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  • Kaukinen, Pasi (Helsingin yliopisto, 2004)
  • Lefebvre, Sylvie (Helsingin yliopisto, 2012)
    Several embryonic organs, such as the hair follicle, develop as appendages of the ectoderm, the outermost layer of the embryo. These organs develop as a result of reciprocal tissue interactions between the surface epithelium and the underlying mesenchyme. The fi rst morphological sign of a developing hair follicle is a thickening of the epithelium called a placode. Several major signaling pathways are important for the development of hair and other ectodermal organs such as Wnts, fi broblast growth factors (Fgfs), Transforming growth factor-beta (TGF-beta), Hedgehogs (Hh) and tumor necrosis factors (TNFs). This thesis focuses on the role of TNFs in hair development and more particularly on one member of the TNF superfamily: Ectodysplasin (Eda). Mutations in Eda pathway components including the TNF ligand Eda, its receptor (Edar), and downstream effectors essential for activation of transcription factor NFbappaB in mouse or human give rise to a disease called hypohidrotic ectodermal dysplasia (HED). HED is an inherited disorder characterized by impaired development of ectodermal organs such as hair, teeth and several exocrine glands. A hallmark of mouse HED (Eda null mouse) is the absence of primary hair placodes that form at embryonic day 14 (E14). In order to identify the direct target genes of Eda, we have performed a microarray analysis on genes differentially expressed upon short exposure to recombinant Eda protein on Eda null skin at E14. Several of the genes identifi ed belong to the major signaling pathways mentioned above and interestingly, include also six chemokines that have not previously been associated with hair follicle morphogenesis. The purpose of this study was to validate whether the upregulated genes were truly transcriptional target genes of Eda/NFkappaB and to study their functional relevance in ectodermal organogenesis, in particular in hair follicle development. Based on these studies, we were able to confirm some Wnt pathway members, such as Dkk4 and Lrp4,TNF family member A20, and two chemokines, cxcl10 and cxcl11, as likely direct target genes of Eda. It is shown that whereas Dkk4 and Lrp4 are expressed in all ectodermal organs, A20 and the two chemokines seem to be hair follicle specific. Further study of Dkk4 and Lrp4 during development led us to conclude that Wnt and Eda pathways interact closely to fine tune the development of hair and other ectodermal organs. The role of A20 seems to be restricted to the termination of NFkappaB signaling induced by the Eda pathway in hair follicles. The lack of cxcl10 and cxcl11 signaling during hair follicle formation leads to more widely spaced hair placodes. This work has revealed an important role of Eda during hair placode induction as a modulator of inhibitors and activators of the major pathways in order to direct the patterning of hair placodes.
  • Li, Chun-Mei (Helsingin yliopisto, 2007)
    The type III secretion system (T3SS) is an essential requirement for the virulence of many Gram-negative bacteria which infect plants, animals and men. Pathogens use the T3SS to deliver effector proteins from the bacterial cytoplasm to the eukaryotic host cells, where the effectors subvert host defenses. The best candidates for directing effector protein traffic are the bacterial type III-associated appendages, called needles or pili. In plant pathogenic bacteria, the best characterized example of a T3SS-associated appendage is the HrpA pilus of the plant pathogen Pseudomonas syringae pv. tomato DC3000. The components of the T3SS in plant pathogens are encoded by a cluster of hrp (hypersensitive reaction and pathogenicity) genes. Two major classes of T3SS-secreted proteins are: harpin proteins such as HrpZ which are exported into extracellular space, and avirulence (Avr) proteins such as AvrPto which are translocated directly to the plant cytoplasm. This study deals with the structural and functional characterization of the T3SS-associated HrpA pilus and the T3SS-secreted harpins. By insertional mutagenesis analysis of HrpA, we located the optimal epitope insertion site in the amino-terminus of HrpA, and revealed the potential application of the HrpA pilus as a carrier of antigenic determinants for vaccination. By pulse-expression of proteins combined with immuno-electron microscopy, we discovered the Hrp pilus assembly strategy as addition of HrpA subunits to the distal end of the growing pilus, and we showed for the first time that secretion of HrpZ occurs at the tip of the pilus. The pilus thus functions as a conduit delivering proteins to the extracellular milieu. By using phage-display and scanning-insertion mutagenesis methods we identified a conserved HrpZ-binding peptide and localized the peptide-binding site to the central domain of HrpZ. We also found that the HrpZ specifically interacts with a host bean protein. Taken together, the current results provide deeper insight into the molecular mechanism of T3SS-associated pilus assembly and effector protein translocation, which will be helpful for further studies on the pathogenic mechanisms of Gram-negative bacteria and for developing new strategies to prevent bacterial infection.
