The Freudian unconscious in the context of the cognitive orientation

For decades psychoanalysis was the discipline studying the unconscious, and other branches of study lacked competence to take a stand on the issues concerning the unconscious. From 1980s onwards intense study of the unconscious has been taken place in the scope of cognitive orientation. Thus, nowadays it is talked about both pyschoanalytic and cognitive unconscious. The aim of this thesis is to integrate psychoanalytic and cognitive views. When the "Freudian" conception of the unconscious is considered, there are four entangled issues: 1) what is the unconscious like, 2) how does the unconsciuos give rise to psychic disorders 3) why and how certain contents are missing from consciousness (repression of contents), 4) the emergence of those contents (becoming conscious of the repressed). The conventional psychoanalytic answer to the first question - and "the cornerstone of psychoanalysis" - is "the unconscious is mental". The issues 2)-4) depend radically on the answer given to the 1): "psychoanalytic" conceptualizations on them rest on the "cornerstone". That ground was challended in study I: it was argued that it has never been clear what does it mean that the unconscious is mental. Thus, it was stated that in the current state of art psychoanalysis should drop out the ephitet "mental" before the term unconscious. That claim creates a pressure to reappraise the convential "psychoanalytic" answers to the other questions, and that reappraisal was the aim of studies II and III. In study II the question 2) is approached in terms of implicit knowledge. Study III focuses on mechanisms, which determine which contents appear in the scope of consciousness, and also cause missing of contents from there (the questions 3) and 4)). In the core of study III there are distinctions concerning the processess occuring in the levels of the brain, consciousness, self-consciousness, and narrative self-consciousness. Studies I-III set "psychoanalytic" topics in the frames of cognitive view. The picture emerging from those studies is not especially useful for a clinican (psychotherapist). Studies IV and V focused that issue. Study IV is a rather serious critique toward neuropsychoanalysis. In it it was claimed that repressive functions of conscious states are in the core of clinical psychoanalysis, and functions in general cannot be reduced to neurophysiological terminology. Thus, the limits of neuropsychoanalysis are more strict than it has been realized: crucial clinical issues remain outside its scope. In study V it was focused on the confusing state of things that although unconscious fantasies do not exist, the idea on them has been an important conceptual tool for clinicans. When put in a larger context, the aim of study V is similar to that of study IV: to determine the relation between psychotherapists' and neuroscientists' terminologies. Studies III, IV and V apply the philosopher Daniel Dennett's model on different levels of explanation.

The structure of Norway spruce (Picea abies [L.] Karst.) stems in relation to wood properties of sawn timber

An important challenge in forest industry is to get the appropriate raw material out from the forests to the wood processing industry. Growth and stem reconstruction simulators are therefore increasingly integrated in industrial conversion simulators, for linking the properties of wooden products to the three-dimensional structure of stems and their growing conditions. Static simulators predict the wood properties from stem dimensions at the end of a growth simulation period, whereas in dynamic approaches, the structural components, e.g. branches, are incremented along with the growth processes. The dynamic approach can be applied to stem reconstruction by predicting the three-dimensional stem structure from external tree variables (i.e. age, height) as a result of growth to the current state. In this study, a dynamic growth simulator, PipeQual, and a stem reconstruction simulator, RetroSTEM, are adapted to Norway spruce (Picea abies [L.] Karst.) to predict the three-dimensional structure of stems (tapers, branchiness, wood basic density) over time such that both simulators can be integrated in a sawing simulator. The parameterisation of the PipeQual and RetroSTEM simulators for Norway spruce relied on the theoretically based description of tree structure developing in the growth process and following certain conservative structural regularities while allowing for plasticity in the crown development. The crown expressed both regularity and plasticity in its development, as the vertical foliage density peaked regularly at about 5 m from the stem apex, varying below that with tree age and dominance position (Study I). Conservative stem structure was characterized in terms of (1) the pipe ratios between foliage mass and branch and stem cross-sectional areas at crown base, (2) the allometric relationship between foliage mass and crown length, (3) mean branch length relative to crown length and (4) form coefficients in branches and stem (Study II). The pipe ratio between branch and stem cross-sectional area at crown base, and mean branch length relative to the crown length may differ in trees before and after canopy closure, but the variation should be further analysed in stands of different ages and densities with varying site fertilities and climates. The predictions of the PipeQual and RetroSTEM simulators were evaluated by comparing the simulated values to measured ones (Study III, IV). Both simulators predicted stem taper and branch diameter at the individual tree level with a small bias. RetroSTEM predictions of wood density were accurate. For focusing on even more accurate predictions of stem diameters and branchiness along the stem, both simulators should be further improved by revising the following aspects in the simulators: the relationship between foliage and stem sapwood area in the upper stem, the error source in branch sizes, the crown base development and the height growth models in RetroSTEM. In Study V, the RetroSTEM simulator was integrated in the InnoSIM sawing simulator, and according to the pilot simulations, this turned out to be an efficient tool for readily producing stand scale information about stem sizes and structure when approximating the available assortments of wood products.

