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  • 151.
    Carlsson, Johanna
    Södertörn University College, School of Life Sciences.
    Sustainable agriculture: A field study from the Babati District in Tanzania2006Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim with this paper is to study the concept of sustainable agriculture. One angle of approach has also been to investigate the role of NGOs, where the organisation FARM-Africa is mostly studied. A field study in the Babati District is the base of the paper.

    Sustainable agriculture is a concept with various definitions and is expressed in different ways. Ecologically sound, economically viable, socially just and humane are some of the keywords within the concept of sustainable agriculture. Over the years, various technologies within the concept have been developed and have proven to be both environmentally friendly and productive, but few of these have been adopted by farmers. Scientists’ experience of agriculture often differs from that of farmers. To get the best result a collaboration between all parts in the society are needed. Participation has a long history within agriculture development. Recent studies have shown that participation is one way to success. People’s participation has therefore become one of the most common concepts within NGOs and also within government departments. Agriculture is an important issue for Tanzania and this is one reason why I have chosen to write about sustainable agriculture.

    My study will show the general oppinion of sustainable agriculture among the interviewees and the general opinion of NGOs like FARM-Africa.

  • 152.
    Carlsson, Michaela
    Södertörn University College, School of Life Sciences.
    Vegetation succession in savanna determined by interaction of grazing, browsing and fire; a comparison between hypotheses.2005Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    Abstract [en]

    Studies in tropical regions have shown that trees and grasses respond differently to fire, grazing and browsing. In African savannas, the responses to fire, grazing and browsing are different, determined by negative or positive correlations. Browsing may have other consequences than grazing because instead of increasing woody biomass it reduces it, causing increase in grass growth, leading to increase in fuel that results in more intense fires and decrease in woody biomass. Fire and herbivory are an important interactive disturbance factors affecting vegetation succession and the tree-grass dynamics in savanna environment. Several of the fire-herbivory interactions are landscape level effects, which is shown in 2 models. My hypothesis is that the tree-grass balances are determined by interactions of both grazing and fire. There have come new scientific data about fire and herbivory and the interaction effects on tree-grass dynamic and succession in the savanna. By analyzing my hypothesis through a comparison between hypotheses, Intermediate disturbance hypothesis, Janzen-Connell hypothesis and the Huston hypothesis, I propose several scenarios of the savanna tree-grass dynamics in East Africa, as a result of this comparison.

  • 153. Castillo, Luisa Eugenia
    et al.
    Martinez, Eduardo
    Ruepert, Clemens
    Savage, Candida
    Gilek, Michael
    Södertörn University, School of Life Sciences. Stockholm University.
    Pinnock, Margareth
    Solis, Efrain
    Water quality and macroinvertebrate community response following pesticide applications in a banana plantation, Limon, Costa Rica2006In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 367, no 1, p. 418-432Article in journal (Refereed)
    Abstract [en]

    Pesticides used in banana production may enter watercourses and pose ecological risks for aquatic ecosystems. The occurrence and effects of pesticides in a stream draining a banana plantation was evaluated using chemical characterization, toxicity testing and macrobenthic community composition. All nematicides studied were detected in the surface waters of the banana plantation during application periods, with peak concentrations following applications. Toxicity tests were limited to the carbofuran application and no toxicity was observed with the acute tests used. However, since pesticide concentrations were generally below the lowest LC50 value for crustaceans but above calculated aquatic quality criteria, there remains a risk of chronic toxicity. Accurate ecological assessments of pesticide use in banana plantations are currently limited by the lack of local short-term chronic toxicity tests and tests using sensitive native species. Relatively constant levels of four pesticides (imazalil, thiabendazole, chlorpyrifos and propiconazole), which had toxic effects according to the 96h hydra and 21d daphnia chronic test, were recorded in the effluent of the packing plant throughout the study, indicating that the solid waste trap used in this facility was not effective in eliminating toxic chemicals. Certain taxa, such as Heterelmis sp. (Elmidae), Heteragrion sp. (Megapodagrionidae, Odonata), Caenis sp. (Caenidae, Ephemerotera), and Smicridea sp. (Hidropsychidae, Trichoptera), were more abundant at reference sites than in the banana farm waters, and may be good candidates for toxicity testing. Multivariate analyses of the macroinvertebrate communities clearly showed that the banana plantation sites were significantly different from the reference sites. Moreover, following the pesticide applications, all the banana plantation sites showed significant changes in community composition, with the same genera being affected at all sites and for all pesticides (terbufas, cadusafos and carbofuran). Consequently, the results presented here show that multivariate analysis of community composition was more sensitive in distinguishing pesticide effects than the toxicity tests and richness and composition measures used. We conclude that monitoring macroinvertebrate communities can be a powerful tool in the assessment of ecological effects of banana production.

  • 154. Ceron, Julian
    et al.
    Swoboda, Peter
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Caenorhabditis elegans comes of age2008In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 9, no 6, p. 312-Article in journal (Other academic)
  • 155.
    Chandrasekar, Gayathri
    et al.
    Södertörn University, School of Life Sciences.
    Lauter, Gilbert
    Södertörn University, School of Life Sciences.
    Hauptmann, Giselbert
    Södertörn University, School of Life Sciences.
    Distribution of corticotropin-releasing hormone in the developing zebrafish brain2007In: Journal of Comparative Neurology, ISSN 0021-9967, E-ISSN 1096-9861, Vol. 505, no 4, p. 337-351Article in journal (Refereed)
    Abstract [en]

    Corticotropin-releasing hormone (CRH) plays a central role in the physiological regulation of the hypothalamus-pituitary-adrenal/interrenal axis mediating endocrine, behavioral, autonomic, and immune responses to stress. Despite the wealth of knowledge about the physiological roles of CRH, the genetic mechanisms by which CRH neurons arise during development are poorly understood. As a first step toward analyzing the molecular and genetic pathways involved in CRH lineage specification, we describe the developmental distribution of CRH neurons in the embryonic zebrafish, a model organism for functional genomics and developmental biology. We searched available zebrafish expressed sequence tag (EST) databases for CRH-like sequences and identified one EST that contained the complete zebrafish CRH open reading frame (ORF). The CRH precursor sequence contained a signal peptide, the CRH peptide, and a cryptic peptide with a conserved sequence motif. RT-PCR analysis showed crh expression in a wide range of adult tissues as well as during embryonic and larval stages. By whole-mount in situ hybridization histochemistry, discrete crh-expressing cell clusters were found in different parts of the embryonic zebrafish brain, including telencephalon, preoptic region, hypothalamus, posterior tuberculum, thalamus, epiphysis, midbrain tegmentum, and rostral hindbrain and in the neural retina. The localization of crh mRNA within the preoptic region is consistent with the central role of CRH in the teleost stress response through activation of the hypothalamic-pituitary-interrenal axis. The widespread distribution of CRH-synthesizing cells outside the preoptic region suggests additional functions of CRH in the embryonic zebrafish brain.

