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  • 201. Ekstam, Börje
    et al.
    Johansson, Beatha
    Dinnetz, Patrik
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Ellström, Patrik
    Predicting risk habitats for the transmission of the small liver fluke, Dicrocoelium dendriticum to grazing ruminants2011In: GEOSPATIAL HEALTH, ISSN 1827-1987, Vol. 6, no 1, p. 125-131Article in journal (Refereed)
    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.

  • 202.
    Ekström, Josephine
    Södertörn University, School of Life Sciences.
    Possibilities and obstacles regarding under-five mortality: A case study in Babati district, Tanzania2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Tanzania is close to reach one of the Millennium Development Goals; to reduce child mortality with two-thirds between 1990 until 2015. This qualitative case study focuses on under-five children’s health in Babati district, situated in the north-west of Tanzania. The empirical data used in this thesis has been collected through interviews with health personnel and mothers during three weeks in February to March 2012. The purpose of the study has been to identify direct and underlying reasons causing child mortality, and to investigate what measures are needed to improve the situation. The most prominent diseases creating death amongst children are pneumonia and malaria, and also diarrheal diseases are common. The prevalence of the diseases differs from wet and dry season, whereas there are more cases of illness and death during the wet season. Malaria and pneumonia are common causes of death during the wet season, and diarrheal diseases are more common during the dry season. Underlying reasons affecting child mortality in Babati district are the lack of infrastructure, such as few well-functioning roads to the main hospitals which affects the rural population in particular. Also the limited access to transport is a vast problem when there is acute illness or childbirth. The clinics available in Babati district are poorly equipped and have a lack of personnel, creating a stressful situation for both healthcare workers and patients. More governmental funds and infrastructure is needed in the area to be able to create a sustainable situation for future children.

  • 203.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institute.
    'Arc' escorts siRNAs in heterochromatin assembly2007In: Nature Structural & Molecular Biology, ISSN 1545-9993, E-ISSN 1545-9985, Vol. 14, no 3, p. 178-179Article in journal (Other academic)
    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.

  • 204.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Epigenetic control of centromere behavior2007In: Annual review of genetics / [ed] Allan Campbell, Wyatt W Anderson, Elizabeth W Jones, Palo Atlo: Annual Reviews , 2007, p. 63-81Chapter in book (Refereed)
    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.

  • 205.
    Ekwall, Karl
    Södertörn University, School of Life Sciences.
    Genome-wide analysis of HDAC function2005In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 21, no 11, p. 608-615Article in journal (Refereed)
    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.

  • 206. El-Beqqali, Aziza
    et al.
    Kussak, Anders
    Södertörn University, School of Life Sciences.
    Abdel-Rehim, Mohamed
    Determination of dopamine and serotonin in human urine samples utilizing microextraction online with liquid chromatography/electrospray tandem mass spectrometry2007In: Journal of Separation Science, ISSN 1615-9306, E-ISSN 1615-9314, Vol. 30, no 3, p. 421-424Article in journal (Refereed)
    Abstract [en]

    A specific LC-MS-MS method for the determination of dopamine and serotonin (5-hydroxytryptamine; 5HT) in human urine is described. The analytes were extracted from urine and preconcentrated by microextraction in a packed syringe (MEPS). The new method is very promising, very easy to use, fully automated, of low cost, and rapid in comparison to previously used methods. The method was validated and the standard curves were evaluated by means of quadratic regression and weighted by inverse of the concentration: 1/x for the calibration range 50-4000 mu g/L. The MEPS applied polymer (silica-C8) could be used more than 300 times. The extraction recovery was about 50%. The results showed close correlation coefficients (r(2) >0.999) for all analytes in the calibration range studied. The accuracy of MEPS-LC-MS-MS was 100-101% for dopamine and 99-100% for 5HT. The interday precision (n = 3 days), expressed as the RSD%, was 6.0-7.7% for dopamine and 6.1-11% for 5HT. MEPS reduced the handling time by 12 times compared to a published method.

  • 207. El-Beqqali, Aziza
    et al.
    Kussak, Anders
    Södertörn University, School of Life Sciences.
    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 water2006In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1114, no 2, p. 234-238Article in journal (Refereed)
    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.

  • 208. El-Beqqali, Aziza
    et al.
    Kussak, Anders
    Södertörn University, School of Life Sciences.
    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 samples2007In: Journal of Liquid Chromatography & Related Technologies, ISSN 1082-6076, E-ISSN 1520-572X, Vol. 30, no 4, p. 575-586Article in journal (Refereed)
    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.

  • 209.
    Elgan, Tobias H.
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Berndt, Kurt D.
    Södertörn University, School of Life Sciences. Karolinska Insitute.
    Quantifying Escherichia coli Glutaredoxin-3 Substrate Specificity Using Ligand-induced Stability2008In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 283, no 47, p. 32839-32847Article in journal (Refereed)
    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.

  • 210.
    Elgán, Tobias H.
    et al.
    Södertörn University, School of Life Sciences. Karlolinska instituet.
    Planson, A. -G
    Beckwith, J.
    Güntert, P.
    Berndt, Kurt D.
    Södertörn University, School of Life Sciences, Chemistry. Karolinska institutet.
    Determinants of activity in glutaredoxins: An in vitro evolved Grx1-like variant of Escherichia coli Grx32010In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 430, no 3, p. 487-495Article in journal (Refereed)
    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 > 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.

