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  • 151. Dzieciatkowska, Monika
    et al.
    Liu, Xin
    Heikema, Astrid P.
    Houliston, R. Scott
    van Belkum, Alex
    Schweda, Elke K. H.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Gilbert, Michel
    Richards, James C.
    Li, Jianjun
    Rapid method for sensitive screening of oligosaccharide epitopes in the lipooligosaccharide from Campylobacter jejuni strains isolated from Guillain-Barre syndrome and Miller Fisher syndrome patients2008Inngår i: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 46, nr 10, s. 3429-3436Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 152. Dzieciatkowska, Monika
    et al.
    Schweda, Elke K. H.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Moxon, E. Richard
    Richards, James C.
    Li, Jianjun
    Characterization of intact lipopolysaccharides from the Haemophilus influenzae strain RM 118 using electrophoresis-assisted open-tubular liquid chromatography-mass spectrometry2008Inngår i: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 29, nr 10, s. 2171-2181Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 153.
    Edin, Michaela
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Grivas, Spiros
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    First synthesis of 6,7-diaminoindole and 1,2,5-selenadiazolo[3,4-g]indole2000Inngår i: ARKIVOC, ISSN 1424-6376, nr 1, s. 1-5Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 154.
    Edlund, Anna
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Microbial diversity in Baltic Sea sediments2007Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

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

  • 155.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Jansson, Janet K.
    SLU.
    Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments2006Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, nr 10, s. 6800-6807Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 156.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Jansson, Janet K.
    SLU.
    Identification of metabolically active phenanthrene transforming bacteria in polluted Baltic Sea sedimentsManuskript (preprint) (Annet vitenskapelig)
  • 157.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Jansson, Janet K.
    Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments2008Inngår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 65, nr 3, s. 513-525Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 158.
    Edlund, Charlotta
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Alvan, G
    Barkholt, L
    Vacheron, F
    Nord, C E
    Pharmacokinetics and comparative effects of telithromycin (HMR 3647) and clarithromycin on the oropharyngeal and intestinal microflora2000Inngår i: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 46, nr 5, s. 741-749Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 159.
    Edlund, Charlotta
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Nord, C E
    Effect on the human normal microflora of oral antibiotics for treatment of urinary tract infections2000Inngår i: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 46, s. 41-48Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 160.
    Edlund, Charlotta
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Nord, C E
    The evaluation and prediction of the ecologic impact of antibiotics in human phase I and II trials2001Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 7, s. 37-41Artikkel i tidsskrift (Fagfellevurdert)
  • 161.
    Edvardsson, Anna
    et al.
    Linköpings universitet.
    Petersson, Ulrika A.
    Södertörns högskola, Institutionen för livsvetenskaper. Stockholms universitet.
    Shapiguzov, Alexey
    Linköpings universitet.
    Schröder, Wolfgang P
    Södertörns högskola, Institutionen för livsvetenskaper. Umeå universitet.
    Vener, Alexander V.
    Linköpings universitet.
    Knockout of the cyclophilin AtCYP20-2 is compensated by oxidative activation of PPIase activity in the thylakoid lumen of Arabidopsis thalianaManuskript (preprint) (Annet vitenskapelig)
  • 162. Edvardsson, Anna
    et al.
    Shapiguzov, Alexey
    Petersson, Ulrika A.
    Södertörns högskola, Institutionen för livsvetenskaper. Stockholm University.
    Schröder, Wolfgang P.
    Vener, Alexander V.
    Immunophilin AtFKBP13 sustains all peptidyl-prolyl isomerase activity in the thylakoid lumen from Arabidopsis thaliana deficient in AtCYP20-22007Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 46, nr 33, s. 9432-9442Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 163.
    Efimenko, Evgeni
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    The study of sensory cilia development in caenorhabditis elegans2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

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

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

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

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

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

  • 164.
    Efimenko, Evgeni
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Blacque, Oliver E.
    Simon Fraser University, Burnaby, British Columbia, Canada.
    Ou, Guangshuo
    University of California, Davis, USA.
    Haycraft, Courtney J.
    University of Alabama at Birmingham Medical Center, Birmingham, USA.
    Yoder, Bradley K.
    University of Alabama at Birmingham Medical Center, Birmingham, USA.
    Scholey, Jonathan M.
    University of California, Davis, USA.
    Leroux, Michel R.
    Simon Fraser University, Burnaby, British Columbia, Canada.
    Swoboda, Peter
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Instiute.
    Caenorhabditis elegans DYF-2, an orthologue of human WDR19, is a component of the intraflagellar transport machinery in sensory Cilia2006Inngår i: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 17, nr 11, s. 4801-4811Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The intraflagellar transport (IFT) machinery required to build functional cilia consists of a multisubunit complex whose molecular composition, organization, and function are poorly understood. Here, we describe a novel tryptophan-aspartic acid (WD) repeat (WDR) containing IFT protein from Caenorhabditis elegans, DYF-2, that plays a critical role in maintaining the structural and functional integrity of the IFT machinery. We determined the identity of the dyf-2 gene by transgenic rescue of mutant phenotypes and by sequencing of mutant alleles. Loss of DYF-2 function selectively affects the assembly and motility of different IFT components and leads to defects in cilia structure and chemosensation in the nematode. Based on these observations, and the analysis of DYF-2 movement in a Bardet-Biedl syndrome mutant with partially disrupted IFT particles, we conclude that DYF-2 can associate with IFT particle complex B. At the same time, mutations in dyf-2 can interfere with the function of complex A components, suggesting an important role of this protein in the assembly of the IFT particle as a whole. Importantly, the mouse orthologue of DYF-2, WDR19, also localizes to cilia, pointing to an important evolutionarily conserved role for this WDR protein in cilia development and function.