From a tree to a stand in Finnish boreal forests: biomass estimation and comparison of methods

There is an increasing need to compare the results obtained with different methods of estimation of tree biomass in order to reduce the uncertainty in the assessment of forest biomass carbon. In this study, tree biomass was investigated in a 30-year-old Scots pine (Pinus sylvestris) (Young-Stand) and a 130-year-old mixed Norway spruce (Picea abies)-Scots pine stand (Mature-Stand) located in southern Finland (61º50' N, 24º22' E). In particular, a comparison of the results of different estimation methods was conducted to assess the reliability and suitability of their applications. For the trees in Mature-Stand, annual stem biomass increment fluctuated following a sigmoid equation, and the fitting curves reached a maximum level (from about 1 kg/yr for understorey spruce to 7 kg/yr for dominant pine) when the trees were 100 years old. Tree biomass was estimated to be about 70 Mg/ha in Young-Stand and about 220 Mg/ha in Mature-Stand. In the region (58.00-62.13 ºN, 14-34 ºE, ≤ 300 m a.s.l.) surrounding the study stands, the tree biomass accumulation in Norway spruce and Scots pine stands followed a sigmoid equation with stand age, with a maximum of 230 Mg/ha at the age of 140 years. In Mature-Stand, lichen biomass on the trees was 1.63 Mg/ha with more than half of the biomass occurring on dead branches, and the standing crop of litter lichen on the ground was about 0.09 Mg/ha. There were substantial differences among the results estimated by different methods in the stands. These results imply that a possible estimation error should be taken into account when calculating tree biomass in a stand with an indirect approach.

Effects of living crown reduction on needle element status of Scots pine

A wide range of biotic and abiotic factors, operating over different time perspectives and intensities, cause defoliation and a rapid decrease in the crown size of trees. Scleroderris canker disease [Gremmeniella abietina (Lagerb.) Morelet] has caused widespread crown reduction and tree mortality in Scots pine (Pinus sylvestris L) in forests in Scandinavia during the last three decades. In the 1980's, attempts were made to show, on the basis of the higher foliar N and S concentrations of affected pines in the diseased area, that sulphur and nitrogen deposition predispose trees to G. abietina. Unfortunately, in many studies on defoliated trees, exceptionally high or low needle mineral nutrient concentrations are still often interpreted as one of the causes of tree injury and not, conversely, as the result. In this thesis, three different field experiments, with foliar analysis as the main study method, were conducted in order to asses the possible long-term effects of living crown reduction on the needle nutrient concentrations of Scots pine trees in southern Finland. The crown ratio and length of the living crown were used to estimate the amount of defoliation in the reduced canopies. The material for the partial studies was collected and a total of 968 foliar samples were analysed individually (15-17 elements/sample) on a total of 488 sample trees (140 diseased, 116 pruned and 232 control trees) during the years 1987-1996 in 13 Scots pine stands. All the three experiments of this thesis provided significant evidence that severe, disease-induced defoliation or artificial pruning of the living branches can induce long-lasting nutritional changes in the foliage of the recovering trees under the typical growing conditions for Scots pine. The foliar concentrations of all the 17 mineral nutrients/elements analysed were affected, to a varying degree, by artificial pruning during the following three years. Although Scots pine, as an evergreen conifer, is considered to have low induced chemical responses to defoliation, this study proved experimentally under natural forest conditions that severe artificial pruning or disease-induced defoliation of Scots pine trees may induce biologically significant changes in the concentrations of most of the important macro- and micronutrients, as well as of carbon, in refoliated needles. Concerning the studies in this thesis, I find the results significant in providing new information about the long-term effects of rapid living crown reduction on the foliar nutrient and element status of Scots pine trees. Key words: Foliar analysis, defoliation, needle loss, pruning, nutrients, Pinus sylvestris, Gremmeniella abietina