  • 211.
    Ellencrona, Ellen
    et al.
    Södertörn University, School of Life Sciences.
    Melik, Wessam
    Södertörn University, School of Life Sciences.
    Johansson, Magnus
    Södertörn University, School of Life Sciences.
    Novel PDZ dependent cell associations of the NS5 proteins of Tick-borne encephalitis virus and West-Nile virusManuscript (preprint) (Other academic)
  • 212.
    Ellencrona, Karin
    Södertörn University, School of Life Sciences.
    Functional characterization of interactions between the flavivirus NS5 protein and PDZ proteins of the mammalian host2009Doctoral thesis, comprehensive summary (Other academic)
    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.

  • 213.
    Ellencrona, Karin
    et al.
    Södertörn University, School of Life Sciences.
    Syed, Asim
    Södertörn University, School of Life Sciences.
    Johansson, Magnus
    Södertörn University, School of Life Sciences, International health. Södertörn University, School of Life Sciences, Chemistry.
    Flavivirus NS5 associates with host-cell proteins zonula occludens-1 (ZO-1) and regulating synaptic membrane exocytosis-2 (RIMS2) via an internal PDZ binding mechanism2009In: Biological chemistry (Print), ISSN 1431-6730, E-ISSN 1437-4315, Vol. 390, no 4, p. 319-323Article in journal (Refereed)
    Abstract [en]

    Dengue virus (DENV) and tick-borne encephalitis virus (TBEV) are flaviviruses, which can cause lethal hemorrhagic fever and encephalitis, respectively. Here, we demonstrate that the TBEV-NS5 and DENV-NS5 proteins use an internal binding mechanism to target human PDZ proteins. TBEV-NS5 has high affinity to regulating synaptic membrane exocytosis-2 (RIMS2) and Scribble, whereas DENV-NS5 binds primarily to the tight junction protein zonula occludens-1 (ZO-1). Targeting of TBEV-NS5 to the plasma membrane is stabilised by ZO-1; however, DENV-NS5 co-localises with ZO-1 in the nucleus. These interactions have potential important roles in the ability of flaviviruses to manipulate cell proliferation, junction permeability and the interferon pathways.

  • 214.
    Elväng, Annelie
    et al.
    Södertörn University, School of Life Sciences, Molecular biology.
    Melik, Wessam
    Södertörn University, School of Life Sciences, Chemistry. Södertörn University, School of Life Sciences, Molecular biology.
    Bertrand, Yann
    Södertörn University, School of Life Sciences, Molecular biology.
    Lönn, Mikael
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Environmental science.
    Johansson, Magnus
    Södertörn University, School of Life Sciences, Chemistry. Södertörn University, School of Life Sciences, International health.
    Sequencing of a Tick-Borne Encephalitis Virus from Ixodes ricinus Reveals a Thermosensitive RNA Switch Significant for Virus Propagation in Ectothermic Arthropods.2011In: Vector Borne and Zoonotic Diseases, ISSN 1530-3667, E-ISSN 1557-7759, Vol. 11, no 6, p. 649-658Article in journal (Refereed)
    Abstract [en]

    Tick-borne encephalitis virus (TBEV) is a flavivirus with major impact on global health. The geographical TBEV distribution is expanding, thus making it pivotal to further characterize the natural virus populations. In this study, we completed the earlier partial sequencing of a TBEV pulled out of a pool of RNA extracted from 115 ticks collected on Torö in the Stockholm archipelago. The total RNA was sufficient for all sequencing of a TBEV genome (Torö-2003), without conventional enrichment procedures such as cell culturing or suckling mice amplification. To our knowledge, this is the first time that the genome of TBEV has been sequenced directly from an arthropod reservoir. The Torö-2003 sequence has been characterized and compared with other TBE viruses. In silico analyses of secondary RNA structures formed by the two untranslated regions revealed a temperature-sensitive structural shift between a closed replicative form and an open AUG accessible form, analogous to a recently described bacterial thermoswitch. Additionally, novel phylogenetic conserved structures were identified in the variable part of the 3'-untranslated region, and their sequence and structure similarity when compared with earlier identified structures suggests an enhancing function on virus replication and translation. We propose that the thermo-switch mechanism may explain the low TBEV prevalence often observed in environmentally sampled ticks. Finally, we were able to detect variations that help in the understanding of virus adaptations to varied environmental temperatures and mammalian hosts through a comparative approach that compares RNA folding dynamics between strains with different mammalian cell passage histories.

  • 215.
    Enberg, Jenny
    Södertörn University College, School of Life Sciences.
    IKEAs etablering i Haparanda: Planerade och förväntade effekter för regionen Haparanda-Torneå2005Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    Abstract [en]

    The aim with my research is to illuminate the meaning of IKEAs settle in Haparanda, for the region Haparanda-Tornio, its economic growth and its inhabitants. The research has been carried out only through qualitative methods. Some interviews with a range of people from varying companies have been conducted.

    Haparanda is a smaller Swedish city situated in the north, on the border to Finland and to a city called Tornio. These two cities, Haparanda and Tornio, has realised they are stronger in pairs, so they initiated cooperation across the border. Haparanda-Tornio is not a region of historically welfare and well-being. At least on the Swedish side, high numbers of unemployment, absence from work and many youngsters leaving the region because of pore prospects for the future, dominates. In this case, something very different happened when IKEA, one of Sweden’s most famous home furnishing companies, chose to settle their new store in Haparanda.

