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Now showing items 3546-3565 of 5209
  • Noschis, Elias (Helsingin yliopisto, 2006)
    The TOTEM experiment at the LHC will measure the total proton-proton cross-section with a precision better than 1%, elastic proton scattering over a wide range in momentum transfer -t= p^2 theta^2 up to 10 GeV^2 and diffractive dissociation, including single, double and central diffraction topologies. The total cross-section will be measured with the luminosity independent method that requires the simultaneous measurements of the total inelastic rate and the elastic proton scattering down to four-momentum transfers of a few 10^-3 GeV^2, corresponding to leading protons scattered in angles of microradians from the interaction point. This will be achieved using silicon microstrip detectors, which offer attractive properties such as good spatial resolution (<20 um), fast response (O(10ns)) to particles and radiation hardness up to 10^14 "n"/cm^2. This work reports about the development of an innovative structure at the detector edge reducing the conventional dead width of 0.5-1 mm to 50-60 um, compatible with the requirements of the experiment.
  • Ronkainen, Tiina (Helsingin yliopisto, 2015)
    Northern peatlands form a large storage of terrestrial carbon and at the same time they provide an important palaeoecological archive to study past climate changes and associated carbon dynamics. One of the most widely used methods to study peatland histories is the plant macrofossil method. However, peat material of the early succession stages, the fens, is often highly decomposed hampering the identification of the fossil plant remains. Thus, current methods may give only a partial view on the past vegetation, and as a result the accuracy of carbon balance estimations and climate implications may remain low. A new promising method to study past plant assemblages from peat is the geochemical plant biomarker method, which has performed well in less decomposed bog peat environments. In my study I assess the applicability of the geochemical plant biomarker method to study past plant assemblages from highly decomposed fen peat. For the first time I apply a living fen plant biomarker training set to study past fen phases. To do this, I collected and analysed two sets of living key fen plants. The training sets included boreal fen, arctic fen and permafrost peat plateau plants. The biomarker analyses on fossil peat were applied in parallel with macrofossil analyses to two boreal and one arctic permafrost peat section, all known to contain highly decomposed peat. The analyses of living plants showed that the biomarker compositions did not differ between the same species collected from different bioclimatic zones, suggesting that, at least to some extent, plant biomarkers can be used universally beyond the geographical areas where the training set was collected. The plant biomarker analyses indicate that the n-alkanes, and their ratios, are the most useful compounds to separate fen plant groups: Sphagnum mosses and vascular plants. Results showed also that biomarker composition of fen plants did not differ substantially from their bog counterparts. However, results indicated that when a wider combination of plants, plant parts and peatland habitats are incorporated into the training set the data interpretation becomes more challenging. For example, the biomarker composition of Sphagnum mosses and sedge roots resembled each other despite their differences in biology. Thus, a larger set of proxies is advisable when plant groups need to be separated more accurately. In the peat sections studied here, the biomarker method performed well in less humified bog peat layers but less well in the highly decomposed fen peat layers. The macrofossil method proved to be most competitive proxy to reconstruct past vegetation assemblages and local environmental conditions through-out the peat sections. However, when macrofossil and biomarker data were interpreted in parallel, it became clear that biomarkers were also able to reflect the major changes in dominating plant groups and in moisture conditions. Accordingly, the analysis separated the most important bog microhabitats and the major regime shifts from fen to bog. I conclude, however, that in fen environments the interpretation of biomarker data can be rather challenging. As a result, it appears that the biomarker method, as applied here, performs the best as a complimentary proxy when used in conjunction with macrofossils, and that the data should be interpreted cautiously.