  • Majaneva, Sanna (Helsingin yliopisto, 2014)
    Gelatinous zooplankton, such as ctenophores, have attracted attention during the last decade,mainly as a result of the enigma around their potentially increased abundances around the world. Despite the increased attention, they remain either understudied or disregarded in most food web investigations and monitoring programs, and are defined as one of the most difficult groups of pelagic animals to study. Consequently, their diversity and ecological role are often grossly oversimplified and misunderstood, leading to biased views of ecosystem functioning. In addition, ctenophores share traits such as voracious predation behavior, the ability to starve and shrink during periods of low food availability and to tolerate increased temperatures, as well as high reproductive capacity, making them likely to take advantage of changing environmental conditions. In the Arctic, earlier ctenophore data consist of sparse abundance estimates and dietary studies lacking a systematic or integrative approach. In the Baltic Sea, despite the wellestablished routine plankton monitoring program conducted by the surrounding nations, the distribution and the role of the Arctic ctenophore Mertensia ovum in this ecosystem has been unknown since its first reported appearance in 2007. In this thesis, the biodiversity of cydippid ctenophores and their role in Svalbard waters and in the Baltic Sea were studied. Extensive in situ sampling, laboratory experiments, morphological and molecular identification analysis, traditional and molecular gut content analysis, as well as several direct measures of the ctenophores and the pelagic communities they inhabit were combined to address system-specific questions and to better understand how important a role the ctenophores might have in marine ecosystems. A combination of morphological species identification and molecular methods revealed Euplokamis sp. and an unidentified mertensiid species to co-occur with the dominating Mertensia ovum in Arctic waters. Similarly, the first recording of the cydippid ctenophore, Euplokamis sp., near the entrance to the Baltic Sea was reported in conjunction with extensive sampling of Mnemiopsis leidyi and Mertensia ovum. Interestingly, Pleurobrachia pileus, earlier reported to commonly co-occur with M. ovum in the Arctic and be present throughout the Baltic Sea (and earlier reported as the only ctenophore species in the northern Baltic Sea), was not present in either study site. It was demonstrated that morphological species identification alone is insufficient. In addition, the lack of proper species descriptions and public sequences limited the identification to the genus, family or order level. Thus, more emphasis should be placed on combining morphological and molecular methods together with photographic vouchers for rigorous taxonomic identification and accurate species descriptions. The lack of historical survey data and accurate abundance estimates of M. ovum have biased interpretations of its role in the Arctic and Baltic ecosystems. According to the results presented in this thesis, the potential predation impact of M. ovum was high when assuming relatively homogenous distributions of M. ovum and its prey, but it was even higher when patchiness of both predators and prey was taken into account. The potential predation impact was further affected by extensive spatial and seasonal migration patterns. Therefore, to adequately model prey predator interactions, more emphasis should be placed on the fine-scale distribution patterns of predators and prey. Also, different populations of a single species can have very different trophic roles in the food web due to the great difference in body size, as exemplified in this thesis with two populations of M. ovum. In the Arctic, M. ovum is a voracious predator of copepods (Calanus spp.), while in the Baltic, the substantially smaller M. ovum individuals mainly prey upon pico- and microplankton. Thus, generalizing and extrapolating ecological traits such as diet and foraging behavior from one population to another can be misleading. Moreover, the future of the two studied populations of M. ovum is likely to differ substantially because their distribution area will be differently affected by climate change; the distribution area is predicted to diminish in the Baltic Sea and remain more or less constant in the Arctic. To conclude, this thesis demonstrates that our current knowledge on the diversity, role, and potential future changes of the ctenophores in pelagic communities is still very incomplete. Thus, to properly understand the ecological impact of ctenophores at present and in the near future, this thesis suggests that all available techniques need to be applied in species identification, and that clear recommendations for a proper assessment of routine ctenophore monitoring are urgently needed.