    The settle of IKEA was a joyful message for the region and for the city of Haparanda in particular. A lot of other Swedish companies are now settling in the city as an effect of IKEAs arrival. It is surprising, though, that IKEA chose Haparanda, because of its low number of inhabitants and its geographical position. But, the increasing welfare in the region, satisfactory communication opportunities and the status on the Russian market, are probably factors behind the settle. Also, the Swedish and Finnish membership in the European Union gives them advantages on trading over the borders. Further, the settle in Haparanda give the company access to high number of consumers in four countries. The personal involvement of IKEAs founder, Mr Kamprad, states how exciting and unique this project is.

    IKEA has become a symbol for the positive development in the region. More people may be offered employment since the municipality believe 1000-1500 new jobs could be the result of IKEA, and other companies settle. The effects on the inhabitants can be described as more opportunities to personal development and a higher well-being, a more shaded life. The region may become central to four countries, not only in consumption, but also in meetings and trade for example. But, the status of the region may grow stronger on the expense of other regions in the north. The language question could also be of high importance again. This is because the majority of the companies are settling on the Swedish side which gives the only Finnish-speaking population limited access to the new jobs.

    The previous critiques to the region may soften, but new could rise. For example a greater load on the environment is inevitable, but also a social and cultural development that could change Haparanda and Tornio essentially.

  • 216. Engskog, Mikael K. R.
    et al.
    Yildirim, Håkan H.
    Södertörn University, School of Life Sciences.
    Li, Jianjun
    Richards, James C.
    Deadman, Mary
    Hood, Derek W.
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences, Chemistry.
    A dual role for the lex2 locus: identification of galactosyltransferase activity in non-typeable Haemophilus influenzae strains 1124 and 20192009In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, no 5, p. 632-641Article in journal (Refereed)
    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.

  • 217.
    Engström, Hanna
    Södertörn University College, School of Life Sciences.
    Molecular and morphological analysis of genetic polymorphisms causing glabrousness in wild populations of Arabidopsis lyrata.2006Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    Trichome formation in Arabidopsis lyrata is a naturally occurring trait with phenotypic polymorphisms within wild populations. In Swedish accessions of A. lyrata, three genetic polymorphisms situated in the coding region of GL1, an important transcription factor in trichome production, have been identified, and these are candidates for being the cause of a glabrous phenotype. In this study a complementation test has been performed to clarify which mutation/mutations that are detrimental for trichome formation. A set of constructs has been transformed into A. thaliana, a close relative to A. lyrata, and subsequent generations of plants were examined for phenotype, genotype and gene expression. A SNP (Single Nucleotide Polymorphism) in the R3 MYB domain of GL1, resulting in a change of an alanine to aspartic acid, was identified as the critical polymorphism. The other two mutations, two indels, were harmless to protein function. The inserted constructs were under control of the native GL1 promoter. Plants that, because of the SNP, lacked trichome production, became totally glabrous.

  • 218.
    Enqvist, Johan
    Södertörn University College, School of Life Sciences.
    Involving forest-dependent communities in climate change mitigation: Obstacles and opportunities for successful implementation of a REDD mechanism in Babati District, Tanzania2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim of this thesis is to identify how forest management in Tanzania can contribute to global climate change mitigation while improving livelihoods of forest-dependent communities.

    A mechanism for reducing emissions from deforestation and forest degradation (REDD) is meant to slow increases of atmospheric CO2 while channelling funds to developing countries. In Tanzania, pioneering work in participatory forest management (PFM) has promoted local-level control over forest resource use. The purpose of this study is to contribute to a linkage between REDD and PFM that maximises benefits for communities, forests and global climate.

    Three PFM projects with relation to REDD have been studied, primarily using semi-structured interviews with villagers, district officials, project facilitators, researchers, consultants and policy-makers. Analysis consists of comparing experiences at different levels and putting them in the theoretical context of climate change and forest conservation.

    The study identifies several issues: local and central government institutions cannot ensure equitable benefit sharing; cross-sectoral co-ordination to address fundamental causes of the problems is lacking; participation of local communities is not satisfactory.

    However, the process is at an early stage. Current activities will hopefully contribute to a future framework that properly addresses these and other obstacles. If this is accomplished, PFM and REDD can complement each other in a positive way.