  • 156.
    Chatila, Nina
    et al.
    Södertörn University College, School of Life Sciences.
    Lindby, Fredrik
    Södertörn University College, School of Life Sciences.
    Symbolism inom turism med Kina som exempel.2006Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 157. Chen, Nansheng
    et al.
    Mah, Allan
    Blacque, Oliver E.
    Chu, Jeffrey
    Phgora, Kiran
    Bakhoum, Mathieu W.
    Newbury, C. Rebecca Hunt
    Khattra, Jaswinder
    Chan, Susanna
    Go, Anne
    Efimenko, Evgeni
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Johnsen, Robert
    Phirke, Prasad
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Swoboda, Peter
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Marra, Marco
    Moerman, Donald G.
    Leroux, Michel R.
    Baillie, David L.
    Stein, Lincoln D.
    Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics2006In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 7, no 12, p. R126-Article in journal (Refereed)
    Abstract [en]

    Background: The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in Caenorhabditis elegans and its sister species. Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes. Results: By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes ( including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of different tissue types and of daf-19(+) and daf-19(-) animals. Finally, we demonstrate that the dye-filling defect of dyf-5( mn400) animals, which is indicative of compromised exposure of cilia to the environment, is caused by a nonsense mutation in the serine/threonine protein kinase gene M04C9.5. Conclusion: Our comparative genomics-based predictions may be useful for identifying genes involved in human ciliopathies, including Bardet-Biedl Syndrome ( BBS), since the C. elegans orthologs of known human BBS genes contain X-box motifs and are required for normal dye filling in C. elegans ciliated neurons.

  • 158. Cheng, Kimberley
    et al.
    Koeck, Philip J. B.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Elmlund, Hans
    Idakieva, Krassimira
    Parvanova, Katja
    Schwarz, Heinz
    Ternström, Tomas
    Hebert, Hans
    Rapana thomasiana hemocyanin (RtH): Comparison of the two isoforms, RtH1 and RtH2, at 19 angstrom 16 angstrom resolution2006In: Micron, ISSN 0968-4328, E-ISSN 1878-4291, Vol. 37, no 6, p. 566-576Article in journal (Refereed)
    Abstract [en]

    Three-dimensional (3D) reconstructions of the two 8.4 MDa Rapana thomasiana hemocyanin isoforms, RtH1 and RtH2, have been obtained by cryoelectron microscopy of molecules embedded in vitreous ice and single particle image processing. The final 3D structures of the RtH1 and RtH2 didecamers at 19 angstrom and 16 angstrom resolution, respectively, are very similar to earlier reconstructions of gastropodan hemocyanins, revealing structural features such as the obliquely oriented subunits, the five- and two-fold symmetrical axes. Three new interactions are defined; two of them connecting the arch and the wall while the third is formed between the collar and the wall. The collar-wall connection and one of the arch-wall connections are positioned between two individual subunit dimers, while the second arch-wall connection is located between two subunits within the subunit dimer. All three interactions establish connections to the first tier of the wall. Furthermore, for each interaction we have allocated two first tier functional units most likely involved in forming the connections.

  • 159.
    Cierlik, Izabela Anna
    Södertörn University College, School of Life Sciences.
    Regulation of callose synthases and beta-1,3-glucanases during aphid infestation on barley cv. Clipper2008Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    Plant resistance hypothesis says that under a period of time when a plant is exposed to powerful herbivore attack it will prioritise defence as a major metabolic function. In theory, induced plant defence (resistance) will provide opportunities for this organism to “invest” in other functions, in example growth when attackers are absent.

    One of the compounds taking part in plant defence is callose. This β-1,3-glucan is synthesised by callose synthase and broken down by β-1,3-glucanase. Deposition of callose occurs as a reaction to aphid attack an varies, depending on cultivars, and aphid species. In this experiment barley (Hordeum vulgare) cultivar Clipper is being infested with two types of aphids: Russian wheat aphid (RWA, Diuraphis noxia) and bird cherry-oat aphid (BCA, Rhopalosiphium padi) over a time period. Infestation by those two insects results in different callose formation and deposition level.

    Six sequences encoding for putative callose synthase genes and nine sequences encoding for β-1,3-glucanase were examined by RT-PCR and Real – Time PCR methods for different expression patterns.

    The results did not show any significant regulation of gene expression during RWA and BCA attack for any of these genes. Thus the pathway regulating aphid – induced callose deposition in barley reminds unresolved.

  • 160. Clarke, A. L.
    et al.
    Weckström, K.
    Conley, D. J.
    Anderson, N. J.
    Adser, F.
    Andrén, Elinor
    Södertörn University, School of Life Sciences.
    Jonge, V. N. de
    Ellegaard, M.
    Juggins, S.
    Kauppila, P.
    Korhola, A.
    Reuss, N.
    Telford, R. J.
    Vaalgamaa, S.
    Long-Term Trends in Eutrophication and Nutrients in the Coastal Zone2006In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 51, no 1, p. 385-397Article in journal (Refereed)
    Abstract [en]

    We used high-resolution paleoecological records of environmental change to study the rate and magnitude of eutrophication over the last century in two contrasting coastal ecosystems. A multiproxy approach using geochemical and biological indicators and diatom-based transfer functions provides a long-term perspective on changes in nutrient concentrations and the corresponding biological and sedimentary responses. In Roskilde Fjord, Denmark, total nitrogen (TN) increased 85% during the last century, with the most rapid increase occurring after the 1950s, corresponding to the postwar increase in N fertilizer use. In Laajalahti Bay, an urban embayment near Helsinki, Finland, total dissolved nitrogen (TDN) increased with growing wastewater inputs and decreased with the remedial actions taken to reduce these discharges. These changes are small relative to the order of magnitude increases in nutrient loading that have occurred in northwestern Europe, where the dissolved inorganic nitrogen (DIN) load has increased more than threefold in certain areas.