  • 165.
    Efimenko, Evgeni
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Bubb, K
    Mak, H Y
    Holzman, T
    Leroux, M R
    Ruvkun, G
    Thomas, J H
    Swoboda, Peter
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Analysis of xbx genes in C-elegans2005Inngår i: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 132, nr 8, s. 1923-1934Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cilia and flagella are widespread eukaryotic subcellular components that are conserved from green algae to mammals. In different organisms they function in cell motility, movement of extracellular fluids and sensory reception. While the function and structural description of cilia and flagella are well established, there are many questions that remain unanswered. In particular, very little is known about the developmental mechanisms by which cilia are generated and shaped and how their components are assembled into functional machineries. To find genes involved in cilia development we used as a search tool a promoter motif, the X-box, which participates in the regulation of certain ciliary genes in the nematode Caenorhabditis elegans. By using a genome search approach for X-box promoter motif-containing genes (xbx genes) we identified a list of about 750 xbx genes (candidates). This list comprises some already known ciliary genes as well as new genes, many of which we hypothesize to be important for cilium structure and function. We derived a C elegans X-box consensus sequence by in vivo expression analysis. We found that xbx gene expression patterns were dependent on particular X-box nucleotide compositions and the distance from the respective gene start. We propose a model where DAF-19, the RFX-type transcription factor binding to the X-box, is responsible for the development of a ciliary module in C elegans, which includes genes for cilium structure, transport machinery, receptors and other factors.

  • 166.
    Eggertsen, Linda
    et al.
    Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Uppsala University, Department of Earth Sciences, Visby, Sweden; Reef Systems Ecology and Conservation Lab, Department of Marine Biology, Fluminense Federal University, Niterói, Brazil.
    Goodell, Whitney
    Fisheries Ecology Research Lab, University of Hawaii, Honolulu, HI, United States; Pristine Seas, National Geographic Society, Washington DC, United States.
    Cordeiro, Cesar A. M. M.
    Reef Systems Ecology and Conservation Lab, Department of Marine Biology, Fluminense Federal University, Niterói, Brazil; Ecology Post Graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
    Cossa, Damboia
    Department of Biological Sciences, Eduardo Mondlane University, Maputo, Mozambique.
    de Lucena, Marcos
    Reef Systems Ecology and Conservation Lab, Department of Marine Biology, Fluminense Federal University, Niterói, Brazil; Ecology Post Graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
    Berkström, Charlotte
    Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden.
    Franco, João N.
    MARE - Marine and Environmental Sciences Centre, ESTM, Politécnico de Leiria, Peniche, 2520-620, Portugal; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, 4450-208, Portugal.
    Ferreira, Carlos E. L.
    Reef Systems Ecology and Conservation Lab, Department of Marine Biology, Fluminense Federal University, Niterói, Brazil.
    Bandeira, Salomão
    Department of Biological Sciences, Eduardo Mondlane University, Maputo, Mozambique.
    Gullström, Martin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Where the grass is greenest in seagrass seascapes depends on life history and simple species traits of fish2022Inngår i: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015, Vol. 266, artikkel-id 107738Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Tropical seagrass meadows are critical habitats for many fish species, yet few studies have investigated the influence of multiple scale-dependent factors and marine protected areas on seagrass fish species of differing life histories. We assessed the influence of fine-scale seagrass meadow characteristics and seascape-scale variables on the abundance of fish in a seagrass-dominated seascape in the Bazaruto Archipelago, Mozambique, particularly examining patterns of nursery- vs. resident species as well as mobile- vs. sedentary species. We found that fish distribution patterns in this seagrass-dominated seascape were dependent on species’ life history characteristics; nursery taxa showed lower abundance in seagrass meadows further from adult reef habitats, while resident species within seagrass meadows occurred in higher abundances far from reefs. For taxa utilizing both mangroves and seagrass meadows as nursery habitat, proximity to mangroves was an important factor. Fish abundances were generally influenced by variables at the seascape scale (km), while sedentary species were predominantly influenced by area variables, and smaller seascapes (<500 m in radius) better explained distribution patterns. The influence of marine protected areas was taxon-specific, with the strongest effects of protection on resident species. Our results indicate that protection efforts in seagrass-dominated seascapes can have varying impacts on fish distribution, depending on the life history of the species present, and the geographical placement of the reserve within the seascape. Further, we suggest that simple species attributes can be utilised to describe generalized abundance patterns of fish in seagrass seascapes.

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    fulltext
  • 167.
    Eggertsen, M.
    et al.
    Stockholm University, Sweden.
    Larsson, Josefine
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Porseryd, Tove
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Åkerlund, C.
    Stockholm University, Sweden.
    Chacin, D. H.
    University of South Florida, USA.
    Berkström, C.
    Stockholm University, Sweden; Swedish University of Agricultural Sciences, Sweden.
    Jiddawi, N.
    Institute of Fisheries Research, Tanzania.
    Kautsky, N.
    Stockholm University, Sweden.
    Halling, C.
    Stockholm University, Sweden.
    Coral-macroalgal interactions: Herbivory and substrate type influence growth of the macroalgae Eucheuma denticulatum (NL Burman) Collins & Hervey, 1917 on a tropical coral reef2021Inngår i: Journal of Experimental Marine Biology and Ecology, ISSN 0022-0981, E-ISSN 1879-1697, Vol. 542, artikkel-id 151606Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Introduced macroalgae becoming invasive may alter ecological functions and habitats in recipient ecosystems. In the Western Indian Ocean (WIO), non-native strains of the native macroalgae Eucheuma denticulatum were introduced for farming practices and consequently spread into the surrounding seascape. We investigated potential effects of non-native and native strains of this macroalgae on a branching coral. We conducted a four-factor field experiment where we examined growth and holdfast development of introduced and native E. denticulatum on live and dead branches of Acropora sp. in the presence and absence of herbivores in Unguja Island, Zanzibar. Moreover, we estimated coral and macroalgae condition by visual examinations, gene expression analyses, and photosynthetic measurements. Macroalgae did not attach to any live coral and coral condition was not impacted by the presence of E. denticulatum, regardless of geographical origin. Instead, necrotic tissue on the macroalgae in areas of direct contact with corals indicated damage inflicted by the coral. The biomass of E. denticulatum did not differ between the replicates attached to live or dead corals in the experiment, yet biomass was strongly influenced by herbivory and replicates without protection from herbivores had a significantly lower biomass. In the absence of herbivory, introduced E. denticulatum had significantly higher growth rates than native algae based on wet weight measurements. These results contribute to an increased understanding of environmental effects by the farming of a non-native strain of algae on corals and stresses the importance to maintain viable populations of macroalgal feeding fishes in such areas.