  • 219.
    Enström Garnström, Åsa
    Södertörn University, School of Life Sciences.
    Science - A fishermen’s friend?: A study of communication and policy legitimacy between researchers and fishermen in Sweden2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Currently available communication studies within fisheries politics largely concern communication between scientists and decision makers, to some extent stakeholders and decision makers, but seldom merely fishermen and scientists. This thesis attempts to discuss the relationship between fishermen and scientists in Sweden, on a more local level. This is carried out through the analysis of the possible barriers blocking communication at the higher levels of the fisheries hierarchy, together with the implication of these barriers on whether fishermen find fisheries policies legitimate or not. The empirical data in this thesis is based upon face-to-face interviews, with four fishermen and four scientists concerning their involvement in communication with the opposite group. The results from these interviews are analysed through the use of a framework resting upon the basis of environmental governance, marine governance and risk communication theory. Within this theoretical base, legitimacy will be used as a central concept. As a part of the theoretical framework, communication barriers indicating a cultural difference will also be examined. In the analysis section of this thesis, indications of several communication barriers are discussed along with the respective potential effects of these barriers on the acceptance of science and the legitimacy of fisheries policies. It was found that in terms of detecting the main functions of risk communication, the lack of a structure for communication between fishermen and scientists may be holding back the full potential of communication between the two groups. The cultural differences spotted in the data are, as far as this study shows, inconclusive and do not seem severe enough to set up any potential communication barriers. Instead, this study did find four major communication barriers: media polarisation; several differing opinions within the Swedish fisheries sector; hierarchy and a lack of a communicational structure between fishermen and scientists. Although all of these communication barriers are seen as risks to legitimacy, the most significant risk appears to be lowered legitimacy due to the difference between experience-based knowledge and research-based knowledge. It is believed that a more structured communication together with cooperative research and / or cooperative management would be able to mend these barriers.Keywords: Cultural barriers, Communication barriers, Media polarisation and Knowledge bases.

  • 220.
    Ericsson, Anna
    Södertörn University College, School of Life Sciences.
    Water Availability and Distribution in Africa: Effects of the IFAD irrigation scheme in Kiru Valley, Tanzania2007Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    Abstract [en]

    The case study was made in the area of Kiru Valley, Tanzania, in order to study the conflicts over the water in the river Dodumera, and also to understand how the villages Mawemairo, Matufa and Mapea have been affected by the construction of the IFAD irrigation scheme. The aim was to connect the conflicts in the area with a general view of how water can create such conflicts. The method used in the case study was semi-structured interviews. The results from the interviews made with farmers and officials in Kiru Valley was analysed through general theories about water conflicts and theories about governing common-pool resources, such as Ostrom’s eight principles and the theory the Tragedy of the Commons. The analysis was also made through the IFAD poverty reduction strategy programme (PRSP). The conclusion made on the basis of this analysis was that the IFAD project, in Kiru Valley, was in correlation with the PRSP and an attempt to reduce poverty in the two villages Mawemairo and Matufa. The project has been very successful and has contributed to an increase of livelihood and development in the villages. However, the scheme has also affected other villages, such as Mapea. The scheme has contributed to a decrease of water availability in the Dodumera River for Mapea. Nowadays they only rely on rain-fed irrigation. The conflicts have been affected by the scheme, not so much in the quantity of the conflicts but more in the target of the conflicts. Before the construction of the scheme the conflicts was directed at the big-scale farmers, now they are directed at the scheme. On the other hand, the scheme has helped reducing the conflicts between the farmers in Mawemairo and Matufa. There are solutions to conflicts and water scarcity, such as more efficient irrigation techniques and Ostrom’s principles on governing the common-pool resources.

  • 221.
    Ericsson, Linda-Mari
    Södertörn University College, School of Life Sciences.
    Mountain Rainforest Management in Babati District, Tanzania.2005Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    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.

  • 222. Eriksen, Bente
    et al.
    Bölter, Manfred
    Breen, Karen
    Henry, Greg
    Lévesque, Esther
    Mattsson, Jan-Eric
    Södertörn University, School of Life Sciences.
    Parker, Carolyn L.
    Rayback, Shelly
    Environment and site descriptions of an ecological baseline study in the Canadian Arctic: The tundra northwest expedition 1999 (Nunavut and Northwest Territories, Canada2003In: Polarforschung, ISSN 0032-2490, Vol. 73, no 2/3, p. 77-88Article in journal (Refereed)
  • 223.
    Eriksson, Johan
    et al.
    Södertörn University, School of Social Sciences, Political science.
    Gilek, MichaelSödertörn University, School of Life Sciences, Environmental science.Rudén, Christina
    Regulating chemical risks: European and global challenges2010Collection (editor) (Other academic)
  • 224.
    Eriksson, Johan
    et al.
    Södertörn University, School of Social Sciences, Political science.
    Karlsson, Mikael
    Södertörn University, School of Life Sciences, Environmental science.
    Reuter, Marta
    Scientific Committees and EU Policy: The Case of SCHER2010In: Regulating chemical risks: European and global challenges / [ed] Johan Eriksson, Michael Gilek, Christina Rudén, Dordrecht: Springer Netherlands, 2010, p. 301-317Chapter in book (Other academic)
  • 225.
    Eriksson, Johan
    et al.
    Södertörn University, School of Social Sciences, Political science.
    Karlsson, Mikael
    Södertörn University, School of Life Sciences, Environmental science.
    Reuter, Marta
    Stockholm University.
    Technocracy, Politicization and Non-Involvement: Politics of Expertise in the European Regulation of Chemicals2010In: Review of Policy Research, ISSN 1541-132X, E-ISSN 1541-1338, Vol. 27, no 2, p. 167-185Article in journal (Refereed)
    Abstract [en]

    This article addresses the relationship between scientific expertise and policy in European chemicals regulation. We argue that the role of scientific expertise in the European regulation of chemicals varies across decision-making levels, countries, and stages of the policy process. Our case study of the role of scientific expertise in the regulation of brominated flame retardants illustrates considerably different manifestations of this interconnected process across regulatory arenas, even though this case concerns a single group of substances. On the European Union level, we find a mix of technocracy and politicization; in Sweden, a clear-cut politicization; and in Poland, noninvolvement. Such differences can be explained by a combination of factors, in particular frame dominance, and mobilization of advocacy coalitions.