  • 161.
    Cortobius Fredriksson, Moa
    Södertörn University, School of Life Sciences.
    Involvement without Influence?: Theoretical and Organisational Premises for Women´s Empowerment in Development Programmes2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The objective of the thesis is to discuss how the theoretical and organisational premises of the gender approaches of development programmes affect their possibilities to empower women and to enhance gender equality. This will be done through a study of the gender approaches of six development programmes for democratic and economic governance in the water and sanitation sector located in Angola, Ecuador, Honduras, Mexico, Paraguay and Philippines respectively. The programmes strive towards the achievement of the UN Millennium Development Goals and are financed by the Spanish Millennium Development Goals Achievement Fund. The programmes‟ gender approaches are defined as: the way the programmes interpret the concepts of women‟s empowerment and gender equality; the way they incorporate the concepts into their programme design and organisational structure, and; the activities and strategies implemented to enhance women‟s empowerment and gender equality in the programme areas. The analysis of the gender approaches of the programmes will be centred on the five theoretical assumptions which together state that a) a gender approach based on a collective postulation, with; b) adequate mechanisms for women‟s influence and; c) a purposeful involvement of men, backed-up by; d) adequate resource and responsibility allocation, and; e) a gender integrated design enabling evaluation and monitoring, is more probable to empower women. The main findings of the thesis are that: 1) all of the six gender approaches of the programmes are fundamentally individualistic and driven by efficiency rationales; 2) women‟s possible influence is generally limited and partial because of inadequate scope of participatory spaces; 3) men are not considered in any of the gender approaches; 4) the responsibility allocation for gender issues is the most important organisational feature for the implementation of the approaches, but it is weak in the majority of the programmes; 5) the integration of gender in the programme design and the funding mechanisms appear to not affect the implementation directly. Based on the results of the thesis it is concluded that both the theoretical and organisational premises of the gender approaches create small possibilities for the programmes to empower women and to enhance gender equality. The results also point to what appears to be fundamental structural weaknesses in the present gender interpretation, integration and implementation of international development agencies.

  • 162.
    Cortobius Fredriksson, Moa
    Södertörn University College, School of Life Sciences.
    ProBenefit: Implementing the Convention on Biological Diversity in the Ecuadorian Amazon2009Independent thesis Basic level (degree of Bachelor), 15 credits / 22,5 HE creditsStudent thesis
    Abstract [en]

    Legislation on benefit sharing dates back to 1992 and the commandment of the UNConvention on Biological Diversity, hence implementation still has few cases to fall back on(CBD, 1992). The case study of the project ProBenefit presented by the thesis highlights howlack of deliberation can undermine a democratic process. The objective of the thesis is thatProBenefit’s attempt to implement the standards of the CBD on access and benefit sharingwill highlight not only problems met by this specific project, but difficulties that generallymeet democratic processes in contexts of high inequality. To define if the project ProBenefitsucceeded in carrying out a deliberative process the project will be analyzed by the criteria:access to information, representation, legitimacy and involvement.The population in the project area of ProBenefit had a long history of social marginalization,which made it hard for foreign projects to gain legitimacy. The lack of independentorganizations and the late establishment of the project, which resulted in time shortage, madeit impossible to prevent the distrust of the local population. The failure of the projectcoordinators to ensure active participation of all stakeholders resulted in a late and lowinvolvement of the local participants. The absence of independent organization also madedemocratic legitimacy of the process questionable. Even if ProBenefit had a vision ofdemocratic deliberation the project was unable to break down the prevailing unequal powerdistribution which resulted in an unsustainable process and failure. The conclusion of thethesis is that the attainment of deliberation foremost depends on how a project deals with theexisting distribution of power and how it succeeds in involving all stakeholders.

  • 163. Crespo, Ana
    et al.
    Kauff, Frank
    Divakar, Pradeep K.
    del Prado, Ruth
    Perez-Ortega, Sergio
    Amo de Paz, Guillermo
    Ferencova, Zuzana
    Blanco, Oscar
    Roca-Valiente, Beatriz
    Nunez-Zapata, Jano
    Cubas, Paloma
    Argueello, Arturo
    Elix, John A.
    Esslinger, Theodore L.
    Hawksworth, David L.
    Millanes, Ana
    Carmen Molina, M.
    Wedin, Mats
    Ahti, Teuvo
    Aptroot, Andre
    Barreno, Eva
    Bungartz, Frank
    Calvelo, Susana
    Candan, Mehmet
    Cole, Mariette
    Ertz, Damien
    Goffinet, Bernard
    Lindblom, Louise
    Luecking, Robert
    Lutzoni, Francois
    Mattsson, Jan-Eric
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Ines Messuti, Maria
    Miadlikowska, Jolanta
    Piercey-Normore, Michele
    Rico, Victor J.
    Sipman, Harrie J. M.
    Schmitt, Imke
    Spribille, Toby
    Thell, Arne
    Thor, Goran
    Upreti, Dalip K.
    Lumbsch, H. Thorsten
    Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence2010In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 59, no 6, p. 1735-1753Article in journal (Refereed)
    Abstract [en]

    Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.

  • 164. Crespo, Ana
    et al.
    Lumbsch, H. Thorsten
    Mattsson, Jan-Eric
    Södertörn University, School of Life Sciences.
    Blanco, Oscar
    Divakar, Pradeep K.
    Articus, Kristina
    Wiklund, Elisabeth
    Bawingan, Paulina A.
    Wedin, Mats
    Naturhistoriska riksmuseet.
    Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 44, no 2, p. 812-824Article in journal (Refereed)
    Abstract [en]

    Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 1.20 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.

  • 165.
    Dahl, Ida
    Södertörn University College, School of Life Sciences.
    Naturvårdshänsyn i boreal bruksskog: En studie om avverkningar och avverkare i skogarna runt Saxdalen i södra Dalarna2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    As the past century’s technological development has progressed the Swedish boreal forests have transformed into dense, highly productive, homogenous and coniferous forests. The area around Saxdalen in Ludvika municipality has long been dominated forests which have been heavily worked since the 18th century. There are in Ludvika 119 000 hectares of productive forest land. Around 70 percent are owned by forest companies and 20 by private forest owners. The forestry is governed by national laws and instructions from the Swedish Forest Agency. Foresters may also choose to abide by certification systems such as FSC and PEFC. 80 percent of Swedish productive forest is certified. This thesis is based on literature review and 8 field studies of regeneration fellings in Saxdalen. The purpose of this thesis is to understand to what degree environmental considerations are taken during regeneration fellings to preserve biodiversity. The focus of the thesis has been the preservation of storm sturdy trees, deciduous trees and standing dread trees, larger tree stumps and protected zones around watercourses. The protected zones were found severely lacking in practically all the observed fellings. The quality the trees preserved varied greatly between the fellings. In this study there were no found links between the ownership form or certification system and the considerations taken during regeneration fellings. A lot of parties are involved in fellings and those responsible aren’t always in full control. The work of preserving boreal forests resilience and biodiversity must be conducted in more strategic and coordinated fashion. There must be common criteria and strategies for large forest areas so that species can spread and survive the forestry, especially considering future climate change.