  • Ahtiainen, Laura (Helsingin yliopisto, 2007)
    Studying neurodegeneration provides an opportunity to gain insights into normal cell physiology, and not just pathophysiology. In this thesis work the focus is on Infantile Neuronal Ceroid Lipofuscinosis (INCL). It is a recessively inherited lysosomal storage disorder. The disease belongs to the neuronal ceroid lipofuscinoses (NCLs), a group of common progressive neurodegenerative diseases of the childhood. Characteristic accumulation of autofluorescent storage material is seen in most tissues but only neurons of the central nervous system are damaged and eventually lost during the course of the disease leaving most other cell types unaffected. The disease is caused by mutations in the CLN1 gene, but the physiological function of the corresponding protein the palmitoyl protein thioesterase (PPT1) has remained elusive. The aim of this thesis work was to shed light on the molecular and cell biological mechanisms behind INCL. This study pinpointed the localization of PPT1 in axonal presynapses of neurons. It also established the role of PPT1 in early neuronal maturation as well as importance in mature neuronal synapses. This study revealed an endocytic defect in INCL patient cells manifesting itself as delayed trafficking of receptor and non-receptor mediated endocytic markers. Furthermore, this study was the first to connect the INCL storage proteins the sphingolipid activator proteins (SAPs) A and D to pathological events on the cellular level. Abnormal endocytic processing and intracellular re-localization was demonstrated in patient cells and disease model knock-out mouse neurons. To identify early affected cellular and metabolic pathways in INCL, knock-out mouse neurons were studied by global transcript profiling and functional analysis. The gene expression analysis revealed changes in neuronal maturation and cell communication strongly associated with the regulated secretory system. Furthermore, cholesterol metabolic pathways were found to be affected. Functional studies with the knock-out mouse model revealed abnormalities in neuronal maturation as well as key neuronal functions including abnormalities in intracellular calcium homeostasis and cholesterol metabolism. Together the findings, introduced in this thesis work, support the essential role of PPT1 in developing neurons as well as synaptic sites of mature neurons. Results of this thesis also elucidate early events in INCL pathogenesis revealing defective pathways ultimately leading to the neurodegenerative process. These results contribute to the understanding of the vital physiological function of PPT1 and broader knowledge of common cellular mechanisms behind neurodegeneration. These results add to the knowledge of these severe diseases offering basis for new approaches in treatment strategies.