  • 226.
    Eriksson, Sofia
    Södertörn University, School of Life Sciences, Environmental science. Stockholms universitet, Institutionen för naturgeografi och kvartärgeologi (INK).
    Cross-scale perspectives on heterogeneity in Swedish boreal forests2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Maintaining species diversity, ecosystem functioning, and socioeconomic values requires continued ecosystem heterogeneity across scales. This thesis aims to bridge gaps between ecological theory, environmental goals, and practical application of sustainable forest management needed to maintain such heterogeneity. Included case studies of boreal Sweden concern three challenges in the cross-scale understanding of heterogeneity: matrix qualities and composition; acquiring and incorporating historical information; and interactions between forest composition and management. Paper I cover three large-scale forest companies in four boreal counties today, outlining available information on matrix qualities and composition from the companies. Papers II-III cover the village scale from 1720s–1850s–present in Dalarna County and papers IV-V the parish scale from 1860s–present in the same county. Geographic Information Systems were used to integrate historical maps with present data, perform spatiotemporal analyses, and extract data for statistical testing in primarily generalized linear models. For the practical realization of sustainable forest management, the results indicate a need for further monitoring across scales to understand matrix composition, especially in relation to small voluntary reservations in a larger spatiotemporal perspective. Historical material can provide information on temporal connectivity and spatial separation between the past and present forest composition from analysis of change trajectories respectively interacting variables. This thesis suggests that models of forest dynamics are more relevant for local implementation of sustainable forest management efforts if including interactions between forest dynamics and ownership as an approximate driver of local change.

  • 227.
    Eriksson, Sofia
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Hammer, Monica
    Södertörn University, School of Life Sciences.
    The challenge of combining timber production and biodiversity conservation for long-term ecosystem functioning: A case study of Swedish boreal forestry2006In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 237, no 1-3, p. 208-217Article in journal (Refereed)
    Abstract [en]

    In this case study of Swedish boreal forestry, we analyze the implementation in practical management of a sustainable forest management that includes the continued capacity of ecosystems to also provide non-timber services. In the Swedish national forest policy, the equal goals of timber production and biodiversity conservation have increased the responsibility of landowners and managers to modify practical management. We compiled written information from three larger FSC-certified forestry companies combined with semi-structured interviews with forest management personnel at regional offices to map what data and information the companies collect and use. We examined to what extent obtainable information from the forest companies captures composition, structure, and function of boreal ecosystems at patch, stand and landscape scale. This was done using 47 indicators compiled from literature and grouped into five categories based on nationally identified deficiencies in the managed boreal forest compared to unmanaged forest. We found that the recording of data describing different aspects of the forest ecosystem were separated in two largely uncoordinated systems, Ecological Landscape Plans and stand registers. While there is a need for conservation-oriented data across scales, collected statistics was largely production-oriented and related to the stand scale. We also identified information gaps regarding different ecosystem structures and their spatial distribution such as dead wood and habitat networks. The knowledge base available to future management decisions also seems to lack information on connectivity in the landscape, habitat at smaller spatial scales and the effectiveness of reserved areas. To reach the ecological goals of sustainable forest management, there is a need to further coordinate existing data and information but also to fill gaps in particular regarding cross-scale information.

  • 228.
    Eriksson, Sofia
    et al.
    Södertörn University, School of Life Sciences, Environmental science. Stockholms universitet.
    Lönn, Mikael
    Södertörn University, School of Life Sciences, Biology.
    Historical perspepctives on landscape representation and forest composition in Woodland Key Habitats compared to formally protected forest in boreal SwedenManuscript (preprint) (Other academic)
    Abstract [en]

    Habitats of Swedish conservation interests are in general small and fragmented following the extensive and intensive forest management history. This study covering 71 000 ha of boreal Sweden investigates how history influences present-day distribution and composition of forests identified as high conservation value habitats and how they are protected. We also investigated if the habitat criteria used to describe reservations differed between reservation types and if habitat criteria were associated with the size of Woodland Key Habitats. The results show strong effects from historical ownership and historical forest type on the probability of an area being set aside as formally protected or as voluntary protected Woodland Key Habitats. We also found that both formal reservations and Woodland Key Habitats primarily cover coniferous forest in the age interval 70-110 years but not the presumably most valuable oldest coniferous category >110 or deciduous forests, which are as common in reservations as in other areas. Old deciduous forests (>110 years) are significantly more rare in formal reservations compared to the forest matrix. When viewed in a context of fragmentation and edge effects the results underline the importance of evaluating reserved areas and Woodland Key Habitats in a wider temporal and larger spatial perspective to optimize conservation management efforts. Maximal representation and biodiversity can be better achieved if new reservations are chosen to represent different ownership and forest history, and if they are selected in a landscape context related to present reservations and the present surrounding production forest.