  • 166.
    Davén, Jonatan
    Södertörn University College, School of Life Sciences.
    Free Primary Education in Tanzania?: A case study on costs and accessibility of primary education in Babati town2008Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    Abstract [en]

    In 2002 Tanzania initiated the implementation of the Primary Education Development Plan (PEDP), in which a substantial capacity expansion and quality improvement of primary education was outlined. The most important measure in the plan was to make primary school free and accessible to all, irrespective of financial capabilities. This thesis is a qualitative policy study, which aims at finding out whether or not primary education is free and equally accessible to all in Tanzania. Besides establishing if it is in fact free and accessible, the thesis identifies the main costs and restraints to access and also brings forward the children’s perceptions on these restraints. The answers to these questions were sought in a case study, conducted in Babati District in Northern Tanzania. Data were collected through semi-structured interviews with households, school staff and primary school children and their responses has been compared to the national policy on primary education. The main conclusions of the study are that: Primary education is not free in Tanzania, as there are significant costs involved to send a child to primary school, such as school uniform, school material and various contributions to the running costs of the school. Neither is primary education equally accessible to all, as children from households, which cannot pay these costs, are sent home from school on a regular basis. Lastly, being sent home has a damaging effect on the children’s school performances and self-esteem.

  • 167. Deadman, Mary E.
    et al.
    Lundström, Susanna L.
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences.
    Moxon, E. Richard
    Hood, Derek W.
    Specific amino acids of the glycosyltransferase LpsA direct the addition of glucose or galactose to the terminal inner core heptose of Haemophilus influenzae lipopolysaccharide via alternative linkages2006In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 281, no 40, p. 29455-29467Article in journal (Refereed)
    Abstract [en]

    Lipopolysaccharide is the major glycolipid of the cell wall of the bacterium Haemophilus influenzae, a Gram-negative commensal and pathogen of humans. Lipopolysaccharide is both a virulence determinant and a target for host immune responses. Glycosyltransferases have high donor and acceptor substrate specificities that are generally limited to catalysis of one unique glycosidic linkage. The H. influenzae glycosyltransferase LpsA is responsible for the addition of a hexose to the distal heptose of the inner core of the lipopolysaccharide molecule and belongs to the glycosyltransferase family 25. The hexose added can be either glucose or galactose and linkage to the heptose can be either beta 1-2 or beta 1-3. Each H. influenzae strain uniquely produces only one of the four possible combinations of linked sugar in its lipopolysaccharide. We show that, in any given strain, a specific allelic variant of LpsA directs the anomeric linkage and the added hexose, glucose, or galactose. Site-directed mutagenesis of a single key amino acid at position 151 changed the hexose added in vivo from glucose to galactose or vice versa. By constructing chimeric lpsA gene sequences, it was shown that the 3' end of the gene directs the anomeric linkage (beta 1-2 or beta 1-3) of the added hexose. The lpsA gene is the first known example where interstrain variation in lipopolysaccharide core structure is directed by the specific sequence of a genetic locus encoding enzymes directing one of four alternative possible sugar additions from the inner core.

  • 168.
    Delp, Gabriele
    et al.
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Molecular biology.
    Gradin, Therese
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Molecular biology.
    Ahman, Inger
    Jonsson, Lisbeth M. V.
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Molecular biology.
    Microarray analysis of the interaction between the aphid Rhopalosiphum padi and host plants reveals both differences and similarities between susceptible and partially resistant barley lines2009In: Molecular Genetics and Genomics, ISSN 1617-4615, E-ISSN 1617-4623, Vol. 281, no 3, p. 233-248Article in journal (Refereed)
    Abstract [en]

    The bird cherry-oat aphid (Rhopalosiphum padi L.) is an important pest on cereals causing plant growth reduction without specific leaf symptoms. Breeding of barley (Hordeum vulgare L.) for R. padi resistance shows that there are several resistance genes, reducing aphid growth. To identify candidate sequences for resistance-related genes, we performed microarray analysis of gene expression after aphid infestation in two susceptible and two partially resistant barley genotypes. One of the four lines is a descendant of two of the other genotypes. There were large differences in gene induction between the four lines, indicating substantial variation in response even between closely related genotypes. Genes induced in aphid-infested tissue were mainly related to defence, primary metabolism and signalling. Only 24 genes were induced in all lines, none of them related to oxidative stress or secondary metabolism. Few genes were down-regulated, with none being common to all four lines. There were differences in aphid-induced gene regulation between resistant and susceptible lines. Results from control plants without aphids also revealed differences in constitutive gene expression between the two types of lines. Candidate sequences for induced and constitutive resistance factors have been identified, among them a proteinase inhibitor, a serine/threonine kinase and several thionins.

  • 169.
    Djupedal, Ingela
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Characterization of RNA polymerase II subunit Rpb7 in silencing and transcription2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The DNA in eukaryotes is arranged in fibres of chromatin. The chromatin may be more or less compacted and the degree of condensation of the chromatin affects the accessibility of the DNA. The accessibility of the DNA, in turn, affects transcription and gene regulation. Genes within inaccessible DNA are commonly repressed whereasgenes within accessible DNA are active and expressed. This thesis concerns the interplay between chromatin and transcription with focus on the function of the RNA polymerase II (pol II) subunit Rpb7. We have demonstrated that processing of centromeric transcripts by the ribonuclease III family protein Dcr1 is required for heterochromatin formation at the centromeres of Schizosaccharomyces pombe. A point mutation in the pol II subunit Rpb7 caused a specific defect in centromeric heterochromatin formation. We have shown i) that the centromeric transcripts that accumulate in dcr1delta cells are products of pol II, ii) the rpbG150D mutation is deficient in recognition and/or initiation of transcription from the centromeric promoter. Transcription by pol II within the centromeres was surprising since insertion of marker genes within these loci normally results in repression of pol II transcription. Here, paradoxically, pol II transcription was required for the construction of the inaccessible heterochromatin structure. Our analysis of sRNA in S. pombe revealed that most centromeric siRNA are originating from two clusters, which are repeated several times within the centromeres. This lead us to propose a model in which centromeric transcripts fold into double stranded structures that are processed by Dcr1. The resulting siRNAs may contribute with the starting signal for the RNAi feedback loop required for heterochromatin formation at the centromeres. Finally, we demonstrate that the genome-wide association of Rpb7 is nearly identical to that of the core pol II subunit Rpb2, indicating a general role for Rpb7 in transcription. We further show that the occupancy pattern of Rpb4, a pol II subunit that forms a subcomplex together with Rpb7, differs from those of Rpb2 and Rpb7. Rpb4 may therefore have a less general function in transcription than Rpb7. Hence, transcription by pol II is required not only for gene expression but also for repression via formation of inaccessible heterochromatin.