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    fulltext
  • 168.
    Eggertsen, M.
    et al.
    Stockholm University, Sweden.
    Tano, S. A.
    Stockholm University, Sweden.
    Chacin, D. H.
    University of South Florida, St. Petersburg, USA.
    Eklöf, J. S.
    Stockholm University, Sweden.
    Larsson, Josefine
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Berkström, C.
    Stockholm University, Swenden ; Swedish University of Agricultural Sciences, Sweden.
    Buriyo, A. S.
    University of Dar Es Salaam, Dar es Salaam, Tanzania.
    Halling, C.
    Stockholm University, Sweden.
    Different environmental variables predict distribution and cover of the introduced red seaweed Eucheuma denticulatum in two geographical locations2021Inngår i: Biological Invasions, ISSN 1387-3547, E-ISSN 1573-1464, Vol. 23, s. 1049-1067Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this study we examined abiotic and biotic factors that could potentially influence the presence of a non-indigenous seaweed, Eucheuma denticulatum, in two locations, one outside (Kane’ohe Bay, Hawai’i, USA) and one within (Mafia Island, Tanzania) its natural geographical range. We hypothesized that the availability of hard substrate and the amount of wave exposure would explain distribution patterns, and that higher abundance of herbivorous fishes in Tanzania would exert stronger top–down control than in Hawai’i. To address these hypotheses, we surveyed E. denticulatum in sites subjected to different environmental conditions and used generalized linear mixed models (GLMM) to identify predictors of E. denticulatum presence. We also estimated grazing intensity on E. denticulatum by surveying the type and the amount of grazing scars. Finally, we used molecular tools to distinguish between indigenous and non-indigenous strains of E. denticulatum on Mafia Island. In Kane’ohe Bay, the likelihood of finding E. denticulatum increased with wave exposure, whereas on Mafia Island, the likelihood increased with cover of coral rubble, and decreased with distance from areas of introduction (AOI), but this decrease was less pronounced in the presence of coral rubble. Grazing intensity was higher in Kane’ohe Bay than on Mafia Island. However, we still suggest that efforts to reduce non-indigenous E. denticulatum should include protection of important herbivores in both sites because of the high levels of grazing close to AOI. Moreover, we recommend that areas with hard substrate and high structural complexity should be avoided when farming non-indigenous strains of E. denticulatum.

  • 169. Ekblom, Robert
    et al.
    Grahn, Mats
    Södertörns högskola, Avdelning Naturvetenskap.
    Höglund, Jacob
    Patterns of polymorphism in the MHC class II of a non-passerine bird, the great snipe (Gallinago media)2003Inngår i: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 54, nr 10, s. 734-741Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 170. Ekblom, Robert
    et al.
    Saether, Stein Are
    Grahn, Mats
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    Major histocompatibility complex variation and mate choice in a lekking bird, the great snipe (Gallinago media)2004Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, nr 12, s. 3821-3828Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 171. Ekblom, Robert
    et al.
    Saether, Stein Are
    Jacobsson, Pär
    Fiske, Peder
    Sahlman, Tobias
    Grahn, Mats
    Södertörns högskola, Institutionen för livsvetenskaper.
    Kålås, John Atle
    Höglund, Jacob
    Spatial pattern of MHC class II variation in the great snipe (Gallinago media)2007Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, nr 7, s. 1439-1451Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism.

  • 172. Ekstam, Börje
    et al.
    Johansson, Beatha
    Dinnetz, Patrik
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Ellström, Patrik
    Predicting risk habitats for the transmission of the small liver fluke, Dicrocoelium dendriticum to grazing ruminants2011Inngår i: GEOSPATIAL HEALTH, ISSN 1827-1987, Vol. 6, nr 1, s. 125-131Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A multiple regression model was used to analyse if the structure of vegetation and soil patches in grazed units (pastures) can be used as explanatory variables to predict the prevalence of Dicrocoelium dendriticum, a common parasite of cattle and sheep, in grazing cattle stocks on the Baltic island of land in southern Sweden. The scale dependency was evaluated by comparing three levels of spatial resolution of patches. Prevalence data were obtained from slaughtered animals. Our models predict that the prevalence of D. dendriticum increases in grazed areas with woody vegetation, whereas moist and wet areas decrease parasite prevalence. The predictive power of the statistical models increased with increasing level of patch resolution. Approximately 42% of the variation in parasite prevalence (angular transformation) was explained by the areal proportion of vegetation types (4th-root-transformed). Based on the results obtained, we believe that our model strategy provides a rational and systematic tool to identify habitats that carry risk for D. dendriticum infection of ruminants, and that it can be applied to other parasites with similar life cycles such as Fasciola hepatica.

  • 173.
    Ekwall, Karl
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    'Arc' escorts siRNAs in heterochromatin assembly2007Inngår i: Nature Structural & Molecular Biology, ISSN 1545-9993, E-ISSN 1545-9985, Vol. 14, nr 3, s. 178-179Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    RNA interference (RNAi) is important in directing heterochromatin assembly at centromeres in fission yeast, which is crucial for maintaining a stable genome through mitotic and meiotic divisions. In this issue, Buker et al. describe a new Argonaute siRNA chaperone (ARC) that converts duplex RNA to single-stranded RNA. This is a previously unknown step in the RNAi-directed heterochromatin-formation pathway.