  • 229.
    Eriksson, Sofia
    et al.
    Södertörn University, School of Life Sciences, Environmental science. Stockholms universitet.
    Lönn, Mikael
    Södertörn University, School of Life Sciences, Biology.
    Interactions between historical forest composition and ownership affect present composition of older forest in boreal SwedenManuscript (preprint) (Other academic)
    Abstract [en]

    In this study we reconstruct forest composition during the 1860s for a 71000 ha area in southern boreal Sweden. The aim is to show how historical ownership and associated anthropogenic disturbances act as a source of heterogeneity in the present-day distribution and composition of coniferous and deciduous forest within the commercial production forest. We use older (>110 years) and mature (70-110 years) forest as response variables in generalized linear models with a binominal error distribution. The explanatory variables include size of zone, historical type of ownership zone (village, company, and farm), amount of forest, and forest type. We focus in particular on investigating effects from interacting explanatory variables. The significant statistical associations in the study indicate that patterns of deciduous and coniferous older patches differ, and that deciduous patches differ in relation to age interval. The oldest deciduous patches, for example, are today more likely on areas that had deciduous cover also in the past and stood on forestland managed by farmers, but less likely on the same habitat managed by companies. We show that there are strong effects on present forest composition from historical ownership and forest composition. We argue that by including local data on past ownership combined with knowledge on use patterns management could be better adapted to local landscape dynamics compared to the application of overly generalized patterns or models of boreal dynamics that excludes interactions with management.

  • 230.
    Eriksson, Sofia
    et al.
    Södertörn University, School of Life Sciences, Environmental science. Stockholm University.
    Skånes, Helle
    Stockholm University.
    Addressing semantics and historical data heterogeneities in ross-temporal landscape analyses2010In: Agriculture, Ecosystems & Environment, ISSN 0167-8809, E-ISSN 1873-2305, Vol. 139, no 4, p. 516-521Article in journal (Refereed)
    Abstract [en]

    The process of recreating historical land cover dynamics, needed to nderstand trends and transient states in ecosystems, includes ifficulties such as the sensitivity of applied spatial analyses to eterogeneities in historical material. This paper compares the handling f quantitatively dominating categories in two matrix analyses of land over change within a Swedish boreal landscape (1725-1859). The focus is n how inconsistencies between historical maps can be handled without iolating the inherent semantic potential. The study shows that analyses f land cover support different indications of change depending on the reatment of dominating categories. The type of landscape and research uestions in focus should therefore be part of choosing matrix method nd classification scheme. The observed patterns need to be evaluated gainst drivers of change and semantic plasticity in classification chemes to separate ecological change from semantic confusion. This aper recommends aggregated classification schemes with maintained riginal relationships between categories in comprehensive analyses. owever, no pathway is persistent over time and categories should be llowed to disappear and new to appear. Analysis of historical dynamics ith extended transition matrixes is recommended to account for the ynamics of small categories in relation to dominating categories within landscape.

  • 231.
    Eriksson, Sofia
    et al.
    Södertörn University, School of Life Sciences, Environmental science. Stockholm University.
    Skånes, Helle
    Hammer, Monica
    Södertörn University, School of Life Sciences, Environmental science.
    Lönn, Mikael
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Current distribution of older and deciduous forests as legacies from historical use patterns in a Swedish boreal landscape (1725–2007)2010In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 260, no 7, p. 1095-1103Article in journal (Refereed)
    Abstract [en]

    We combine historical maps and satellite derived data to reconstruct the development of a Swedish boreal landscape over the past 300 years. The aim is to understand legacies from past use patterns in present-day forest composition and consequences for conservation objectives from a landscape perspective. We analyze landscape development in cross-tabulation matrixes, building change trajectories. These trajectories are tested in linear models to explain the distribution of present-day landscape composition of coniferous, mixed, and deciduous forests >110 years. Of 49 tested change trajectories, 11 showed a significant association. Associations for mixed and coniferous forests were similar and linked to characteristics such as forest continuity, which characterized the studied landscape. Deciduous older forests did not show any association to forest continuity but were more likely to occur on areas that specifically shifted from forests with grazing in the 1720s to open impediment (likely indicating low tree coverage) in the 1850s. There were large shifts and spatial redistribution in ownerships over time. Use patterns and legacies varied between small- and large-scale ownership categories as well as within small-scale categories. The legacies found in the study indicate a complex origin of heterogeneous landscape elements such as older deciduous forests. Additionally, the origin of the legacies indicates a potential need to diversify conservation management based on the influence of past use patterns. Despite large inconsistencies in historical and contemporary data we argue that this type of analysis could be used to further understand the distribution of landscape elements important for conservation objectives.

  • 232.
    Fagerström-Billai, Fredrik
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Genome wide analysis of the Ssn6-Tup11/Tup12 co-repressor complex in the fission yeast Schizosaccharomyces pombe2007Doctoral thesis, comprehensive summary (Other academic)
    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.

  • 233.
    Fagerström-Billai, Fredrik
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Durand-Dubief, Mikael
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Individual Subunits of the Ssn6-Tup11/12 corepressor are selectively required for repression of different target genes2007In: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 27, no 3, p. 1069-1082Article in journal (Refereed)
    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.

  • 234.
    Fagerström-Billai, Fredrik
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Wright, Anthony P H
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Functional comparison of the Tup11 and Tup12 transcriptional corepressors in fission yeast2005In: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 25, no 2, p. 716-727Article in journal (Refereed)
    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.