  • Vauramo, Saara (Helsingin yliopisto, 2011)
    Continuing urbanization is a crucial driver of land transformation, having widespread impacts on virtually all ecosystems. Terrestrial ecosystems, including disturbed ones, are dependent on soils, which provide a multitude of ecosystem services. As soils are always directly and/or indirectly impacted through land transformation, land cover change causes soil change. Knowledge of ecosystem properties and functions in soils is increasing in importance as humans continue to concentrate into already densely-populated areas. Urban soils often have hampered functioning due to various disturbances resulting from human activity. Innovative solutions are needed to bring the lacking ecosystem services and quality of life to these urban environments. For instance, the ecosystem services of the urban green infrastructure may be substantially improved through knowledge of their functional properties. In the research forming this thesis, the impacts of four plant species (Picea abies, Calluna vulgaris, Lotus corniculatus and Holcus lanatus) on belowground biota and regulatory ecosystem services were investigated in two different urban soil types. The retention of inorganic nitrogen and phosphorus in the plant-soil system, decomposition of plant litter, primary production, and the degradation of polycyclic aromatic hydrocarbons (PAHs) were examined in the field and under laboratory conditions. The main objective of the research was to determine whether the different plant species (representing traits with varying litter decomposability) will give rise to dissimilar urban belowground communities with differing ecological functions. Microbial activity as well as the abundance of nematodes and enchytraeid worm biomass was highest below the legume L. corniculatus. L. corniculatus and the grass H. lanatus, producing labile or intermediate quality litter, enhanced the proportion of bacteria in the soil rhizosphere, while the recalcitrant litter-producing shrub C. vulgaris and the conifer P. abies stimulated the growth of fungi. The loss of nitrogen from the plant-soil system was small for H. lanatus and the combination of C. vulgaris + P. abies, irrespective of their energy channel composition. These presumably nitrogen-conservative plant species effectively diminished the leaching losses from the plant-soil systems with all the plant traits present. The laboratory experiment revealed a difference in N allocation between the plant traits: C. vulgaris and P. abies sequestered significantly more N in aboveground shoots in comparison to L. corniculatus and H. Lanatus. Plant rhizosphere effects were less clear for phosphorus retention, litter decomposition and the degradation of PAH compounds. This may be due to the relatively short experimental durations, as the maturation of the plant-soil system is likely to take a considerably longer time. The empirical studies of this thesis demonstrated that the soil communities rapidly reflect changes in plant coverage, and this has consequences for the functionality of soils. The energy channel composition of soils can be manipulated through plants, which was also supported by the results of the separate meta-analysis conducted in this thesis. However, further research is needed to understand the linkages between the biological community properties and ecosystem services in strongly human-modified systems.
  • Ranta, Pertti (Helsingin yliopisto, 2012)
    Man is now an urban species, because most of the mankind lives in cities.In cities, the only thing permanent is change. There are several agents of change in operation in cities, producing environmental disturbances at various temporal and spatial scales and regimes. This affects the living conditions of both man and other urban species. This study was an ecological stress tests how different urban habitats and species survived the actions of the agents of change. The disturbances can be divided into pulse disturbances and press disturbances.In this study, air and water pollution were typical pulse disturbances.The ecosystems may have enough adaptive capacity to renew and remain in a stable state, but they may also shift to a new state. The ecosystems that maintain their stable state have high resilience, but others shift into a new,possibly undesirable domain (from the perspective of biodiversity conservation and ecosystem services). The pulse of air pollution caused a temporary disappearance of urban epiphytic lichens in the city of Tampere (Finland). After ameliorating the air quality, the lichens returned, albeit in a reorganised combination of species.Thus, the ecosystem showed resilience as it was able to recover after the disturbance ended. Enough of external ecological memory was available and most of the lichens returned after the pollution episode was over. Within a period of 100 years, water pollution and other disturbances of the urban lake of Iidesjärvi (in Tampere) caused a shift from one stability domain (a clear-water state) to a new domain (turbid-water state). This domain shift presents a challenge for urban environmental management. A deadlock situation was created because the shift back to the desirable state would require