The efficacy and potential risks of controlling sprouting in Finnish birches (Betula spp.) with the fungal decomposer Chondrostereum purpureum

Sprouting of fast-growing broad-leaved trees causes problems in young coniferous stands, under power transmission lines and along roads and railways. Public opinion and the Finnish Forest Certification System oppose the use of chemical herbicides to control sprouting, which means that most areas with problems rely on mechanical cutting. However, cutting is a poor control method for many broad-leaved species because the removal of leaders can stimulate the sprouting of side branches and cut stumps quickly re-sprout. In order to be effective, cutting must be carried out frequently but each cut increases the costs, making this control method increasingly difficult and expensive once begun. As such, alternative methods for sprout control that are both effective and environmentally sound represent a continuing challenge to managers and research biologists. Using biological control agents to prevent sprouting has been given serious consideration recently. Dutch and Canadian researchers have demonstrated the potential of the white-rot fungus Chondrostereum purpureum (Pers. ex Fr.) Pouzar as a control agent of stump sprouting in many hardwoods. These findings have focused the attention of the Finnish forestry community on the utilization of C. purpureum for biocontrol purposes. Primarily, this study sought determines the efficacy of native C. purpureum as an inhibitor of birch stump sprouting in Finland and to clarify its mode of action. Additionally, genotypic variation in Finnish C. purpureum was examined and the environmental risks posed by a biocontrol program using this fungus were assessed. Experimental results of the study demonstrated that C. purpureum clearly affects the sprouting of birch: both the frequency of living stumps and the number of living sprouts per stump were effectively reduced by the treatment. However, the treatment had no effect on the maximum height of new sprouts. There were clear differences among fungal isolates in preventing sprouting and those that possessed high oxidative activities as measured in the laboratory inhibited sprouting most efficiently in the field. The most effective treatment time during the growing season was in early and mid summer (May July). Genetic diversity in Nordic and Baltic populations of C. purpureum was found to be high at the regional scale but locally homogeneous. This natural distribution of diversity means that using local genotypes in biocontrol programs would effectively prevent the introduction of novel genes or genotypes. While a biocontrol program using local strains of C. purpureum would be environmentally neutral, pruned birches that are close to the treatment site would have a high susceptibility to infect by the fungus during the early spring.

Tropical dryland agroforestry on clay soils: : Analysis of systems based on Acacia senegal in the Blue Nile region, Sudan