  • 235.
    Falk, Karl
    Södertörn University College, School of Life Sciences.
    Baltic 21 kontra Helcom: Hållbarhet eller Modernisering2006Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    Abstract [en]

    The purpose with the essay is to point out how the main differences of the Helsinkicommission, Helcom and Baltic 21 can be explained from a general perspective and with a specific focus on two of their ongoing projects: Baltic 21 Lighthouse projects and The Baltic Sea Joint Comprehensive Environmental Action Plan. And to investigate how the organisations them selves formulates the purpose of the two projects. This will be an indication on why environmental problems are handled with in a traditional matter although the rhetoric of the environmental politics is permeated by the concept of Sustainable Development.

    This dilemma is being treated from the theoretical approaches of Ecological Modernisation and Sustainable Development and linked to how these organisations actually carried out their work and how the historical heritage have a role to play in this complex of problems. The results of the essay shows that concrete differences exists in the way that the two organisations are constructed and how their ongoing projects are designed and formulated. These differences can be derived to the theoretical platforms Ecological Modernisation and Sustainable Development and be explained by in witch political context the organisations were created. Helcom and The Baltic Sea Joint Comprehensive Environmental Action Plan are operating within the framework of Ecological Modernisation and Baltic 21 and the Lighthouse projects within Sustainable Development.

  • 236.
    Falk, Karolina
    Södertörn University, School of Life Sciences.
    Pilotprojekt Drevfjällen, vägen till en hållbar regional utveckling?2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This study is based on a case study of Pilotprojekt Drevfjällen, a project whose ambition is tofind ways to secure nature conservation in a local context. This is promoted at governmentlevel, which says that a local connection is needed to achieve sustainable regionaldevelopment. The study, based on a theoretical background of the concept of governance,intends to evaluate whether Pilotprojekt Drevfjällen can contribute to a sustainable regionaldevelopment.This study is based on meeting documentations, semi-structured interviews with variousstakeholders in the project, field studies and participant observation at an informativemeeting. The region of interest, north Dalarna, was visited twice to obtain the specificconditions that Pilotprojekt Drevfjällen have. The interviews revealed positive attitude to theincreased dialogue and cooperation that Pilotprojekt Drevfjällen has meant for theparticipants. Some questions were raised among respondents about the concept of localmanagement and its definition as well as for the representativeness of the parish unions.The conclusions, based on the conceptual framework, is that the Pilotprojekt Drevfjällen hasmany attributes to succeed with a local connection, however, with the exception that therepresentativeness should be reviewed and elaborated further. To stimulate sustainabledevelopment the social dimension needs to be further integrated into the discussions. Theconcept of local management can´t be defined at this point. To make the process moveforward and to prevent speculation among stakeholders local management needs to be definedin a near future.

  • 237.
    Farzin, Maziar
    Södertörn University College, School of Life Sciences.
    Det svenska områdesskyddet: Ett samspel mellan diskurs och institutioner2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Sweden has had laws protecting nature for about a hundred years. In this paper the views of nature and the values that serve as a rationale for protective measures are analyzed as results of a social process characterized by the dialectic relationship between institutions and discourse. Critical discourse analysis (CDA) is used to study this relationship and the discursive practices used by institutions, which reproduce or reshape views of nature that define the relationship between society and nature. Institutional design contributes to shaping discourse in the field of nature protection, while being originally shaped by discourse. In Sweden, the national park is an institution that reproduces a view of nature as the wild and untamed opposite of society, and the natural reserves reproduce a view of nature as holder of a multi-faceted set of values intertwined with society. However, the most recently formed national park, the marine national park of the Koster sea includes resource values that threaten the hegemony of arcadian discourse within the institution and indicates social change.

  • 238.
    Fatahi, Robar
    Södertörn University College, School of Life Sciences.
    Sockerproduktionens skilda utveckling i u-länder: En jämförande fallstudie av Moçambique och Tanzania2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    How affected are the sugar production in Mozambique and Tanzania by EU sugar regime? What does the EU sugar reform constitute in these countries?

    Using theories regarding free trade and anti-free trade, I am able to answer these questions. The aim of this paper is to study how the various sugar agreements with EU affect the sugar production in Mozambique and Tanzania. Therefore I am using a method called a most similar system design in this comparative case study. The conclusion is that the EU sugar regime is the main reason to how the sugar productions in developing countries are. This conclusion is drawn since the difference in their developed sugar production is based on the importance of an advantageous sugar agreement. This can be applied to the case in Tanzania, which had a higher sugar export when the country had an advantageous sugar agreement with EU. Now when the trade has been more liberalized with the sugar reform the country does not have the same advantageous agreements with EU and the sugar export has been smaller. Compared to Tanzania Mozambique has had a better development in their sugar production, since their trade agreements with EU is better today than before 2001.

  • 239.
    Ferreira, Monica E.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska institutet.
    Studies of transcription factor domains and their interactions with other transcription factors2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

  • 240.
    Ferreira, Monica E.
    et al.
    Södertörn University, School of Life Sciences, Molecular biology.
    Berndt, Kurt D.
    Södertörn University, School of Life Sciences, Chemistry.
    Nilsson, Johan
    Södertörn University, School of Life Sciences, Molecular biology.
    Wright, Anthony P. H.
    Södertörn University, School of Life Sciences, Molecular biology.
    WD40 Domain Divergence Is Important for Functional Differences between he Fission Yeast Tup11 and Tup12 Co-Repressor Proteins2010In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 5, no 6, article id e11009Article in journal (Refereed)
    Abstract [en]