  • 170.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Durand-Dubief, M.
    Babraham Institute, Cambridge, IK.
    Sinha, Indranil
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Differential Genome-wide Occupancies of RNA Polymerase II Subunits Rpb4 and Rpb7 in Fission YeastManuscript (preprint) (Other academic)
  • 171.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences.
    Ekwall, Karl
    Södertörn University, School of Life Sciences, Molecular biology.
    Epigenetics: heterochromatin meets RNAi2009In: Cell Research, ISSN 1001-0602, E-ISSN 1748-7838, Vol. 19, no 3, p. 282-295Article in journal (Refereed)
    Abstract [en]

    The term epigenetics refers to heritable changes not encoded by DNA. The organization of DNA into chromatin fibers affects gene expression in a heritable manner and is therefore one mechanism of epigenetic inheritance. Large parts of eukaryotic genomes consist of constitutively highly condensed heterochromatin, important for maintaining genome integrity but also for silencing of genes within. Small RNA, together with factors typically associated with RNA interference (RNAi) targets homologous DNA sequences and recruits factors that modify the chromatin, commonly resulting in formation of heterochromatin and silencing of target genes. The scope of this review is to provide an overview of the roles of small RNA and the RNAi components, Dicer, Argonaute and RNA dependent polymerases in epigenetic inheritance via heterochromatin formation, exemplified with pathways from unicellular eukaryotes, plants and animals.

  • 172.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences.
    Ekwall, Karl
    Södertörn University, School of Life Sciences.
    Molecular biology - The paradox of silent heterochromatin2008In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 320, no 5876, p. 624-625Article in journal (Other academic)
  • 173.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Kos-Braun, Isabelle C.
    University of Edinburgh, Edinburgh, UK / Universität Heidelberg, Heidelberg, Germany.
    Mosher, Rebecca A.
    University of Cambridge, Cambridge, UK.
    Söderholm, Niklas
    Karolinska Institutet.
    Simmer, Femke
    University of Edinburgh, Edinburgh, UK.
    Hardcastle, Thomas J.
    University of Cambridge, Cambridge, UK.
    Fender, Aurelie
    Uppsala universitet.
    Heidrich, Nadja
    Uppsala universitet.
    Kagansky, Alexander
    University of Edinburgh, Edinburgh, UK.
    Bayne, Elizabeth
    University of Edinburgh, Edinburgh, UK.
    Wagner, E. Gerhart H.
    Uppala universitet.
    Baulcombe, David C.
    University of Cambridge, Cambridge, UK.
    Allshire, Robin C.
    University of Edinburgh, Edinburgh, UK.
    Ekwall, Karl
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA2009In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 28, no 24, p. 3832-3844Article in journal (Refereed)
    Abstract [en]

    The formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 50-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1D cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity. The EMBO Journal (2009) 28, 3832-3844. doi: 10.1038/emboj.2009.351; Published online 26 November 2009

  • 174.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Portoso, M
    University of Edinburgh, Edinburgh, UK.
    Spåhr, H
    Karolinska Institutet.
    Bonilla, Carolina
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Gustafsson, C M
    Karolinska Institutet.
    Allshire, R C
    University of Edinburgh, Edinburgh, UK.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing2005In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 19, no 19, p. 2301-2306Article in journal (Refereed)
    Abstract [en]

    Fission yeast centromeric repeats are transcribed into small interfering RNA (siRNA) precursors (pre-siRNAs), which are processed by Dicer to direct heterochromatin formation. Recently, Rpb1 and Rpb2 subunits of RNA polymerase II (RNA Pol II) were shown to mediate RNA interference (RNAi)-directed chromatin modification but did not affect pre-siRNA levels. Here we show that another Pol II subunit, Rpb7 has a specific role in presiRNA transcription. We define a centromeric presiRNA promoter from which initiation is exquisitely sensitive to the rpb7-G150D mutation. In contrast to other Pol II subunits, Rpb7 promotes pre-siRNA transcription required for RNAi-directed chromatin silencing.

  • 175. Dreyer, Marion
    et al.
    Sellke, Piet
    Boström, Magnus
    Södertörn University, School of Life Sciences, Environmental science.
    Jönsson, Anna-Maria
    Södertörn University, School of Culture and Communication, Media and Communication Studies.
    Structures and processes of stakeholder and public communication on Baltic Seaenvironmental risks: RISKGOV Deliverable 102011Report (Other academic)
  • 176.
    Dristig, Caroline
    et al.
    Södertörn University College, School of Life Sciences.
    Mattsson, Therese
    Södertörn University College, School of Life Sciences.
    Panna-rye, Woraporn
    Södertörn University College, School of Life Sciences.
    Rymdturismen och dess lokala påverkan på Kiruna ur ett hållbarhetsperspektiv: en explorativ studie2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This paper contributes to a greater understanding of the new phenomenon that has occurred in tourism, thus space tourism. The intention with the paper is to study the phenomenon of space tourism and its impacts on the local community of Kiruna based on the practice of sustainable development. Our essay illustrates how the persons involved see on this attraction. It also reflects what needs to be done and what can be improved in order that space tourism not only develops to be an exciting experience, but also above all a sustainable one. The paper is exploratory and the method applied in the study is a qualitative study with a hermeneutic approach. Eight interviews with persons who can provide us facts, information and knowledge in the field of space tourism have been carried out. In the theoretical section, elements of tourism impacts concerning environmental, economic, socialand cultural aspects along with space tourism as a phenomenon and its progression are presented. This contributes to a deeper insight into what space tourism is. In the empirical part of the paper, space tourism as an experience and how space tourism in Kiruna is in the present are described. In the same section, there is a description of our informants and their activities, followed by our collected interview material divided into space tourism's impacts on Kiruna regarding environmental, economic, social and cultural aspects. In the analysis, the progression of space tourism and how the space tourism can affect Kiruna based on the three aspects concerning sustainability are discussed. In conclusion, we find that in order to develop a desirable basis for sustainable space tourism, Kiruna needs clearer guidance andactive responsibility taking. The reached result is that the participants involved must strive to create balance in all aspects of sustainable development. Focus should not only be on the economic aspect. We believe that further action is needed in the space tourism branch and wehave thus set out recommendations on how to create a sustainable development of space tourism in Kiruna. Finally, proposals for continued research are presented.