Acacia senegal, the gum arabic producing tree, is the most important component in traditional dryland agroforestry systems in the Blue Nile region, Sudan. The aim of the present study was to provide new knowledge on the potential use of A. senegal in dryland agroforestry systems on clay soils, as well as information on tree/crop interaction, and on silvicultural and management tools, with consideration on system productivity, nutrient cycling and sustainability. Moreover, the aim was also to clarify the intra-specific variation in the performance of A. senegal and, specifically, the adaptation of trees of different origin to the clay soils of the Blue Nile region. In agroforestry systems established at the beginning of the study, tree and crop growth, water use, gum and crop yields, nutrient cycling and system performance were investigated for a period of four years (1999 to 2002). Trees were grown at 5 x 5 m and 10 x 10 m spacing alone or in mixture with sorghum or sesame; crops were also grown in sole culture. The symbiotic biological N2 fixation by A. senegal was estimated using the 15N natural abundance (δ15N) procedure in eight provenances collected from different environments and soil types of the gum arabic belt and grown in clay soil in the Blue Nile region. Balanites aegyptiaca (a non-legume) was used as a non-N-fixing reference tree species, so as to allow 15N-based estimates of the proportion of the nitrogen in trees derived from the atmosphere. In the planted acacia trees, measurements were made on shoot growth, water-use efficiency (as assessed by the δ13C method) and (starting from the third year) gum production. Carbon isotope ratios were obtained from the leaves and branch wood samples. The agroforestry system design caused no statistically significant variation in water use, but the variation was highly significant between years, and the highest water use occurred in the years with high rainfall. No statistically significant differences were found in sorghum or sesame yields when intercropping and sole crop systems were compared (yield averages were 1.54 and 1.54 ha-1 for sorghum and 0.36 and 0.42 t ha-1 for sesame in the intercropped and mono-crop plots, respectively). Thus, at an early stage of agroforestry system management, A. senegal had no detrimental effect on crop yield, but the pattern of resource capture by trees and crops may change as the system matures. Intercropping resulted in taller trees and larger basal and crown diameters as compared to the development of sole trees. It also resulted in a higher land equivalent ratio. When gum yields were analysed it was found that a significant positive relationship existed between the second gum picking and the total gum yield. The second gum picking seems to be a decisive factor in gum production and could be used as an indicator for the total gum yield in a particular year. In trees, the concentrations of N and P were higher in leaves and roots, whereas the levels of K were higher in stems, branches and roots. Soil organic matter, N, P and K contents were highest in the upper soil stratum. There was some indication that the P content slightly increased in the topsoil as the agroforestry plantations aged. At a stocking of 400 trees ha-1 (5 x 5 m spacing), A. senegal accumulated in the biomass a total of 18, 1.21, 7.8 and 972 kg ha-1of N, P, K and OC, respectively. Trees contributed ca. 217 and 1500 kg ha-1 of K and OC, respectively, to the top 25-cm of soil over the first four years of intercropping. Acacia provenances of clay plain origin showed considerable variation in seed weight. They also had the lowest average seed weight as compared to the sandy soil (western) provenances. At the experimental site in the clay soil region, the clay provenances were distinctly superior to the sand provenances in all traits studied but especially in basal diameter and crown width, thus reflecting their adaptation to the environment. Values of δ13C, indicating water use efficiency, were higher in the sand soil group as compared to the clay one, both in leaves and in branch wood. This suggests that the sand provenances (with an average value of -28.07 ) displayed conservative water use and high drought tolerance. Of the clay provenances, the local one (Bout) displayed a highly negative (-29.31 ) value, which indicates less conservative water use that resulted in high productivity at this particular clay-soil site. Water use thus appeared to correspond to the environmental conditions prevailing at the original locations for these provenances. Results suggest that A. senegal provenances from the clay part of the gum belt are adapted for a faster growth rate and higher biomass and gum productivity as compared to provenances from sand regions. A strong negative relationship was found between the per-tree gum yield and water use efficiency, as indicated by δ13C. The differences in water use and gum production were greater among provenance groups than within them, suggesting that selection among rather than within provenances would result in distinct genetic gain in gum yield. The relative δ15N values ( ) were higher in B. aegyptiaca than in the N2-fixing acacia provenances. The amount of Ndfa increased significantly with age in all provenances, indicating that A. senegal is a potentially efficient nitrogen fixer and has an important role in t agroforestry development. The total above-ground contribution of fixed N to foliage growth in 4-year-old A. senegal trees was highest in the Rahad sand-soil provenance (46.7 kg N ha-1) and lowest in the Mazmoom clay-soil provenance (28.7 kg N ha-1). This study represents the first use of the δ15N method for estimating the N input by A. senegal in the gum belt of Sudan. Key words: Acacia senegal, agroforestry, clay plain, δ13C, δ15N, gum arabic, nutrient cycling, Ndfa, Sorghum bicolor, Sesamum indicum