  • 174.
    Ekwall, Karl
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Epigenetic control of centromere behavior2007Inngår i: Annual review of genetics / [ed] Allan Campbell, Wyatt W Anderson, Elizabeth W Jones, Palo Atlo: Annual Reviews , 2007, s. 63-81Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    The centromere is the DNA region that ensures genetic stability and is therefore of vital importance. Paradoxically, centromere proteins and centromeric structural domains are conserved despite that fact that centromere DNA sequences are highly variable and are not conserved. Remarkably, heritable states at the centromere can be propagated independent of the underlying centromeric DNA sequences. This review describes the epigenetic mechanisms governing centromere behavior, i.e., the mechanisms that control centromere assembly and propagation. A centromeric histone variant, CenH3, and histone modifications play key roles at centromeric chromatin. Histone modifications and RNA interference are important in assembly of pericentric heterochromatin structures. The molecular machinery that is directly involved in epigenetic control of centromeres is shared with regulation of gene expression. Nucleosome remodeling factors, histone chaperones, histone-modifying enzymes, transcription factors, and even RNA polymerase II itself control epigenetic states at centromeres.

  • 175.
    Ekwall, Karl
    Södertörns högskola, Institutionen för livsvetenskaper.
    Genome-wide analysis of HDAC function2005Inngår i: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 21, nr 11, s. 608-615Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This article focuses on new developments in the genome-wide analysis of histone deacetylase (HDAC) function in yeast. HDACs are highly conserved in many organisms; therefore, their basic functions can be investigated using experimentally tractable model organisms, such as the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. New microarray techniques have enabled the systematic study of HDACs by identifying their direct and indirect gene targets in addition to their physiological functions and enzymatic specificity. These new approaches have already provided new surprising insights into the basic function of HDACs.

  • 176.
    Ekwall, Karl
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Karolinska Institute.
    The RITS complex - A direct link between small RNA and heterochromatin2004Inngår i: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 13, nr 3, s. 304-305Artikkel i tidsskrift (Fagfellevurdert)
  • 177.
    Ekwall, Karl
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Karolinska Institute.
    The roles of histone modifications and small RNA in centromere function2004Inngår i: Chromosome Research, ISSN 0967-3849, E-ISSN 1573-6849, Vol. 12, nr 6, s. 535-542Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 178. El-Beqqali, Aziza
    et al.
    Kussak, Anders
    Södertörns högskola, Institutionen för livsvetenskaper.
    Abdel-Rehim, Mohamed
    Fast and sensitive environmental analysis utilizing microextraction in packed syringe online with gas chromatography-mass spectrometry - Determination of polycyclic aromatic hydrocarbons in water2006Inngår i: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1114, nr 2, s. 234-238Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new sensitive, selective, fast and accurate technique for online sample preparation was developed. Microextraction in a packed syringe (MEPS) is a new miniaturised, solid-phase extraction (SPE) technique that can be connected online to GC or LC without any modifications. In MEPS approximately 1 mg of the solid packing material is inserted into a syringe (100-250 ml) as a plug. Sample preparation takes place on the packed bed. The bed can be coated to provide selective and suitable sampling conditions. The new method is very promising. It is very easy to use, fully automated, of low cost and rapid in comparison with previously used methods. The determination of polycyclic hydrocarbons (PAHs) in water was performed using MEPS as sample preparation method online with gas chromatography and mass spectrometry (MEPS-GC-MS). The results from MEPS as sample preparation were compared with other techniques such as stir bar sorptive extraction (SBSE) and solid-phase microextraction (SPME). The method was validated and the standard curves were evaluated by the means of quadratic regression and weighted by inverse of the concentration: 1/x for the calibration range 5-1000 ng/L. The MEPS applied polymer (silica-C8) could be used more than 400 times before the syringe was discarded. The extraction recovery was about 70%. The results showed close correlation coefficients (R > 0.998) for all analytes in the calibration range studied. The accuracy of MEPS-GC-MS was between 90 and 113% and the inter-day precision (n = 3 days), expressed as the relative standard deviation (RSD%), was 8-16%. MEPS reduced the handling time by 30 and 100 times compared to SPME and SBSE, respectively.

  • 179. El-Beqqali, Aziza
    et al.
    Kussak, Anders
    Södertörns högskola, Institutionen för livsvetenskaper.
    Blomberg, Lars
    Abdel-Rehim, Mohamed
    Microextraction in packed syringe/liquid chromatography/electrospray tandem mass spectrometry for quantification of acebutolol and metoprolol in human plasma and urine samples2007Inngår i: Journal of Liquid Chromatography & Related Technologies, ISSN 1082-6076, E-ISSN 1520-572X, Vol. 30, nr 4, s. 575-586Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The aim of the present investigation was to develop a simple, fast, and sensitive method for the determination of acebutolol and metoprolol in human plasma and urine samples. The determination of acebutolol and metoprolol in plasma and urine was performed using micro extraction in packed syringe (MEPS) as a sample preparation method, online with high performance liquid chromatography and tandem mass spectrometry (LC-MS/MS). In MEPS the sampling sorbent was 1 mg polystyrene polymer, which was inserted in a 250 mu L syringe. The lower limits of quantification (LLOQ) for acebutolol and metoprolol were set to 1.0 ng/mL. The accuracy of quality control samples (QC) varied by +/- 10%, and precision (R.S.D.) had a deviation of 1.4-12% for plasma and urine samples. The calibration curve was obtained within the concentration range 1.0-100 ng/mL in both plasma and urine. The regression correlation coefficients (R-2) for plasma and urine samples were >= 0.999 for all runs. The present method is miniaturized, fully automated, robust, and can be easily used for pharmacokinetic and pharmacodynamic studies of acebutolol and metoprolol.

  • 180.
    Elgan, Tobias H.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Insitute.
    Quantifying Escherichia coli Glutaredoxin-3 Substrate Specificity Using Ligand-induced Stability2008Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 283, nr 47, s. 32839-32847Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Traditionally, quantification of protein-ligand affinity is performed using kinetic or equilibrium measurements. However, if the binding reaction proceeds via a stable covalent complex, these approaches are often limited. By exploiting the fact that the conformational stabilization of a protein is altered upon ligand binding due to specific interactions, and using an array of selectively chosen ligand analogs, one can quantify the contribution individual interactions have on specificity. We have used ligand-induced stability as a basis to dissect the interaction between glutaredoxin-3 (Grx3) and one of its native substrates, the tripeptide glutathione. Taking advantage of the fact that Grx3 can be trapped in a covalent mixed disulfide to glutathione or to selected synthetic glutathione analogs as part of the natural catalytic cycle, individual contributions to binding of specific molecular groups can be quantified by changes in ligand-induced stability. These changes in conformational stability are interpreted in terms of interaction energies (i.e. specificity) of the particular groups present on the ligand analog. Our results illustrate that although Grx3 recognizes glutathione predominantly through independent and additive ionic interactions at the N- and C-terminal of glutathione, van der Waals interactions from the unique gamma-glutamate moiety of glutathione also play an important role. This study places us closer to understanding the complex task of accommodating multiple substrate specificities in proteins of the thioredoxin superfamily and underscores the general applicability of ligand-induced stability to probe substrate specificity.