  • Tarmi, Sanna (Helsingin yliopisto, 2011)
    Agri-environmental schemes have so far resulted in only minor positive implications for the biodiversity of agricultural environments, in contrast to what has been expected. Land-use intensification has decreased landscape heterogeneity and the amount of semi-natural habitats. Field margins are uncultivated areas of permanent vegetation located adjacent to fields. Since the number of these habitats is high, investing in their quality may result in more diverse agricultural landscapes. Field margins can be considered as multifunctional habitats providing agronomic, environmental and wildlife services. This thesis aimed at examining the plant communities of different types of field margin habitats and the factors affecting their species diversity and composition. The importance of edaphic, spatial and management factors was studied on regional, landscape and habitat scales. Vegetation surveys were conducted on regional and landscape scales and a field experiment on cutting management was conducted on a habitat scale. In field margin plant communities, species appeared to be indicators of high or intermediate soil fertility and moist soil conditions. The plant species diversity found was rather low, compared with most species-rich agricultural habitats in Finland, such as dry meadows. Among regions, land-use history, main production line, natural species and human induced distribution, climate and edaphic factors were elements inducing differences in species composition. The lowest regional species diversity of field margins was related to intensive and long-term cereal production. Management by cutting and removal or grazing had a positive effect on plant species diversity. The positive effect of cutting and removal on species richness was also dependent on the adjacent source of colonizing species. Therefore, in species-poor habitats and landscapes, establishment of margins with diverse seed mixtures can be recommended for enhancing the development of species richness. However, seed mixtures should include only native species preferably local origin. Management by cutting once a year for 5 years did not result in a decline in dominance of a harmful weed species, Elymus repens, showing that E. repens probably needs cutting more frequently than once per year. Agri-environmental schemes should include long-term contracts with farmers for the establishment, and management by cutting and removal or grazing, of field margins that are several metres wide. In such schemes, the timing and frequency of management should be planned so as not to harm other taxa, such as the insects and birds that are dependent on these habitats. All accidental herbicide drifts to field margins should be avoided when spraying the cultivated area to minimize the negative effects of sprayings on vegetation. The harmful effects of herbicides can be avoided by organic farming methods.
  • Vahisalu, Triin (Helsingin yliopisto, 2010)
    Plants are rooted to their growth place; therefore it is important that they react adequately to changes in environmental conditions. Stomatal pores, which are formed of a pair of guard cells in leaf epidermis, regulate plant gas-exchange. Importantly, guard cells protect the plant from desiccation in drought conditions by reducing the aperture of the stomatal pore. They serve also as the first barrier against the major air pollutant ozone, but the behaviour of guard cells during ozone exposure has not been sufficiently addressed. Aperture of the stomatal pore is regulated by the influx and efflux of osmotically active ions via ion channels and transporters across the guard cell membrane, however the molecular identity of guard cell plasma membrane anion channel has remained unknown. In the frame of this study, guard cell behaviour during ozone exposure was studied using the newly constructed Arabidopsis whole-rosette gas-exchange system. Ozone induced a Rapid Transient Decrease (RTD) in stomatal conductance within 10 min from the start of exposure, which was followed by a recovery in the conductance within the next 40 min. The decrease in stomatal conductance was dependent on the applied ozone concentration. Three minutes of ozone exposure was sufficient to induce RTD and further ozone application during the closure-recovery process had no effect on RTD, demonstrating that the whole process is programmed within the first three minutes. To address the molecular components responsible for RTD, the ozone response was measured in 59 different Arabidopsis mutants involved in guard cell signalling. Four of the tested mutants slac1 (originally rcd3), ost1, abi1-1 and abi2-1 lacked RTD completely. As the ozone sensitive mutant slac1 lacked RTD, the next aim of this study was to identify and characterize SLAC1. SLAC1 was shown to be a central regulator in response to all major factors regulating guard cell aperture: CO2, light/darkness transitions, ozone, relative air humidity, ABA, NO, H2O2, and extracellular Ca2+. It encodes the first guard cell plasma membrane slow type anion channel to be identified at the molecular level. Interestingly, the rapid type anion conductance was intact in slac1 mutant plants. For activation, SLAC1 needs to be phosphorylated. Protein kinase OST1 was shown to phosphorylate several amino acids in the N-terminal tail of SLAC1, Ser120 was one of its main targets, which led to SLAC1 activation. The lack of RTD in type 2C protein phosphatase mutants abi1-1 and abi2-1, suggests that these proteins have a regulatory role in ozoneinduced activation of the slow type anion channel.