Use of biomass fuels in the brick-making industries of Sudan: Implications for deforestation and greenhouse gas emission

The study focuses on the potential roles of the brick making industries in Sudan in deforestation and greenhouse gas emission due to the consumption of biofuels. The results were based on the observation of 25 brick making industries from three administrative regions in Sudan namely, Khartoum, Kassala and Gezira. The methodological approach followed the procedures outlined by the Intergovernmental Panel on Climate Change (IPCC). For predicting a serious deforestation scenario, it was also assumed that all of wood use for this particular purpose is from unsustainable sources. The study revealed that the total annual quantity of fuelwood consumed by the surveyed brick making industries (25) was 2,381 t dm. Accordingly, the observed total potential deforested wood was 10,624 m3, in which the total deforested round wood was 3,664 m3 and deforested branches was 6,961 m3. The study observed that a total of 2,990 t biomass fuels (fuelwood and dung cake) consumed annually by the surveyed brick making industries for brick burning. Consequently, estimated total annual emissions of greenhouse gases were 4,832 t CO2, 21 t CH4, 184 t CO, 0.15 t N20, 5 t NOX and 3.5 t NO while the total carbon released in the atmosphere was 1,318 t. Altogether, the total annual greenhouse gases emissions from biomass fuels burning was 5,046 t; of which 4,104 t from fuelwood and 943 t from dung cake burning. According to the results, due to the consumption of fuelwood in the brick making industries (3,450 units) of Sudan, the amount of wood lost from the total growing stock of wood in forests and trees in Sudan annually would be 1,466,000 m3 encompassing 505,000 m3 round wood and 961,000 m3 branches annually. By considering all categories of biofuels (fuelwood and dung cake), it was estimated that, the total emissions from all the brick making industries of Sudan would be 663,000 t CO2, 2,900 t CH4, 25,300 t CO, 20 t N2O, 720 t NOX and 470 t NO per annum, while the total carbon released in the atmosphere would be 181,000 t annually.

Regulation of strawberry growth and development

Strawberries (Fragaria sp.) are adapted to diverse environmental conditions from the tropics to about 70ºN, so different responses to environmental conditions can be found. Most genotypes of garden strawberry (F. x ananassa Duch.) and woodland strawberry (F. vesca L.) are short-day (SD) plants that are induced to flowering by photoperiods under a critical limit, but also various photoperiod x temperature interactions can be found. In addition, continuously flowering everbearing (EB) genotypes are found. In addition to flowering, axillary bud differentiation in strawberry is regulated by photoperiod. In SD conditions, axillary buds differentiate to rosette-like structures called "branch crowns", whereas in long-day conditions (LD) they form runners, branches with 2 long internodes followed by a daughter plant (leaf rosette). The number of crown branches determines the yield of the plant, since inflorescences are formed from the apical meristems of the crown. Although axillary bud differentiation is an important developmental process in strawberries, its environmental and hormonal regulation has not been characterized in detail. Moreover, the genetic mechanisms underlying axillary bud differentiation and regulation of flowering time in these species are almost completely unresolved. These topics have been studied in this thesis in order to enhance strawberry research, cultivation and breeding. The results showed that 8-12 SD cycles suppressed runner initiation from the axillary buds of the garden strawberry cv. Korona with the concomitant induction of crown branching, and 3 weeks of SD was sufficient for the induction of flowering in the main crown. Furthermore, a second SD treatment given a few weeks after the first SD period can be used to induce flowering in the primary branch crowns and to induce the formation of secondary branches. Thus, artificial SD treatments effectively stimulate crown branching, providing one means for the increase of cropping (yield) potential in strawberry. It was also shown by growth regulation applications, quantitave hormone analysis and gene expression analysis that gibberellin (GA) is one of the key signals involved in the photoperiod control of shoot differentiation. The results indicate that photoperiod controls GA activity specifically in axillary buds, thereby determining bud fate. It was further shown that chemical control of GA biosynthesis by prohexadione-calcium can be utilized to prevent excessive runner formation and induce crown branching in strawberry fields. Moreover, ProCa increased berry yield up to 50%, showing that it is an easier and more applicable alternative to artificial SD treatments for controlling strawberry crown development and yield. Finally, flowering gene pathways in Fragaria were explored by searching for homologs of 118 Arabidopsis thaliana flowering-time genes. In total, 66 gene homologs were identified, and they distributed to all known flowering pathways, suggesting the presence of these pathways also in strawberry. Expression analysis of selected genes revealed that the mRNA of putative floral identity gene APETALA1 accumulated in the shoot apex of the EB genotype after the induction of flowering, whereas it was absent in vegetative SD genotype, indicating the usefulness of this gene product as the marker of floral initiation. The present data enables the further exploration of strawberry flowering pathways with genetic transformation, gene mapping and transcriptomics methods.