  • 177. Dryselius, Rikard
    et al.
    Nikravesh, Abbas
    Kulyté, Agné
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Goh, Shan
    Good, Liam
    Variable coordination of cotranscribed genes in Escherichia coli following antisense repression2006In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 6, p. 97-Article in journal (Refereed)
    Abstract [en]

    Background: A majority of bacterial genes belong to tight clusters and operons, which complicates gene functional studies using conventional knock-out methods. Antisense agents can down-regulate the expression of genes without disrupting the genome because they bind mRNA and block its expression. However, it is unclear how antisense inhibition affects expression from genes that are cotranscribed with the target. Results: To examine the effects of antisense inhibition on cotranscribed genes, we constructed a plasmid expressing the two reporter genes gfp and DsRed as one transcriptional unit. Incubation with antisense peptide nucleic acid (PNA) targeted to the mRNA start codon region of either the upstream gfp or the downstream DsRed gene resulted in a complete expression discoordination from this artificial construct. The same approach was applied to the three cotranscribed genes in the endogenously expressed lac-operon (lacZ, Y and A) and partial downstream expression coordination was seen when the lacZ start codon was targeted with antisense PNA. Targeting the lacY mRNA start codon region showed no effect on the upstream lacZ gene expression whereas expression from the downstream lacA gene was affected as strongly as the lacY gene. Determination of lacZ and lacY mRNA levels revealed a pattern of reduction that was similar to the Lac-proteins, indicating a relation between translation inhibition and mRNA degradation as a response to antisense PNA treatment. Conclusion: The results show that antisense mediated repression of genes within operons affect cotranscribed genes to a variable degree. Target transcript stability appears to be closely related to inhibition of translation and presumably depends on translating ribosomes protecting the mRNA from intrinsic decay mechanisms. Therefore, for genes within operons and clusters it is likely that the nature of the target transcript will determine the inhibitory effects on cotranscribed genes. Consequently, no simple and specific methods for expression control of a single gene within polycistronic operons are available, and a thorough understanding of mRNA regulation and stability is required to understand the results from both knock-down and knock-out methods used in bacteria.

  • 178. Dunleavy, Elaine M.
    et al.
    Pidoux, Alison L.
    Monet, Marie
    Bonilla, Carolina
    Richardson, William
    Hamilton, Georgina L.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institute.
    McLaughlin, Paul J.
    Allshire, Robin C.
    A NASP (N1/N2)-related protein, Sim3, binds CENP-A and is required for its deposition at fission yeast Centromeres2007In: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 28, no 6, p. 1029-1044Article in journal (Refereed)
    Abstract [en]

    A defining feature of centromeres is the presence of the histone H3 variant CENP-A(Cnp1). It is not known how CENP-A(Cnp1) is specifically delivered to, and assembled into, centromeric chromatin. Through a screen for factors involved in kinetochore integrity in fission yeast, we identified Sim3. Sim3 is homologous to known histone binding proteins NASP(Human) and N1/N2(Xenopus) and aligns with Hif1(S. cerevisiae), defining the SHNi-TPR family. Sim3 is distributed throughout the nucleoplasm, yet it associates with CENP-A(Cnp1) and also binds H3. Cells defective in Sim3 function have reduced levels of CENP-A(CnP1) at centromeres (and increased H3) and display chromosome segregation defects. Sim3 is required to allow newly synthesized CENP-A(Cnp1) to accumulate at centromeres in S and G2 phase-arrested cells in a replication-independent mechanism. We propose that one function of Sim3 is to act as an escort that hands off CENP-A(Cnp1) to chromatin assembly factors, allowing its incorporation into centromeric chromatin.

  • 179.
    Durand-Dubief, Mickael
    et al.
    Södertörn University, School of Life Sciences.
    Ekwall, Karl
    Södertörn University, School of Life Sciences.
    Heterochromatin tells CENP-A where to go2008In: Bioessays, ISSN 0265-9247, E-ISSN 1521-1878, Vol. 30, no 6, p. 526-529Article in journal (Refereed)
    Abstract [en]

    The centromere is the region of the chromosome where the kinetochore forms. Kinetochores are the attachment sites for spindle microtubules that separate duplicated chromosomes in mitosis and meiosis. Kinetochore formation depends on a special chromatin structure containing the histone H3 variant CENP-A. The epigenetic mechanisms that maintain CENP-A chromatin throughout the cell cycle have been studied extensively but little is known about the mechanism that targets CENP-A to naked centromeric DNA templates. In a recent report published in Science,((1)) such de novo centromere assembly of CENP-A is shown to be dependent on heterochromatin and the RNA interference pathway.

  • 180.
    Durand-Dubief, Mickael
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Sinha, Indranil
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Fagerström-Billai, Fredrik
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Bonilla, Carolina
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Wright, Anthony
    Södertörn University, School of Life Sciences. Karolinska Instiutet.
    Grunstein, Michael
    University of California, Los Angeles, CA, USA.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation and retrotransposon silencing2007In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 26, no 10, p. 2477-2488Article in journal (Refereed)
    Abstract [en]

    Expression profiling, ChiP-CHIP and phenotypic analysis were used to investigate the functional relationships of class III NAD(+)-dependent HDACs (Sirtuins) in fission yeast. We detected significant histone acetylation increases in Sirtuin mutants at their specific genomic binding targets and were thus able to identify an in vivo substrate preference for each Sirtuin. At heterochromatic loci, we demonstrate that although Hst2 is mainly cytoplasmic, a nuclear pool of Hst2 colocalizes with the other Sirtuins at silent regions (cen, mat, tel, rDNA), and that like the other Sirtuins, Hst2 is required for rDNA and centromeric silencing. Interestingly we found specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation. Hst2 directly represses genes involved in transport and membrane function, whereas Hst4 represses amino-acid biosynthesis genes and Tf2 retrotransposons. A specific role for Hst4 in Tf2 50 mRNA processing was revealed. Thus, Sirtuins share functions at many genomic targets, but Hst2 and Hst4 have also evolved unique functions in gene regulation.

  • 181. Dzieciatkowska, Monika
    et al.
    Liu, Xin
    Heikema, Astrid P.
    Houliston, R. Scott
    van Belkum, Alex
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences.
    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 patients2008In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 46, no 10, p. 3429-3436Article in journal (Refereed)
    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.

  • 182. Dzieciatkowska, Monika
    et al.
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences.
    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 spectrometry2008In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 29, no 10, p. 2171-2181Article in journal (Refereed)
    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.

  • 183.
    Edestav, Johanna
    Södertörn University College, School of Life Sciences.
    Water Management of River Basins: A Case Study in Kiru Valley, Tanzania2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This case study was made in Kiru Valley in the northeast Tanzania in order to study the water management to get a picture of which institutions that are involved, how conflicts are resolved, and also to see if all farmers in the area have an influence in the management. The area consists of big-scale farmers, small-scale farmers with IFAD irrigation scheme and small-scale farmers without irrigation scheme. The irrigation scheme was built in 2004 in the villages Mawemairo and Matufa. Mapea village is located downstream and has got less water after the scheme was built. The case study was conducted by semi-structured interviews with some officials at different institutions in the District, Mawemairo and Mapea and also with some farmers in Mawemairo. The results were mainly analysed with Integrated Water Resources Management approach which have been adapted by Tanzania government. Mawemairo and Matufa have established a Water Users Association (WUA) and the water management seems to work quite good for those who are members of this. But those farmers who are not members of a WUA seem to be outside of the management of the rivers in Kiru Valley. What is missing is a platform where all relevant stakeholders in Kiru Valley, like farmers, can participate in the decision-making and where conflicts can be resolved.