  • Jauni, Miia (Helsingin yliopisto, 2012)
    Plant invasions cause a serious threat to native biodiversity. Agricultural habitats are highly disturbed and often invaded by the alien plant species. Generally, the success of a plant invader depends on the abiotic (e.g. climate, habitat properties) and biotic factors (e.g. the characteristics of the invader and interaction with the resident species). In this thesis, I determined the invasion level of alien plant species in Finnish agricultural habitats. In addition, I assessed the environmental conditions and species characteristics affecting plant invasions, and the alien species impact on native species richness and diversity. The invasion level of alien plant species varied between different types of semi-natural agricultural habitats, geographical regions and study years. Generally, more frequently disturbed and more intensively managed habitats (e.g. field and road verges) were more often invaded by alien plants than infrequently disturbed and managed habitats (e.g. grassland). However, the effect of disturbance regime tended to depend on residence time of the alien plant species, and vary among the alien plant species. The invasion level decreased towards north with decreasing temperature and increased towards east with increasing continentality. The geographical trends may be explained by climate, migration history and land-use intensity. In addition, alien plant species diversity increased with higher native plant species diversity. Thus, the results suggest that species interactions, especially competition, with resident plant species do not limit plant invasions in semi-natural agricultural habitats. The positive relationship between native and alien species may be caused by both suitable environmental conditions and spatial heterogeneity in environmental conditions partly created by disturbance of agricultural habitats. The species traits of alien plant species are habitat-specific and strongly related environmental conditions. I did not find evidence that alien plants species cause a severe threat to native plant diversity in Finnish semi-natural habitats. The most harmful invasive plant species are still rare in Finnish agricultural landscape. In the future, the pressure of establishment and spread of alien species can be assumed to increase. Thus, regular monitoring is needed for early detection of new species and detection of the changes in the distribution and the spread of established alien species. The fact that plant invasions are species-specific and depended on environmental characteristics calls for habitat- and species-specific studies on the impacts of alien species and on the determinants of plant invasion at multiple spatial scales.
  • Kanerva, Sanna (2007)
    The aim of this study was to explore soil microbial activities related to C and N cycling and the occurrence and concentrations of two important groups of plant secondary compounds, terpenes and phenolic compounds, under silver birch (Betula pendula Roth), Norway spruce (Picea abies (L.) Karst) and Scots pine (Pinus sylvestris L.) as well as to study the effects of volatile monoterpenes and tannins on soil microbial activities. The study site, located in Kivalo, northern Finland, included ca. 70-year-old adjacent stands dominated by silver birch, Norway spruce and Scots pine. Originally the soil was very probably similar in all three stands. All forest floor layers (litter (L), fermentation layer (F) and humified layer (H)) under birch and spruce showed higher rates of CO2 production, greater net mineralisation of nitrogen and higher amounts of carbon and nitrogen in microbial biomass than did the forest floor layers under pine. Concentrations of mono-, sesqui-, di- and triterpenes were higher under both conifers than under birch, while the concentration of total water-soluble phenolic compounds as well as the concentration of condensed tannins tended to be higher or at least as high under spruce as under birch or pine. In general, differences between tree species in soil microbial activities and in concentrations of secondary compounds were smaller in the H layer than in the upper layers. The rate of CO2 production and the amount of carbon in the microbial biomass correlated highly positively with the concentration of total water-soluble phenolic compounds and positively with the concentration of condensed tannins. Exposure of soil to volatile monoterpenes and tannins extracted and fractionated from spruce and pine needles affected carbon and nitrogen transformations in soil, but the effects were dependent on the compound and its molecular structure. Monoterpenes decreased net mineralisation of nitrogen and probably had a toxic effect on part of the microbial population in soil, while another part of the microbes seemed to be able to use monoterpenes as a carbon source. With tannins, low-molecular-weight compounds (also compounds other than tannins) increased soil CO2 production and nitrogen immobilisation by soil microbes while the higher-molecular-weight condensed tannins had inhibitory effects. In conclusion, plant secondary compounds may have a great potential in regulation of C and N transformations in forest soils, but the real magnitude of their significance in soil processes is impossible to estimate.