Kymijoen vaelluskalojen nousureittien avaamisen kustannusten ja hyötyjen arviointi

The objective of this thesis is to evaluate different means of increasing natural reproduction of migratory fish, especially salmon, in the river Kymijoki. The original stocks of migratory fish in Kymijoki were lost by the 1950s because of hydropower plants and worsened quality of water in the river. Nowadays the salmon stocks is based on hatchery-reared fish, even though there is significant potential of natural smolt production in the river. The main problem in the natural reproduction is that the migratory fish cannot ascend to the reproduction areas above the Korkeakoski and Koivukoski hydropower plants. In this thesis alternative projects which aim to open these ascencion routes and their costs and benefits are evaluated. The method used in the evaluation is social cost-benefit analysis. The alternative projects evaluated in this thesis consist of projects that aim to change the flow patterns between the eastern branches of Kymijoki and projects that involve building a fish ladder. Also different combinations of these projects are considered. The objective of this thesis is to find the project that is the most profitable to execute; this evaluation can be done in comparing the net present values of the projects. In addition to this, a sensitivity analysis will be made on the parameter values that are most uncertain. We compare the net present values of the projects with the net present values of hatchery-reared smolt releases, so we can evaluate, if the projects or the smolt releases are more socially profitable in the long term. The results of this thesis indicate that especially the projects that involve building a fish ladder next to the Korkeakoski hydropower plant are the most socially profitable. If this fish ladder would be built, the natural reproduction of salmon in the Kymijoki river could become so extensive, that hatchery-reared smolt releases could even be stopped. The results of the sensivity analysis indicate that the net present values of the projects depend especially on the initial smolt survival rate of wild salmon and the functioning of the potential fish ladder in Korkeakoski. Also the changes of other parameter values influence the results of the cost-benefit analysis, but not as significantly. When the net present values of the projects and the smolt releases are compared, the results depend on which period of time is selected to count the average catches of reared salmon. If the average of the last 5 years catches is used in counting the net benefits of smolt releases, all the alternative projects are more profitable than the releases. When the average of the last 10 years is used, only building of the fish ladder in Korkeakoski and all the project combinations are more profitable than the smolt releases.

Studies on metal complex formation of environmentally friendly aminopolycarboxylate chelating agents