  • 184.
    Edholm, Fredrik
    Södertörn University College, School of Life Sciences.
    Education for all in Tanzania: A case study of the MDG footprint in Babati2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim of this paper is to investigate the impact of free education for all on the primary schools in Babati, Tanzania. The study is based on the fieldwork carried out in Babati district Tanzania, where information was gathered through qualitative methods. The empirical findings are analysed using a World Bank model of how educational inputs affects welfare outcomes. The study examines the millennium development goal with respect to giving every child an education. The study shows that a bigger impact can be seen in an increased enrolment in schools. That was the result of removing the primary school fees. This has resulted in overcrowding in the primary schools, lack of enough teachers, classrooms and learning material. However, over time the performances have improved. In the short term, the removal of school fees increased enrolment but resulted in poor quality of the education. In the long term, these problems are decreasing and the educational sector can now provide education to children that could not afford it before.

  • 185.
    Edlund, Anna
    Södertörn University, School of Life Sciences. SLU.
    Microbial diversity in Baltic Sea sediments2007Doctoral thesis, comprehensive summary (Other academic)
    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.

  • 186.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Hårdeman, Fredrik
    Södertörn University, School of Life Sciences. Karolinska institutet.
    Jansson, Janet K.
    SLU / Lawrence Berkeley National Laboratory, Berkeley, USA.
    Sjöling, Sara
    Södertörn University, School of Life Sciences.
    Active bacterial community structure along vertical redox gradients in Baltic Sea sediment2008In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, no 8, p. 2051-2063Article in journal (Refereed)
    Abstract [en]

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, -64 and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  • 187.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Jansson, Janet K.
    SLU.
    Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments2006In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, no 10, p. 6800-6807Article in journal (Refereed)
    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.

  • 188.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Jansson, Janet K.
    SLU.
    Identification of metabolically active phenanthrene transforming bacteria in polluted Baltic Sea sedimentsManuscript (preprint) (Other academic)
  • 189.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences.
    Jansson, Janet K.
    Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments2008In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 65, no 3, p. 513-525Article in journal (Refereed)
    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.

  • 190.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Soule, T
    Sjöling, Sara
    Södertörn University, School of Life Sciences.
    Jansson, J K
    Microbial community structure in polluted Baltic Sea sediments2006In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 8, no 2, p. 223-232Article in journal (Refereed)
    Abstract [en]

    Nearly half the seabed of the Baltic Proper is incapable of supporting life of higher organisms as a consequence of oxygen depletion resulting from eutrophication. However, these areas are actually teeming with microbial life. Here we used terminal-restriction fragment length polymorphism (T-RFLP) to investigate the dominant archaeal and bacterial groups, with respect to community structure, in surface layers of bottom sediments of the Baltic Sea along a coastal pollution gradient. Both archaeal and bacterial communities formed distinct clusters along the pollution gradient and the community compositions were different at the polluted sites compared with the relatively clean reference sites. The structures of the bacterial communities were most strongly correlated to water depth, followed by organic carbon, oxygen, salinity and silicate levels. In contrast, the structures of the archaeal communities were most strongly correlated to oxygen, salinity, organic carbon, silicate and nitrate levels. Some members of the microbial communities were identified using a combination of traditional and molecular approaches. Isolates obtained on different culture media were identified by partial sequencing of their 16S rRNA genes and some novel species were found. In addition, we developed a computer program, APLAUS, to elucidate the putative identities of the most dominant community members by T-RFLP.

  • 191.
    Edvardsson, Anna
    et al.
    Linköpings universitet.
    Petersson, Ulrika A.
    Södertörn University, School of Life Sciences. Stockholms universitet.
    Shapiguzov, Alexey
    Linköpings universitet.
    Schröder, Wolfgang P
    Södertörn University, School of Life Sciences. 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 thalianaManuscript (preprint) (Other academic)
  • 192. Edvardsson, Anna
    et al.
    Shapiguzov, Alexey
    Petersson, Ulrika A.
    Södertörn University, School of Life Sciences. 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 AtCYP20-22007In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 46, no 33, p. 9432-9442Article in journal (Refereed)
    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.

  • 193.
    Eek, Eleonor
    Södertörn University College, School of Life Sciences.
    Stockholms kommuns klimatanpassningsarbete2008Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    I den här uppsatsen görs en studie av vilka förväntade effekter vid en klimatförändring som kan drabba Stockholms kommun, hur kommunens klimatanpassningsarbete ser ut samt vilka prioriteringar som görs i kommunens klimatanpassningsarbete. I studien har jag valt att även ta med en annan aktör, Stockholm Vatten på grund av att de äger och sköter vatten- och avloppsnäten och vattenreservoarerna i Stockholm och är därmed en viktig aktör i Stockholms kommuns klimatanpassningsarbete. Syftet är att göra en studie av Stockholms kommun för att ta reda på hur kommunen kan komma att påverkas av en klimatförändring och hur kommunens klimatanpassningsarbete ser ut. För att komma fram till resultatet har en person intervjuats på miljöförvaltningen, mailkontakt med en person som jobbar inom Stockholm Vatten är genomförd och sekundära källor har också använts. I teoridelen har jag använt mig av Ekologisk hållbarhet, Ekonomisk hållbarhet, Social hållbarhet samt proaktiv och reaktiv planering för att analysera resultatet.

    En klimatförändring kan påverka Stockholms kommun på många sätt och effekterna som kan drabba kommunen kan bli många, bland annat en ökad nederbörd, översvämningar, utslagen dricksvattenförsörjning, föroreningar, ökad påfrestning på samhällsystemen, ökad risk för ras och skred, temperaturförändringar och påverkan på hela ekosystemet. Sverige kommer att få ett klimat med att få kalla dagar och många extremt varma dagar och detta är en stor hälsorisk på grund av att många människor inte kommer att klara av temperaturförändringen och värmen kommer även att göra att smittor och sjukdomar sprids lättare. Många verksamheter kommer att påverkas i andra länder och detta kommer i sin tur att påverka utvecklingen och behovet av anpassning i Sverige. Om inga åtgärder görs kommer Mälardalen år 2020 att ha en medeltemperatur som dagens Skåne.