  • 181.
    Elgán, Tobias H.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karlolinska instituet.
    Planson, A. -G
    Beckwith, J.
    Güntert, P.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi. Karolinska institutet.
    Determinants of activity in glutaredoxins: An in vitro evolved Grx1-like variant of Escherichia coli Grx32010Inngår i: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 430, nr 3, s. 487-495Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Escherichia coli glutaredoxins 1 and 3 (Grx1 and Grx3) are structurally similar (37% sequence identity), yet have different activities in vivo. Unlike Grx3, Grx1 efficiently reduces protein disulfides in proteins such as RR (ribonucleotide reductase), whereas it is poor at reducing S-glutathionylated proteins. An E. coli strain lacking genes encoding thioredoxins 1 and 2 and Grx1 is not viable on either rich or minimal medium; however, a M43V mutation in Grx3 restores growth under these conditions and results in a Grx1-like protein [Ortenberg, Gon, Porat and Beckwith (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 7439-7944]. To uncover the structural basis of this change in activity, we have compared wild-type and mutant Grx3 using CD and NMR spectroscopy. Ligand-induced stability measurements demonstrate that the Grx3(M43V/C65Y) mutant has acquired affinity for RR. Far-UV CD spectra reveal no significant differences, but differences are observed in the near-UV region indicative of tertiary structural changes. NMR 1H- 15N HSQC (heteronuclear single quantum coherence) spectra show that approximately half of the 82 residues experience significant (Δδ &gt; 0.03 p.p.m.) chemical shift deviations in the mutant, including nine residues experiencing extensive (Δδ ≥ 0.15 p.p.m.) deviations. To test whether the M43V mutation alters dynamic properties of Grx3, H/D (hydrogen/deuterium) exchange experiments were performed demonstrating that the rate at which backbone amides exchange protons with the solvent is dramatically enhanced in the mutant, particularly in the core of the protein. These data suggest that the Grx1-like activity of the Grx3(M43V/C65Y) mutant may be explained by enhanced intrinsic motion allowing for increased specificity towards larger substrates such as RR.

  • 182.
    Ellencrona, Ellen
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Melik, Wessam
    Södertörns högskola, Institutionen för livsvetenskaper.
    Johansson, Magnus
    Södertörns högskola, Institutionen för livsvetenskaper.
    Novel PDZ dependent cell associations of the NS5 proteins of Tick-borne encephalitis virus and West-Nile virusManuskript (preprint) (Annet vitenskapelig)
  • 183.
    Ellencrona, Karin
    Södertörns högskola, Institutionen för livsvetenskaper.
    Functional characterization of interactions between the flavivirus NS5 protein and PDZ proteins of the mammalian host2009Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Flaviviruses are found all over the world and affect and infect millions of people every year. Flavivirus infection can lead to severe clinical outcomes resulting in neuronal damages e.g. Tick-borne encephalitis virus (TBEV), or severe hemorrhagic fevers e.g. Dengue virus (DENV). In order to effectively treat infected patients and to prevent these diseases we must understand how these viruses work and how they interfere with the mammalian host. This thesis is focusing on interactions between the virus protein NS5 and human host cell proteins. The interactions presented here might be key factors for out-come of viral disease. NS5 is the largest of the non-structural proteins and is essential for the replication and the capping as it contains both RNA dependent RNA polymerase and Methyltransferase domains. We found that TBEV NS5 interacts with human PDZ domain protein Scribble, a polarization protein important e.g. in regulating membrane trafficking. We determined that the interaction depend on a novel internal motif in TBEVNS5. This interaction could be correlated to NS5s ability to interfere with the immune system as absence of Scribble prevented NS5 from blocking phosphorylation of STAT upon Interferon induction. The role of NS5 in human PDZ domain targeting was addressed further by using a PDZ array system. Both TBEVNS5 and DENVNS5 bind additional PDZ domains using the internal motif. The tight junction protein ZO-1 binds both DENVNS5 and TBEVNS5. DENVNS5 is mainly present in the nucleus and co-localize with ZO-1 in un-polarized cells. In polarized cells TBEVNS5 and ZO-1 co-localize at the plasmamembrane. Putative C-terminal PDZ binding motifs of TBEVNS5 and WNVNS5 were characterized using the PDZ array system. This detected four novel binding partners of TBEVNS5 but numerous of potential WNVNS5 binding partners. We found that TBEVNS5 co-localizes with ZO-2 in the cellular membrane. Further, we found that TBEVNS5 induce the AP-1 by a 2 fold over the control.

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  • 184.
    Elma, Eylem
    et al.
    Newcastle University, UK; Stockholm University, Sweden.
    Gullström, Martin
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Yahya, Saleh A.S.
    University of Dar es Salaam, Tanzania.
    Jouffray, Jean-Baptiste
    Stockholm University, Sweden.
    East, Holly K.
    Northumbria University, UK.
    Nyström, Magnus
    Stockholm University, Sweden.
    Post-bleaching alterations in coral reef communities2023Inngår i: Marine Pollution Bulletin, ISSN 0025-326X, E-ISSN 1879-3363, Vol. 186, artikkel-id 114479Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We explored the extent of post-bleaching impacts, caused by the 2014–2016 El Niño Southern Oscillation (ENSO) event, on benthic community structure (BCS) and herbivores (fish and sea urchins) on seven fringing reefs, with differing protection levels, in Zanzibar, Tanzania. Results showed post-bleaching alterations in BCS, with up to 68 % coral mortality and up to 48 % increase in turf algae cover in all reef sites. Herbivorous fish biomass increased after bleaching and was correlated with turf algae increase in some reefs, while the opposite was found for sea urchin densities, with significant declines and complete absence. The severity of the impact varied across individual reefs, with larger impact on the protected reefs, compared to the unprotected reefs. Our study provides a highly relevant reference point to guide future research and contributes to our understanding of post-bleaching impacts, trends, and evaluation of coral reef health and resilience in the region.