Aminopolykarboksyylaatteja, kuten etyleenidiamiinitetraetikkahappoa (EDTA), on käytetty useiden vuosikymmenien ajan erinomaisen metalli-ionien sitomiskyvyn vuoksi kelatointiaineena lukuisissa sovelluksissa sekä analytiikassa että monilla teollisisuuden aloilla. Näiden yhdisteiden biohajoamattomuus on kuitenkin herättänyt huolta viime aikoina, sillä niiden on havaittu olevan hyvin pysyviä luonnossa. Tämä työ on osa laajempaa tutkimushanketta, jossa on tavoitteena löytää korvaavia kelatointiaineita EDTA:lle. Tutkimuksen aiheena on kuuden kelatointiaineen metalli-ionien sitomiskyvyn kartoitus. EDTA:a paremmin luonnossa hajoavina nämä ovat ympäristöystävällisiä ehdokkaita korvaaviksi kelatointiaineiksi useisiin sovelluksiin. Työssä tutkittiin niiden kompleksinmuodostusta useiden metalli-ionien kanssa potentiometrisella titrauksella. Metalli-ionivalikoima vaihteli hieman kelatointiaineesta riippuen sisältäen magnesium-, kalsium-, mangaani-, rauta-, kupari-, sinkki-, kadmium-, elohopea-, lyijy- ja lantaani-ionit. Tutkittavat metallit oli valittu tähtäimessä olevien sovellusten, synteesissä ilmenneiden ongelmien tai ympäristönäkökohtien perusteella. Tulokset osoittavat näiden yhdisteiden metallinsitomiskyvyn olevan jonkin verran heikompi kuin EDTA:lla, mutta kuitenkin riittävän useisiin sovelluksiin kuten sellunvalkaisuprosessiin. Myrkyllisten raskasmetallien, kadmiumin, elohopen ja lyijyn kohdalla EDTA:a heikompi sitoutuminen on eduksikin, koska se yhdistettynä parempaan biohajoavuuteen saattaa alentaa tutkittujen yhdisteiden kykyä mobilisoida kyseisiä metalleja sedimenteistä. Useimmilla tutkituista yhdisteistä on ympäristönäkökulmasta etuna myös EDTA:a pienempi typpipitoisuus.

Forest inventory-based large-scale forest biomass and carbon budget assessment: new enhanced methods and use of remote sensing for verification

In recent years, concern has arisen over the effects of increasing carbon dioxide (CO2) in the earth's atmosphere due to the burning of fossil fuels. One way to mitigate increase in atmospheric CO2 concentration and climate change is carbon sequestration to forest vegeta-tion through photosynthesis. Comparable regional scale estimates for the carbon balance of forests are therefore needed for scientific and political purposes. The aim of the present dissertation was to improve methods for quantifying and verifying inventory-based carbon pool estimates of the boreal forests in the mineral soils. Ongoing forest inventories provide a data based on statistically sounded sampling for estimating the level of carbon stocks and stock changes, but improved modelling tools and comparison of methods are still needed. In this dissertation, the entire inventory-based large-scale forest carbon stock assessment method was presented together with some separate methods for enhancing and comparing it. The enhancement methods presented here include ways to quantify the biomass of understorey vegetation as well as to estimate the litter production of needles and branches. In addition, the optical remote sensing method illustrated in this dis-sertation can be used to compare with independent data. The forest inventory-based large-scale carbon stock assessment method demonstrated here provided reliable carbon estimates when compared with independent data. Future ac-tivity to improve the accuracy of this method could consist of reducing the uncertainties regarding belowground biomass and litter production as well as the soil compartment. The methods developed will serve the needs for UNFCCC reporting and the reporting under the Kyoto Protocol. This method is principally intended for analysts or planners interested in quantifying carbon over extensive forest areas.

Finitary Abstract Elementary Classes

The research in model theory has extended from the study of elementary classes to non-elementary classes, i.e. to classes which are not completely axiomatizable in elementary logic. The main theme has been the attempt to generalize tools from elementary stability theory to cover more applications arising in other branches of mathematics. In this doctoral thesis we introduce finitary abstract elementary classes, a non-elementary framework of model theory. These classes are a special case of abstract elementary classes (AEC), introduced by Saharon Shelah in the 1980's. We have collected a set of properties for classes of structures, which enable us to develop a 'geometric' approach to stability theory, including an independence calculus, in a very general framework. The thesis studies AEC's with amalgamation, joint embedding, arbitrarily large models, countable Löwenheim-Skolem number and finite character. The novel idea is the property of finite character, which enables the use of a notion of a weak type instead of the usual Galois type. Notions of simplicity, superstability, Lascar strong type, primary model and U-rank are inroduced for finitary classes. A categoricity transfer result is proved for simple, tame finitary classes: categoricity in any uncountable cardinal transfers upwards and to all cardinals above the Hanf number. Unlike the previous categoricity transfer results of equal generality the theorem does not assume the categoricity cardinal being a successor. The thesis consists of three independent papers. All three papers are joint work with Tapani Hyttinen.