excessive technical and economic resources. The upstream, nonpolluted lake of Kaukajärvi in the samem catchment area remained in a clear water state with rich flora of elodeids and isoetids. The dynamic macrophyte species pool (1902 2008) of Iidesjärvi consisted of 48 species, some of which disappeared temporarily and later returned.The shallow species-rich lakes in the region may occasionally experience species turnover; a species that disappears may recolonise later from other lakes. The gradient paradigm provides a useful basis for studies in cities to quantify the intensity of urbanisation. In the present study, a 21 km long string of grid cells was established through the city of Tampere. The aim of the gradient study was to examine the distribution of native and alien plants along the gradient line and to find the most important variables, which determine the location and abundance of species along it. The urban forest fragment under study (1.27 ha in the city of Tampere) had enough adaptive capacity to remain in the same stability domain since it has been isolated 120 years ago. The urban pressure affected the forest in several cumulative ways and domain shift will occur in the foreseeable future. A special feature of boreal cities is the presence of remnants of seminatural habitats,mostly forests, close to central business districts. As a result, Nordic cities are resilient and show remarkably low extinction rates of plants. The urban traffic corridors were compared with a river corridor on the municipal level. Despite their small area, the corridors are very rich in species.The corridor plants in the City of Vantaa represented 61 percent of the total number of species of the biogeographical province of Uusimaa. Disturbance regimes were the common denominator of the ecological profiles of traffic corridors and river corridors. In spite of the richness in species, urban corridors are not included in the networks of protected areas. The Finnish cities showed a high degree of resilience in spite of the concomitant actions of several agents of change. This was a result of the urban structure of the Finnish cities. In Finland,fragments of original nature of different types are embedded in the urban structure. Keywords: urban ecology, monitoring, disturbance, resilience, ecological memory
  • Lehvävirta, Susanna (Helsingin yliopisto, 2005)
  • Yli-Pelkonen, Vesa (Helsingin yliopisto, 2006)
    Urbanization leads to irreversible land-use change, which has ecological consequences such as the loss and fragmentation of green areas, and structural and functional changes in terrestrial and aquatic ecosystems. These consequences diminish ecosystem services important for human populations living in urban areas. All this results in a conflict situation: how to simultaneously meet the needs of city growth and the principles of sustainable development, and especially conserve important green areas within and around built-up areas? Urban planners and decisionmakers have an important role in this, since they must use the ecological information mainly from species and biotope inventories and biodiversity impact assessments in determining the conservation values of green areas. The main aim of this thesis was to study the use of ecological information in the urban land-use planning and decisionmaking process in the Helsinki Metropolitan Area, Finland. At first, the literature on ecological-social systems linkages related to urban planning was reviewed. Based on the review, a theoretical and conceptual framework for the research on Finnish urban setting was adapted. Secondly, factors determining the importance and effectiveness of incorporation of ecological information into the urban planning process, and the challenges related to the use of ecological information were studied. Thirdly, the importance and use of Local Ecological Knowledge in urban planning were investigated. Then, factors determining the consideration of urban green areas and related ecological information in political land-use decisionmaking were studied. Finally, in a case study illustrating the above considerations, the importance of urban stream ecosystems in the land-use planning was investigated. This thesis demonstrated that although there are several challenges in using ecological information effectively, it is considered as an increasingly important part of the basic information used in urban planning and decisionmaking process. The basic determinants for this are the recent changes in environmental legislation, but also the increasing appreciation of green areas and their conservation values by all the stakeholders. In addition, Local Ecological Knowledge in its several forms can be a source of ecological information for planners if incorporated effectively into the process. This study also showed that rare or endangered species and biotopes, and related ecological information receive priority in the urban planning process and usually pass through the decisionmaking system. Furthermore, the stream Rekolanoja case indicates that planners and residents see the value of urban stream ecosystem as increasingly important for the local health and social values, such as recreation and stress relief.