  • Eeva, Manu (Helsingin yliopisto, 2010)
    A reversed-phase, high-performance liquid chromatographic method (RP-HPLC) with atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) detection was developed utilising Turbo Method Development® and DryLab® programmes for the separation and identification of coumarins in Peucedanum palustre L. (Moench) and Angelica archangelica (L.) var. archangelica both belonging to the endemic flora of Finland. Fifteen coumarins were identified both in P. palustre and in A. archangelica. This is the first report on the xanthotoxin, isopimpinellin, pimpinellin, and coumarin composition of the umbels of P. palustre. The coumarin composition of Finnish P. palustre populations was analyzed and verified chromatographically. The main coumarin in roots was oxypeucedanin, and in aerial parts peulustrin/isopeulustrin. The highly varying total coumarin concentration was the highest in umbels and the lowest in stems. Leaves and roots contained comparable amounts of coumarins. The total coumarin concentration decreased towards the north. As regards the aerial parts, the coumarin content of the umbels and leaves resembled each other the most. The effective temperature sum clearly correlated with the coumarin concentrations of the aerial parts, but not with the roots of the plant. The study did not support the existence of chemotypes in Finnish P. palustre populations. A spontaneously embryogenic cell line of A. archangelica was established from seedlings via callus formation. The highest coumarin production was achieved after three weeks of cultivation in the medium containing 3.0% sucrose. Cryopreservation was found to be a suitable method for storing the cell line. Plantlets propagated in an air-sparged bioreactor were transferable directly to soil. The coumarin composition and levels in the regenerated plants were comparable to those in intact plants. A mathematical computer-aided model CELLOP was constructed in which the desirability functions in a three-dimensional experimental design are used for optimising the growing conditions for plant cultures. The calcium, inorganic nitrogen, and sucrose concentrations in the medium were optimised for coumarin-producing, spontaneously embryogenic cell lines of A. archangelica and P. palustre. In comparison to the reference, the dry mass for A. archangelica was 24.7% and the coumarin concentration 40.5% higher in the optimised conditions, and the dry mass for P. palustre 61.8% and the coumarin concentration 58.1% higher. For A. archangelica the highest embryogenic activity occurred in the medium containing 1.25 mM calcium and for P. palustre in the medium containing 50.0 mM NO3- and 4.01 mM NH4+.
  • Ma, Maohua (Helsingin yliopisto, 2006)
    Buffer zones are vegetated strip-edges of agricultural fields along watercourses. As linear habitats in agricultural ecosystems, buffer strips dominate and play a leading ecological role in many areas. This thesis focuses on the plant species diversity of the buffer zones in a Finnish agricultural landscape. The main objective of the present study is to identify the determinants of floral species diversity in arable buffer zones from local to regional levels. This study was conducted in a watershed area of a farmland landscape of southern Finland. The study area, Lepsämänjoki, is situated in the Nurmijärvi commune 30 km to the north of Helsinki, Finland. The biotope mosaics were mapped in GIS. A total of 59 buffer zones were surveyed, of which 29 buffer strips surveyed were also sampled by plot. Firstly, two diversity components (species richness and evenness) were investigated to determine whether the relationship between the two is equal and predictable. I found no correlation between species richness and evenness. The relationship between richness and evenness is unpredictable in a small-scale human-shaped ecosystem. Ordination and correlation analyses show that richness and evenness may result from different ecological processes, and thus should be considered separately. Species richness correlated negatively with phosphorus content, and species evenness correlated negatively with the ratio of organic carbon to total nitrogen in soil. The lack of a consistent pattern in the relationship between these two components may be due to site-specific variation in resource utilization by plant species. Within-habitat configuration (width, length, and area) were investigated to determine which is more effective for predicting species richness. More species per unit area increment could be obtained from widening the buffer strip than from lengthening it. The width of the strips is an effective determinant of plant species richness. The increase in species diversity with an increase in the width of buffer strips may be due to cross-sectional habitat gradients within the linear patches. This result can serve as a reference for policy makers, and has application value in agricultural management. In the framework of metacommunity theory, I found that both mass effect(connectivity) and species sorting (resource heterogeneity) were likely to explain species composition and diversity on a local and regional scale. The local and regional processes were interactively