    Fulltekst (pdf)
    fulltext
  • 185. Elmroth, K
    et al.
    Erkell, L J
    Nygren, Jonas
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Hultborn, R
    Radiation and hypothermia: Changes in DNA supercoiling in human diploid fibroblasts1999Inngår i: Anticancer Research, ISSN 0250-7005, E-ISSN 1791-7530, Vol. 19, nr 6B, s. 5307-5311Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 186.
    Elofsson, Katarina
    et al.
    Swedish University of Agricultural Sciences.
    Gren, I. -M
    Swedish University of Agricultural Sciences.
    Regulating invasive species with different life history2015Inngår i: Journal of Bioeconomics, ISSN 1387-6996, E-ISSN 1573-6989, Vol. 17, nr 2, s. 113-136Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Invasive species often cause economic damage due to their impact on economically valuable resident species. We study optimal regulation in terms of simultaneous control and adaptation when the purpose is to manage an invasive species which competes for scarce resources with a resident species. The optimal policy includes both subsidies for control of an invasive species with zero commercial value, and harvesting taxes on the resident species which are adjusted in the presence of an invasion. A numerical age-structured optimization model is used to analyze the role of species’ life history, i.e. the degree of evolutionary specialization in survival or reproduction, for the choice of strategy and the associated economic instruments. Results show that, irrespective of life history, both policies are implemented in efficient solutions, but subsidies for controlling the invader are used to a larger extent when it is possible to target specific age classes of the invader. If a resident species is harvested non-selectively, the optimal subsidy for control of the invader is lower, and if the invader is specialized in survival the control subsidy mirrors the resident species harvest cycle. © 2014, The Author(s).

  • 187.
    Elofsson, Katarina
    et al.
    Södertörns högskola, Institutionen för samhällsvetenskaper, Nationalekonomi. Aarhus University, Denmark.
    Hiron, M.
    Swedish University of Agricultural Sciences, Sweden.
    Kačergytė, I.
    Swedish University of Agricultural Sciences, Sweden.
    Pärt, T.
    Swedish University of Agricultural Sciences, Sweden.
    Ecological compensation of stochastic wetland biodiversity: National or regional policy schemes?2023Inngår i: Ecological Economics, ISSN 0921-8009, E-ISSN 1873-6106, Vol. 204, artikkel-id 107672Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The aim of this study is to compare policy schemes for ecological compensation applied at national and regional levels, using exploited inland wetlands as an example. We study whether uncertainty, due to natural variability and measurement difficulties, motivates compensation that is carried out in the same region as that of the exploited site, or whether it rather motivates nationwide compensation schemes. For this purpose, we develop an empirical, chance-constrained programming model of cost-effective wetland management. The model is spatially differentiated and accounts for heterogeneity in wetland quality across wetland types and regions. Wetland quality is defined by three alternative biodiversity indices: species richness, population-weighted species richness, and red-listed species richness, estimated from voluntarily reported data on breeding bird species observations. Results show that regional schemes are more expensive, in particular if the policy maker dislikes uncertainty and wants to prioritize uncommon species. Contrary to expectations from the theoretical analysis, regional schemes would lead to a higher risk-adjusted level of biodiversity at the national level. However, regionalization also implies that targets cannot be achieved if a high safety margin is imposed. Trading ratios are robust to the choice of wetland quality index.

    Fulltekst (pdf)
    fulltext
  • 188.
    Elväng, Annelie M.
    et al.
    Stockholms universitet.
    Westerberg, Karolina
    Stockholms universitet.
    Jernberg, Cecilia
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Jansson, Janet K
    Södertörns högskola, 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 soil2001Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 3, nr 1, s. 32-42Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 189. Engel, Katja
    et al.
    Ashby, Deborah
    Brady, Sean F.
    Cowan, Don A.
    Doemer, John
    Edwards, Elizabeth A.
    Fiebig, Klaus
    Martens, Eric C.
    McCormac, Dennis
    Mead, David A.
    Miyazaki, Kentaro
    Moreno-Hagelsieb, Gabriel
    O'Gara, Fergal
    Reid, Alexandra
    Rose, David R.
    Simonet, Pascal
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Smalla, Kornelia
    Streit, Wolfgang R.
    Tedman-Jones, Jennifer
    Valla, Svein
    Wellington, Elizabeth M. H.
    Wu, Cheng-Cang
    Liles, Mark R.
    Neufeld, Josh D.
    Sessitsch, Angela
    Charles, Trevor C.
    Meeting Report: 1st International Functional Metagenomics Workshop May 7-8, 2012, St. Jacobs, Ontario, Canada2013Inngår i: Standards in Genomic Sciences, E-ISSN 1944-3277, Vol. 8, nr 1, s. 106-111Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo.