  • Pessa, Heli (Helsingin yliopisto, 2010)
    The removal of non-coding sequences, introns, is an essential part of messenger RNA processing. In most metazoan organisms, the U12-type spliceosome processes a subset of introns containing highly conserved recognition sequences. U12-type introns constitute less than 0,5% of all introns and reside preferentially in genes related to information processing functions, as opposed to genes encoding for metabolic enzymes. It has previously been shown that the excision of U12-type introns is inefficient compared to that of U2-type introns, supporting the model that these introns could provide a rate-limiting control for gene expression. The low efficiency of U12-type splicing is believed to have important consequences to gene expression by limiting the production of mature mRNAs from genes containing U12-type introns. The inefficiency of U12-type splicing has been attributed to the low abundance of the components of the U12-type spliceosome in cells, but this hypothesis has not been proven. The aim of the first part of this work was to study the effect of the abundance of the spliceosomal snRNA components on splicing. Cells with a low abundance of the U12-type spliceosome were found to inefficiently process U12-type introns encoded by a transfected construct, but the expression levels of endogenous genes were not found to be affected by the abundance of the U12-type spliceosome. However, significant levels of endogenous unspliced U12-type intron-containing pre-mRNAs were detected in cells. Together these results support the idea that U12-type splicing may limit gene expression in some situations. The inefficiency of U12-type splicing has also promoted the idea that the U12-type spliceosome may control gene expression, limiting the mRNA levels of some U12-type intron-containing genes. While the identities of the primary target genes that contain U12-type introns are relatively well known, little has previously been known about the downstream genes and pathways potentially affected by the efficiency of U12-type intron processing. Here, the effects of U12-type splicing efficiency on a whole organism were studied in a Drosophila line with a mutation in an essential U12-type spliceosome component. Genes containing U12-type introns showed variable gene-specific responses to the splicing defect, which points to variation in the susceptibility of different genes to changes in splicing efficiency. Surprisingly, microarray screening revealed that metabolic genes were enriched among downstream effects, and that the phenotype could largely be attributed to one U12-type intron-containing mitochondrial gene. Gene expression control by the U12-type spliceosome could thus have widespread effects on metabolic functions in the organism. The subcellular localization of the U12-type spliceosome components was studied as a response to a recent dispute on the localization of the U12-type spliceosome. All components studied were found to be nuclear indicating that the processing of U12-type introns occurs within the nucleus, thus clarifying a question central to the field. The results suggest that the U12-type spliceosome can limit the expression of genes that contain U12-type introns in a gene-specific manner. Through its limiting role in pre-mRNA processing, the U12-type splicing activity can affect specific genetic pathways, which in the case of Drosophila are involved in metabolic functions.
  • Lahdenranta, Johanna (Helsingin yliopisto, 2004)
  • Wirzenius, Maria (Helsingin yliopisto, 2007)
    The circulatory system consists of the blood and lymphatic vessels. While blood vessels transport oxygen, cells, and nutrients to tissues, the lymphatic vessels collect fluid, cells, and plasma proteins from tissues to return back to the blood circulation. Angiogenesis, the growth of new blood vessels from pre-existing ones, is an important process involved in several physiological conditions such as inflammation, wound healing, and embryonic development. Furthermore, angiogenesis is found in many pathological conditions such as atherosclerosis and the growth and differentiation of solid tumors. Many tumor types spread via lymphatic vessels to form lymph node metastasis. The elucidation of the molecular players coordinating development of the vascular system has provided an array of tools for further insight of the circulatory system. The discovery of the Vascular Endothelial Growth Factor (VEGF) family members and their tyrosine kinase receptors (VEGFRs) has facilitated the understanding of the vasculature in different physiological and pathological situations. The VEGFRs are expressed on endothelial cells and mediate the growth and maintenance of both the blood and lymphatic vasculatures. This study was undertaken to address the role of VEGFR-2 specific signaling in maturation of blood vessels during neoangiogenesis and in lymphangiogenesis. We also wanted to differentiate between VEGFR-2 and VEGFR-3 specific signaling in lymphangiogenesis. We found that specific VEGFR-2 stimulation alone by gene therapeutic methods is not sufficient for production of mature blood vessels. However, VEGFR-2 stimulation in combination with expression of platelet-derived growth factor D (PDGF-D), a recently identified member of the PDGF growth factor family, was capable of stabilizing these newly formed vessels. Signaling through VEGFR-3 is crucial during developmental lymphangiogenesis, but we showed that the lymphatic vasculature becomes independent of VEGFR-3 signaling after the postnatal period. We also found that VEGFR-2 specific stimulation cannot rescue the loss of lymphatic vessels when VEGFR-3 signaling is blocked and that VEGFR-2 specific signals promote lymphatic vessel enlargement, but are not involved in vessel sprouting to generate new lymphatic vessels in vivo, in contrast to the VEGFR-2 dependent sprouting observed in blood vessels. In addition, we compared the inhibitory effects of a small molecular tyrosine kinase inhibitor of VEGFR-2 vs. VEGFR-3 specific signaling in vitro and in vivo. Our results showed that the tyrosine kinase inhibitor could equally affect physiological and pathological processes dependent on VEGFR-2 and VEGFR-3 driven angiogenesis or lymphangiogenesis. These results provide new insights into the VEGFR specific pathways required for pre- and postnatal angiogenesis as well as lymphangiogenesis, which could provide important targets and therapies for treatment of diseases characterized by abnormal angiogenesis or lymphangiogenesis.