    Kommunen har tagit del av utredningar och rapporter, men än har inte klimatanpassningsarbetet kommit igång. De arbeten som pågår idag är främst byggandet av energieffektiva bostäder samt att markprover har gjorts i vissa områden för att analysera markföroreningar. De prioriteringar som kommunen gör i klimatanpassningsarbetet är energieffektiviseringar i byggnader samt att informera befolkningen för att kunna minska utsläppen genom beteendeförändringar. Slussen är även en prioritering eftersom att området ligger i riskzonen för översvämning och detta skulle få stora konsekvenser för dricksvattnet. Stockholms kommun med sin unika natur och naturvärden måste anpassa stadsplaneringen för en större befolkning samtidigt som en klimatanpassning måste ske och detta ställer höga krav på kommunens klimatanpassningsarbete. En större befolkning kommer öka kommunens påfrestning på miljön och åtgärder måste göras för att påfrestningen blir så liten som möjligt.

    Målen i det kommande miljöprogrammet, i översiktsplanen och i vision 2030 förverkligar en ekologisk hållbarhet, ekonomisk hållbarhet, social hållbarhet samt en proaktiv planering som gör att en hållbar samhällsutveckling och samhällsplanering kan uppfyllas. Mycket arbete är dock kvar innan alla målen är uppfyllda och kommunen har en minimal miljöpåverkan.

  • 194.
    Efimenko, Evgeni
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    The study of sensory cilia development in caenorhabditis elegans2008Doctoral thesis, comprehensive summary (Other academic)
    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.

  • 195.
    Efimenko, Evgeni
    et al.
    Södertörn University, School of Life Sciences. 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
    Södertörn University, School of Life Sciences. Karolinska Instiute.
    Caenorhabditis elegans DYF-2, an orthologue of human WDR19, is a component of the intraflagellar transport machinery in sensory Cilia2006In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 17, no 11, p. 4801-4811Article in journal (Refereed)
    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.

  • 196.
    Efimenko, Evgeni
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Bubb, K
    Mak, H Y
    Holzman, T
    Leroux, M R
    Ruvkun, G
    Thomas, J H
    Swoboda, Peter
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Analysis of xbx genes in C-elegans2005In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 132, no 8, p. 1923-1934Article in journal (Refereed)
    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.

  • 197.
    Ekane, Duone
    Södertörn University College, School of Life Sciences.
    The Exploitation and Conservation of prunus africana in the Mount Cameroon Region of Cameroon2008Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The exploitation of natural resources in general and biodiversity in particular by human beings, is remarked to be associated with unsustainable practices that place the survival of these resources at stake. An assessment of the exploitation of prunus africana around the mount Cameroon region can be linked with the trend of unsustainable exploitation prevailing in other parts of the world. Prunus africana, is a tree cherished by the local population for its varied values, with its medicinal values propelling it to international popularity. This has been characterized by the massive demand for its bark by western pharmaceutical companies. The huge demand of the tree in the international market is remarked to be a major factor that contributed to the tree’s mass unsustainable exploitation by the local population in the studied region. This paper has looked at the factors responsible for the mass unsustainable exploitation of prunus and the measures that local based organizations, MOCAP-CIG and MCP had adopted to promote participatory management of the tree. Three major factors; poverty, the issuing of 50 exploitation permits and international demand were identified to have contributed to the involvement of the local population in unsustainable exploitation of the tree. The concept of sustainable development was used as the theoretical framework to examine if the three dimensions can be attained without one affecting the other. The results showed that it is quite difficult to achieve this especially in the case of  the exploitation and conservation of prunus africana.

  • 198. Ekblom, Robert
    et al.
    Saether, Stein Are
    Jacobsson, Pär
    Fiske, Peder
    Sahlman, Tobias
    Grahn, Mats
    Södertörn University, School of Life Sciences.
    Kålås, John Atle
    Höglund, Jacob
    Spatial pattern of MHC class II variation in the great snipe (Gallinago media)2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 7, p. 1439-1451Article in journal (Refereed)
    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.

  • 199.
    Ekedahl, Sanna
    Södertörn University, School of Life Sciences.
    Trädet, tillståndet, turerna: Konflikten i samband med beslutet om TV-ekens fällning2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In the autumn of 2011 a veteran oak of protective value, ”TV-eken”, located on Oxenstiernsgatan in the city district Östermalm in Stockholm, was felled. The decision to fell the tree – officially a technical decision to fell a high-risk tree, whereas protesting people interpeted the decision completely different – caused a conflict between responsible decision-takers and people fighting to preserve the tree. The aim of this study is to understand what events and processes lead up to the conflict arising from the decision to fell the ”TV-eken” tree. Responsible decision-taking public official at the traffic administration in the city of Stockholm has been interviewed as well as three oak activists. The interviews have been complemented by reviews of some relevant documents. Due to the background of the conflicting parties and the parties' preconceived view of the opposite party, the conflict developed to be all about more questions than the factual question (i.e. the felling of the oak). New studies that were performed in order to examine the state of the oak exacerbated the conflict as none of the studies were considered legitimate by both parties. Both parties have expressed substantial suspiciousness towards the other party and many actings have been interpreted as strategical. Inadequate communication between the parties is the general explanation to the origin and increase of the conflict.

  • 200.
    Eklund, Jessica
    Södertörn University College, School of Life Sciences.
    Agroforestry as a tool toward sustainable development in Babati district2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In Babati district, Tanzania, agro-forestry land use system has been traditionally used for hundreds of years. It is a multi layer system with trees and/or bushes integrated with crops. That knowledge has been extended in the district through the land management programme, LAMP. It is said to be a “win-win” system with both economic and ecologic benefits. For a land use system to be sustainable, three spheres have to incorporate to reach a balanced development; the economic sphere, the ecologic sphere and the social sphere. To achievesustainable development, one sphere can not develop without the others. This study aims tosee if agro-forestry in Babati district balances all three spheres, if it is a proper tool toward sustainable development. It is a qualitative case study with semi-structured interviews with farmers in Babati and one interview in Sweden. The fieldwork in Babati where held under two weeks, based on interviews with farmers who practice agro-forestry and farmers who do not, and their opinion about it. The result indicates that it employs a lot of people and that the economy among farmers in the district has improved. Most farmers say their economy is more secure, because it is a multipurpose system and most people can adopt the technologies because high costs or advanced technology are not required. Farmers benefit from the ecosystem services provided from agro-forestry, for example water catchment and decreased soil erosion which also improves the environment. Soils regain their fertility and the land use becomes more resilient when trees integrate with crops. Many farmers believe the equity between gender has improved and that condition for women improves when fuel wood can be gathered from trees on the farm instead of walking long distances to a forest. The conclusion is that agro-forestry in Babati district fulfill more or less all three sustainability spheres and is a useful tool towards sustainable development, but has not yet reached full potential, there are possibilities for improvements and to scale up for greater benefits for all three spheres.

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