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

  • 241.
    Ferreira, Monica E
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Hermann, Stefan
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Prochasson, P
    Stowers Institute for Medical Research, Kansas City, USA.
    Workman, J L
    Stowers Institute for Medical Research, Kansas City, USA.
    Berndt, Kurt D
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Wright, Athony P H
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Mechanism of transcription factor recruitment by acidic activators2005In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 280, no 23, p. 21779-21784Article in journal (Refereed)
    Abstract [en]

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

  • 242.
    Ferreira, Monica E.
    et al.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Nilsson, Johan
    Södertörn University, School of Life Sciences, Molecular biology.
    Berndt, Kurt D.
    Södertörn University, School of Life Sciences, Chemistry. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Protein domains underlying functional divergence between the Tup11 and Tup12 co-repressor proteins in fission yeastManuscript (preprint) (Other academic)
  • 243.
    Ferreira, Monica E.
    et al.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska instiutet.
    Prochasson, Philippe
     Stowers Institute for Medical Research, Kansas City, MO, USA.
    Berndt, Kurt D.
    Södertörn University, School of Life Sciences, Chemistry. Karolinska institutet.
    Workman, Jerry L.
    Stowers Institute for Medical Research, Kansas City, MO, USA.
    Wright, Anthony P. H.
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska institutet.
    Activator-binding domains of the SWI/SNF chromatin remodeling complex characterized in vitro are required for its recruitment to promoters in vivo2009In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 276, no 9, p. 2557-2565Article in journal (Refereed)
    Abstract [en]

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

  • 244.
    Figueroa, Ricardo
    et al.
    Södertörn University, School of Life Sciences, Molecular biology. Karloinska institutet.
    Gudise, Santhosh
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska institutet.
    Larsson, Veronica
    Karloinska institutet.
    Hallberg, Einar
    Södertörn University, School of Life Sciences, Molecular biology.
    A transmembrane inner nuclear membrane protein in the mitotic spindle2010In: Nucleus, ISSN 1949-1042, Vol. 1, no 3, p. 249-253Article in journal (Refereed)
    Abstract [en]

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

  • 245. Fisher, Linda
    et al.
    Samuelsson, Malin
    Jiang, Yang
    Ramberg, Veronica
    Figueroa, Ricardo
    Södertörn University, School of Life Sciences.
    Hallberg, Einar
    Södertörn University, School of Life Sciences.
    Langel, Ulo
    Iverfeldt, Kerstin
    Targeting cytokine expression in glial cells by cellular delivery of an NF-kappa B decoy2007In: Journal of Molecular Neuroscience, ISSN 0895-8696, E-ISSN 1559-1166, Vol. 31, no 3, p. 209-219Article in journal (Refereed)
    Abstract [en]

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

  • 246.
    Flygge, Mikaela
    Södertörn University College, School of Life Sciences.
    Invisible children in the Dominican Republic: A Minor Field Study on obstacles to birth registration2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Birth registration is a fundamental key in ensuring several essential rights of the child; including the right to a name and a nationality, the right to education and health care, and protection from abuse and exploitation among others. The United Nation’s Convention on the Right of the Child establishes that the child shall be registered immediately after birth and have the right to a name and a nationality. A total of 22 % of the Dominican children under the age of five are lacking an official proof of their existence within the Dominican society and in the world. A Minor Field study was conducted during a period of two months in 2009 with the aim of clarifying what obstacles to birth registration exist in the South-western part of the Dominican Republic. This clarification will contribute to a wider understanding of the causes to non-registration and the birth registration process in the country. Semi-structured interviews have been conducted with parents to unregistered children, civil registry officials and other relevant actors in the Dominican society. The findings of the study present a wide range of obstacles to birth registration and it is clear that the reasons behind non-registration in this region are numerous, complex and often inter-related. According to most parents, officials and other informants the main obstacle to birth registration was found to be the parents’ lack of a Dominican identification card, a cédula. The lack of awareness about the importance of being registered and neglect by the parents were two other significant barriers to birth registration. The Minor Field Study was conducted with the support of the child rights organisation Plan International - República Dominicana.

  • 247.
    Folkesson, Malin
    Södertörn University College, School of Life Sciences.
    How the Community Affects a Community-Based Forest Management: Based on a Case Study in Tanzania2008Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
  • 248.
    Forsberg, Lars
    Södertörn University, School of Life Sciences.
    Genetic Aspects of Sexual Selection and Mate Choice in Salmonids2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

  • 249.
    Forsberg, Lars A.
    et al.
    Södertörn University, School of Life Sciences. Uppsala University.
    Dannewitz, J.
    Petersson, E.
    Grahn, Mats
    Södertörn University, School of Life Sciences.
    Influence of genetic dissimilarity in the reproductive success and mate choice of brown trout - females fishing for optimal MHC dissimilarity2007In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 20, no 5, p. 1859-1869Article in journal (Refereed)
    Abstract [en]

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

  • 250.
    Forsberg, Lars
    et al.
    Södertörn University, School of Life Sciences.
    Brockmark, Sofia
    Dannewitz, Johan
    Dahl, Jonas
    Preestegard, Tore
    Petersson, Erik
    Grahn, Mats
    Södertörn University, School of Life Sciences.
    Mate choice in brown trout (Salmo trutta L.) - females prefer MHC intermediate males in a fluviariumArticle in journal (Refereed)
2345678 201 - 250 of 901
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