  • Jeltsch, Michael (Helsingin yliopisto, 2002)
  • Pietiäinen, Vilja (Helsingin yliopisto, 2005)
  • Sundell, Janne (Helsingin yliopisto, 2002)
  • Kallio, Kari (Helsingin yliopisto, 2012)
    In lake-rich regions, the gathering of information about water quality is challenging because only a small proportion of the lakes can be assessed each year by conventional methods. One of the techniques for improving the spatial and temporal representativeness of lake monitoring is remote sensing from satellites and aircrafts. The experimental material included detailed optical measurements in 11 lakes, air- and spaceborne remote sensing measurements with concurrent field sampling, automatic raft measurements and a national dataset of routine water quality measurements from over 1100 lakes. The analyses of the spatially high-resolution airborne remote sensing data from eutrophic and mesotrophic lakes showed that one or a few discrete water quality observations using conventional monitoring can yield a clear over- or underestimation of the overall water quality in a lake. The use of TM-type satellite instruments in addition to routine monitoring results substantially increases the number of lakes for which water quality information can be obtained. The preliminary results indicated that coloured dissolved organic matter (CDOM) can be estimated with TM-type satellite instruments, which could possibly be utilised as an aid in estimating the role of lakes in global carbon budgets. Based on the results of reflectance modelling and experimental data, MERIS satellite instrument has optimal or near-optimal channels for the estimation of turbidity, chlorophyll a and CDOM in Finnish lakes. MERIS images with a 300 m spatial resolution can provide water quality information in different parts of large and medium-sized lakes, and in filling in the gaps resulting from conventional monitoring. Algorithms that would not require simultaneous field data for algorithm training would increase the amount of remote sensing-based information available for lake monitoring. The MERIS Boreal Lakes processor, trained with the optical data and concentration ranges provided by this study, enabled turbidity estimations with good accuracy without the need for algorithm correction with field measurements, while chlorophyll a and CDOM estimations require further development of the processor. The accuracy of interpreting chlorophyll a via semi empirical algorithms can be improved by classifying lakes prior to interpretation according to their CDOM level and trophic status. Optical modelling indicated that the spectral diffuse attenuation coefficient can be estimated with reasonable accuracy from the measured water quality concentrations. This provides more detailed information on light attenuation from routine monitoring measurements than is available through the Secchi disk transparency. The results of this study improve the interpretation of lake water quality by remote sensing and encourage the use of remote sensing in lake monitoring.