    Fulltekst (pdf)
    fulltext
  • 190. Engskog, Mikael K. R.
    et al.
    Yildirim, Håkan H.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Li, Jianjun
    Richards, James C.
    Deadman, Mary
    Hood, Derek W.
    Schweda, Elke K. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi.
    A dual role for the lex2 locus: identification of galactosyltransferase activity in non-typeable Haemophilus influenzae strains 1124 and 20192009Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, nr 5, s. 632-641Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lipopolysaccharide (LPS) of Haemophilus influenzae comprises a conserved tri-L-glycero-D-manno-heptosyl inner-core moiety (L-alpha-D-Hepp-(1 -> 2)-[PEtn -> 6]-L-alpha-D-Hepp-(1 -> 3)-[beta-D-Glclp-(1 -> 4)]-L-alpha-D-Hepp-(1 -> 5)-alpha-Kdop) to which addition of beta-D-Glcp to O-4 of Glcl in serotype b strains is controlled by the gene lex2B. In non-typeable H. influenzae strains 1124 and 2019, however, a beta-D-Galp is linked to O-4 of Glcl. In order to test the hypothesis that the 1ex2 locus is involved in the expression Of beta-D-Galp-(1 -> 4-beta-D-Glcp-(1 -> - from Hepl, 1ex2B was inactivated in strains 1124 and 2019, and LPS glycoform populations from the resulting mutant strains were investigated. Detailed structural analyses using NMR techniques and electrospray-ionisation mass spectrometry (ESIMS) on O-cleacylated LPS and core oligosaccharide material (OS), as well as ESIMS" on permethylated dephosphorylated OS, indicated both lex2B mutant strains to express only beta-D-Glcp extensions from Hepl. This provides strong evidence that Lex2B functions as a galactosyltransferase adding a beta-D-Galp to O-4 of Glcl in these strains, indicating that allelic polymorphisms in the lex2B sequence direct alternative functions of the gene product.

  • 191.
    Ericsson, Linda-Mari
    Södertörns högskola, Institutionen för livsvetenskaper.
    Mountain Rainforest Management in Babati District, Tanzania.2005Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    This paper deals with Community Based Forest Management in Mountain rainforests in Babati. This form of management is when the Communities are managing the forest with some help from the Government.

    I have made a field study to see how the managing is working the mountain forests. I made interviews with chairmen, guards and district council. The purpose with the interview is to give answers to my questions about CBFM and how it is working. I want to see if the CBFM is sustainable in Babati and know if the villagers are satisfied with it. To answer the sustainability questions, studies in Ostroms eight principles for sustainable forest management is made.

    The main conclusions of the study are: Babati will have a sustainable management if they follow the rules and laws that are made for Community Based Forest Management, if the community gets some kind of benefits for being the manager and they want to take care of the forest in a good way when they are the owners. If there are threats against the villagers like pressure from others villages or corruptions this sustainability can be destroyed.

    CBFM needs supporting systems, help from the Government, clearly defined boundaries and the basic needs like food and shelter is fulfilled before they can think of the ecosystem health and sustainability.

    Fulltekst (pdf)
    FULLTEXT01
  • 192. Eriksson, AnnaCarin
    et al.
    Glaser, Elzbieta
    Sjöling, Sara
    A general processing proteinase of spinach leaf mitochondria is a membrane bound enzyme1993Inngår i: Plant Mitochondria: with emphasis on RNA editing and cytoplasmic male sterility / [ed] Brennicke, Axel and Kuch, U, VCH Verlag , 1993, s. 233-241Kapittel i bok, del av antologi (Annet vitenskapelig)
    Abstract [en]

    The book summarizes our current knowledge in the molecular biology of plant mitochondria. It covers such topics as: - RNA editing - mitochondrial gene organization and expression - protein synthesis and transport - cytoplasmic male sterility Specific emphasis is placed on RNA editing. Different systems known to date in mitochondria and plastids are compared. In addition, their connection with the molecular biology involved with the functional analysis is delineated. Another major topic is the molecular biology of mitochondrial genomes of cytoplasmic male sterile (cms) plants. The similarities observed in different cms systems not only promote our understanding of those processes which lead to male sterile plants but are also helpful for breeding strategies. Concise and timely, this book is a unique collaboration of researchers from different fields.

  • 193. Eriksson, AnnaCarin
    et al.
    Sjöling, Sara
    Glaser, Elzbieta
    Characterization of the bifunctional mitochondrial processing peptidase (MPP)/bc1 complex in Spinacia oleracea1996Inngår i: Journal of Bioenergetics and Biomembranes, ISSN 0145-479X, E-ISSN 1573-6881, Vol. 28, nr 3, s. 285-292Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The mitochondrial general processing peptidase (MPP) in plant mitochondria constitutes an integral part of the cytochromebc 1 complex of the respiratory chain. Here we present a characterization of this bifunctional complex from spinach leaf mitochondria. The purified MPP/bc 1 complex has a molecular mass of 550 kDa, which corresponds to a dimer. Increased ionic strength results in partial dissociation of the dimer as well as loss of the processing activity. Micellar concentrations of nonionic and zwitterionic detergents stimulate the activity by decreasing the temperature optimum of the processing reaction, whereas anionic detergents totally suppress the activity. MPP is a metalloendopeptidase. Interestingly, hemin, a potent regulator of mitochondrial and cytosolic biogenesis and inhibitor of proteosomal degradation, inhibits the processing activity. Measurements of the processing activity at different redox states of the bc 1 complex show that despite bifunctionality of the MPP/bc 1 complex, there is no correlation between electron transfer and protein processing.