dominated by the degree to which dispersal perturbs local communities. In the lowly and intermediately connected regions, species sorting was of primary importance to explain species diversity, while the mass effect surpassed species sorting in the highly connected region. Increasing connectivity in communities containing high habitat heterogeneity can lead to the homogenization of local communities, and consequently, to lower regional diversity, while local species richness was unrelated to the habitat connectivity. Of all species found, Anthriscus sylvestris, Phalaris arundinacea, and Phleum pretense significantly responded to connectivity, and showed high abundance in the highly connected region. We suggest that these species may play a role in switching the force from local resources to regional connectivity shaping the community structure. On the landscape context level, the different responses of local species richness and evenness to landscape context were investigated. Seven landscape structural parameters served to indicate landscape context on five scales. On all scales but the smallest scales, the Shannon-Wiener diversity of land covers (H') correlated positively with the local richness. The factor (H') showed the highest correlation coefficients in species richness on the second largest scale. The edge density of arable field was the only predictor that correlated with species evenness on all scales, which showed the highest predictive power on the second smallest scale. The different predictive power of the factors on different scales showed a scaledependent relationship between the landscape context and local plant species diversity, and indicated that different ecological processes determine species richness and evenness. The local richness of species depends on a regional process on large scales, which may relate to the regional species pool, while species evenness depends on a fine- or coarse-grained farming system, which may relate to the patch quality of the habitats of field edges near the buffer strips. My results suggested some guidelines of species diversity conservation in the agricultural ecosystem. To maintain a high level of species diversity in the strips, a high level of phosphorus in strip soil should be avoided. Widening the strips is the most effective mean to improve species richness. Habitat connectivity is not always favorable to species diversity because increasing connectivity in communities containing high habitat heterogeneity can lead to the homogenization of local communities (beta diversity) and, consequently, to lower regional diversity. Overall, a synthesis of local and regional factors emerged as the model that best explain variations in plant species diversity. The studies also suggest that the effects of determinants on species diversity have a complex relationship with scale.
  • Sipilä, Timo (Helsingin yliopisto, 2009)
    Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.
  • Siljander, Pia (Helsingin yliopisto, 2000)
  • Tirri, Henry (Helsingin yliopisto, 1997)
  • Kulikov, Vadim (Helsingin yliopisto, 2011)
    The most prominent objective of the thesis is the development of the generalized descriptive set theory, as we call it. There, we study the space of all functions from a fixed uncountable cardinal to itself, or to a finite set of size two. These correspond to generalized notions of the universal Baire space (functions from natural numbers to themselves with the product topology) and the Cantor space (functions from natural numbers to the {0,1}-set) respectively. We generalize the notion of Borel sets in three different ways and study the corresponding Borel structures with the aims of generalizing classical theorems of descriptive set theory or providing counter examples. In particular we are interested in equivalence relations on these spaces and their Borel reducibility to each other. The last chapter shows, using game-theoretic techniques, that the order of Borel equivalence relations under Borel reduciblity has very high complexity. The techniques in the above described set theoretical side of the thesis include forcing, general topological notions such as meager sets and combinatorial games of infinite length. By coding uncountable models to functions, we are able to apply the understanding of the generalized descriptive set theory to the model theory of uncountable models. The links between the theorems of model theory (including Shelah's classification theory) and the theorems in pure set theory are provided using game theoretic techniques from Ehrenfeucht-Fraïssé games in model theory to cub-games in set theory. The bottom line of the research declairs that the descriptive (set theoretic) complexity of an isomorphism relation of a first-order definable model class goes in synch with the stability theoretical complexity of the corresponding first-order theory. The first chapter of the thesis has slightly different focus and is purely concerned with a certain modification of the well known Ehrenfeucht-Fraïssé games. There we (me and my supervisor Tapani Hyttinen) answer some natural questions about that game mainly concerning determinacy and its relation to the standard EF-game