  • Van Teeffelen, Astrid (Helsingin yliopisto, 2007)
    Ongoing habitat loss and fragmentation threaten much of the biodiversity that we know today. As such, conservation efforts are required if we want to protect biodiversity. Conservation budgets are typically tight, making the cost-effective selection of protected areas difficult. Therefore, reserve design methods have been developed to identify sets of sites, that together represent the species of conservation interest in a cost-effective manner. To be able to select reserve networks, data on species distributions is needed. Such data is often incomplete, but species habitat distribution models (SHDMs) can be used to link the occurrence of the species at the surveyed sites to the environmental conditions at these locations (e.g. climatic, vegetation and soil conditions). The probability of the species occurring at unvisited location is next predicted by the model, based on the environmental conditions of those sites. The spatial configuration of reserve networks is important, because habitat loss around reserves can influence the persistence of species inside the network. Since species differ in their requirements for network configuration, the spatial cohesion of networks needs to be species-specific. A way to account for species-specific requirements is to use spatial variables in SHDMs. Spatial SHDMs allow the evaluation of the effect of reserve network configuration on the probability of occurrence of the species inside the network. Even though reserves are important for conservation, they are not the only option available to conservation planners. To enhance or maintain habitat quality, restoration or maintenance measures are sometimes required. As a result, the number of conservation options per site increases. Currently available reserve selection tools do however not offer the ability to handle multiple, alternative options per site. This thesis extends the existing methodology for reserve design, by offering methods to identify cost-effective conservation planning solutions when multiple, alternative conservation options are available per site. Although restoration and maintenance measures are beneficial to certain species, they can be harmful to other species with different requirements. This introduces trade-offs between species when identifying which conservation action is best applied to which site. The thesis describes how the strength of such trade-offs can be identified, which is useful for assessing consequences of conservation decisions regarding species priorities and budget. Furthermore, the results of the thesis indicate that spatial SHDMs can be successfully used to account for species-specific requirements for spatial cohesion - in the reserve selection (single-option) context as well as in the multi-option context. Accounting for the spatial requirements of multiple species and allowing for several conservation options is however complicated, due to trade-offs in species requirements. It is also shown that spatial SHDMs can be successfully used for gaining information on factors that drive a species spatial distribution. Such information is valuable to conservation planning, as better knowledge on species requirements facilitates the design of networks for species persistence. This methods and results described in this thesis aim to improve species probabilities of persistence, by taking better account of species habitat and spatial requirements. Many real-world conservation planning problems are characterised by a variety of conservation options related to protection, restoration and maintenance of habitat. Planning tools therefore need to be able to incorporate multiple conservation options per site, in order to continue the search for cost-effective conservation planning solutions. Simultaneously, the spatial requirements of species need to be considered. The methods described in this thesis offer a starting point for combining these two relevant aspects of conservation planning.
  • Ghobad-Nejhad, Masoomeh (Helsingin yliopisto, 2011)
    The Caucasus region is a hotspot of biodiversity and is one of the few areas in the Northern Hemisphere which harbor Pleistocene glacial refugia. The region encompasses Armenia, Azerbaijan, Georgia, the southernmost European Russia, NE Turkey, and northern Iran. The study on fungal composition of the Caucasus region and its connection and possible contribution to the present mycota of Europe has largely escaped empirical scrutiny. Using taxonomic surveys, phylogenetic reconstruction methods, haplotype analysis, and similarity tests, this study has aimed to, 1) summarize the knowledge on the occurrence of corticioids and polypores in the Caucasus region, 2) resolve the phylogenetic relationships of selected, resupinate wood-inhabiting basidiomycetes for which the Caucasus region is currently the mere, or one of the noteworthy areas of distribution, and, 3) assess the similarity of Caucasian corticioid fungi to those of Europe and important areas in the Northern Hemisphere, and to examine the significance of the Caucasus region as a glacial refugium for these fungi. This study provides the first catalogue of corticioids and polypores (635 species) occurring in the Caucasus region. The phylogeny and systematics of the Caucasian resupinate taxa in focus has been resolved and the usefulness of some morphological characters has been re-evaluated. In this context, four new genera and two new species were described and five new combinations were proposed, two of which were supplemented with modern descriptions. The species composition of corticioids in the Caucasus region is found to be distinctly more similar to Europe and North America than to East Asia and India. The highest molecular diversity and within population pairwise distance for Peniophorella praetermissa has been detected in the Caucasus and East Asia, with the isolates of the latter area being highly divergent from the European ones. This, and the assignment of root haplotype to the Caucasian isolates in a haplotype network for Phlebia tuberucalta and P. livida, call attention to the role of the Caucasus region in shaping the current mycota of Europe.