  • 194.
    Eriksson, Charlotta
    et al.
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Karolinska Institute.
    Rustum, Cecilia
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Stockholm University.
    Hallberg, Einar
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Dynamic properties of nuclear pore complex proteins in gp210 deficient cells2004Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 572, nr 1-3, s. 261-265Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 195. Eriksson, S
    et al.
    Nygren, Jonas
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Ahnström, G
    Matrix association of early- and late-replicating chromatin studied by single-cell electrophoresis2002Inngår i: Biochimica et Biophysica Acta. Molecular Cell Research, ISSN 0167-4889, E-ISSN 1879-2596, Vol. 1590, nr 1-3, s. 103-108Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 196. Facanha, A L O
    et al.
    Appelgren, Henrik
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Tabish, Mohammad
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Okorokov, L
    Ekwall, Karl
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    The endoplasmic reticulum cation P-type ATPase Cta4p is required for control of cell shape and microtubule dynamics2002Inngår i: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 157, nr 6, s. 1029-1039Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 197.
    Fagerström-Billai, Fredrik
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Genome wide analysis of the Ssn6-Tup11/Tup12 co-repressor complex in the fission yeast Schizosaccharomyces pombe2007Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In this study, we have investigated the fission yeast Ssn6-Tup11 /Tup 12 transcriptional corepressor which is involved in regulation of many genes important for a wide variety of processes. In contrast to the well characterised budding yeast Tup1 protein there are two paralogous proteins present in fission yeast, namely Tup11 and Tup12. We have shown that the two proteins can interact with each other and are expressed at similar levels, which is in line with a reported redundant function. Sequence analysis shows that the intermediate proposed histone interacting domain is highly variable between Tup11 and Tup12 indicating a diversification. Interestingly, we show that tup11 and tup12 mutants have different phenotypes on media containing KC1 and CaC12. Consistent with this functional difference, we identify a number of target genes by genome wide expression profiling that are differentially affected by tup11 - and tup12. Many of these genes are Tup12 dependent and correlate with genes that have previously been shown to respond to a range of different environmental stress conditions. The observed different physiological roles of Tup11 and Tup12 can not be explained by differential recruitment of Ssn6 which can interact independently with both Tup11 and Tup12. Most interestingly we show that the Ssn6 protein is essential in fission yeast and therefore must have a distinct role separated from Tup11 and Tup12. Surprisingly, a conditional ssn6HA-ts mutant displays the same growth phenotype as tup12, indicating a role in Tup12 dependent stress response. Consistent with the diverse phenotypes of the individual co-repressor proteins, we identify a group of genes that requires Ssn6 for their regulation which is overlapping but distinct from the group of genes that depend on Tup11 or Tup12. Genome wide chromatin immunoprecipitation shows that Ssn6 is almost invariably found in the same genomic locations as Tup11 and/or Tup12. All three co-repressor subunits are generally bound to genes that are selectively regulated by Ssn6 or Tup11/12, and thus, likely in the context of a co-repressor complex containing all three subunits. The co-repressor binds to both the intergenic and coding regions of genes, but differential localization of the co-repressor within genes does not appear to account for the selective dependence of target genes on the Ssn6 or Tup11/12 subunits. Ssn6, Tup11, and Tup12 are preferentially found at genomic locations at which histones are deacetylated, primarily by the Clr6 class I HDAC. A subset of co-repressor target genes, including direct target genes affected by Ssn6 overexpression, is in addition associated with the function of class II (Clr3) and III (Hst4 and Sir2) HDACs. Interestingly, many specific Hst4 repressed ORF targets involved in amino acid biosynthesis are also direct targets for the Ssn6-Tup11/12 co-repressor, suggesting an association with the class ill sirtuins which has not been reported previously.

  • 198.
    Fagerström-Billai, Fredrik
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Durand-Dubief, Mikael
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Ekwall, Karl
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Individual Subunits of the Ssn6-Tup11/12 corepressor are selectively required for repression of different target genes2007Inngår i: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 27, nr 3, s. 1069-1082Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Saccharomyces cerevisiae Ssn6 and Tup1 proteins form a corepressor complex that is recruited to target genes by DNA-bound repressor proteins. Repression occurs via several mechanisms, including interaction with hypoacetylated N termini of histones, recruitment of histone deacetylases (HDACs), and interactions with the RNA polymerase II holoenzyme. The distantly related fission yeast, Schizosaccharomyces pombe, has two partially redundant Tup1-like proteins that are dispensable during normal growth. In contrast, we show that Ssn6 is an essential protein in S. pombe, suggesting a function that is independent of Tup11 and Tup12. Consistently, the group of genes that requires Ssn6 for their regulation overlaps but is distinct from the group of genes that depend on Tup11 or Tup12. Global chip-on-chip analysis shows that Ssn6 is almost invariably found in the same genomic locations as Tup11 and/or Tup12. All three corepressor subunits are generally bound to genes that are selectively regulated by Ssn6 or Tup11/12, and thus, the subunit specificity is probably manifested in the context of a corepressor complex containing all three subunits. The corepressor binds to both the intergenic and coding regions of genes, but differential localization of the corepressor within genes does not appear to account for the selective dependence of target genes on the Ssn6 or Tup11/12 subunits. Ssn6, Tup11, and Tup12 are preferentially found at genomic locations at which histones are deacetylated, primarily by the Clr6 class I HDAC. Clr6 is also important for the repression of corepressor target genes. Interestingly, a subset of corepressor target genes, including direct target genes affected by Ssn6 overexpression, is associated with the function of class II (CIr3) and III (Hst4 and Sir2) HDACs.

  • 199.
    Fagerström-Billai, Fredrik
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Wright, Anthony P H
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Functional comparison of the Tup11 and Tup12 transcriptional corepressors in fission yeast2005Inngår i: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 25, nr 2, s. 716-727Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gene duplication is considered an important evolutionary mechanism. Unlike many characterized species, the fission yeast Schizosaccharomyces pombe contains two paralogous genes, tup11(+) and tup12(+), that encode transcriptional corepressors similar to the well-characterized budding yeast Tup1 protein. Previous reports have suggested that Tup11 and Tup12 proteins play redundant roles. Consistently, we show that the two Tup proteins can interact together when expressed at normal levels and that each can independently interact with the Ssn6 protein, as seen for Tup1 in budding yeast. However, tup11(-) and tup12(-) mutants have different phenotypes on media containing KCl and CaCl2. Consistent with the functional difference between tup11(-) and tup12- mutants, we identified a number of genes in genome-wide gene expression experiments that are differentially affected by mutations in the tup11(+) and tup12(+) genes. Many of these genes are differentially derepressed in tup11(-) mutants and are over-represented in genes that have previously been shown to respond to a range of different stress conditions. Genes specifically derepressed in tup12(-) mutants require the Ssn6 protein for their repression. As for Tupl.2, Ssn6 is also required for efficient adaptation to KCI- and CaCl2-mediated stress. We conclude that Tup11 and Tup12 are at least partly functionally diverged and suggest that the Tup12 and Ssn6 proteins have adopted a specific role in regulation of the stress response.

  • 200.
    Fang, Hong
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Univesity Hospital, Huddinge.
    Edlund, Charlotta
    Södertörns högskola, 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 susceptibility2002Inngår i: Anaerobe, ISSN 1075-9964, E-ISSN 1095-8274, Vol. 8, nr 2, s. 55-61Artikkel i tidsskrift (Fagfellevurdert)
    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.

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