Mechanisms for alphavirus nonstructural polyprotein processing

Replication and transcription of the RNA genome of alphaviruses relies on a set of virus-encoded nonstructural proteins. They are synthesized as a long polyprotein precursor, P1234, which is cleaved at three processing sites to yield nonstructural proteins nsP1, nsP2, nsP3 and nsP4. All the four proteins function as constitutive components of the membrane-associated viral replicase. Proteolytic processing of P1234 polyprotein is precisely orchestrated and coordinates the replicase assembly and maturation. The specificity of the replicase is also controlled by proteolytic cleavages. The early replicase is composed of P123 polyprotein intermediate and nsP4. It copies the positive sense RNA genome to complementary minus-strand. Production of new plus-strands requires complete processing of the replicase. The papain-like protease residing in nsP2 is responsible for all three cleavages in P1234. This study addressed the mechanisms of proteolytic processing of the replicase polyprotein in two alphaviruses Semliki Forest virus (SFV) and Sindbis virus (SIN) representing different branches of the genus. The survey highlighted the functional relation of the alphavirus nsP2 protease to the papain-like enzymes. A new structural motif the Cys-His catalytic dyad accompanied with an aromatic residue following the catalytic His was described for nsP2 and a subset of other thiol proteases. Such an architecture of the catalytic center was named the glycine specificity motif since it was implicated in recognition of a specific Gly residue in the substrate. In particular, the presence of the motif in nsP2 makes the appearance of this amino acid at the second position upstream of the scissile bond a necessary condition for the cleavage. On top of that, there were four distinct mechanisms identified, which provide affinity for the protease and specifically direct the enzyme to different sites in the P1234 polyprotein. Three factors RNA, the central domain of nsP3 and the N-terminus of nsP2 were demonstrated to be external modulators of the nsP2 protease. Here I suggest that the basal nsP2 protease specificity is inherited from the ancestral papain-like enzyme and employs the recognition of the upstream amino acid signature in the immediate vicinity of the scissile bond. This mechanism is responsible for the efficient processing of the SFV nsP3/nsP4 junction. I propose that the same mechanism is involved in the cleavage of the nsP1/nsP2 junction of both viruses as well. However, in this case it rather serves to position the substrate, whereas the efficiency of the processing is ensured by the capability of nsP2 to cut its own N-terminus in cis. Both types of cleavages are demonstrated here to be inhibited by RNA, which is interpreted as impairing the basal papain-like recognition of the substrate. In contrast, processing of the SIN nsP3/nsP4 junction was found to be activated by RNA and additionally potentiated by the presence of the central region of nsP3 in the protease. The processing of the nsP2/nsP3 junction in both viruses occurred via another mechanism, requiring the exactly processed N-terminus of nsP2 in the protease and insensitive to RNA addition. Therefore, the three processing events in the replicase polyprotein maturation are performed via three distinct mechanisms in each of two studied alphaviruses. Distinct sets of conditions required for each cleavage ensure sequential maturation of P1234 polyprotein: nsP4 is released first, then the nsP1/nsP2 site is cut in cis, and liberation of the nsP2 N-terminus activates the cleavage of the nsP2/nsP3 junction at last. The first processing event occurs differently in SFV and SIN, whereas the subsequent cleavages are found to be similar in the two viruses and therefore, their mechanisms are suggested to be conserved in the genus. The RNA modulation of the alphavirus nonstructural protease activity, discovered here, implies bidirectional functional interplay between the alphavirus RNA metabolism and protease regulation. The nsP2 protease emerges as a signal transmitting moiety, which senses the replication stage and responds with proteolytic cleavages. A detailed hypothetical model of the alphavirus replicase core was inferred from the data obtained in the study. Similar principles in replicase organization and protease functioning are expected to be employed by other RNA viruses.

Peroxidases in lignifying xylem of Norway spruce, Scots pine and silver birch

Lignin is a complex plant polymer synthesized through co-operation of multiple intracellular and extracellular enzymes. It is deposited to plant cell walls in cells where additional strength or stiffness are needed, such as in tracheary elements (TEs) in xylem, supporting sclerenchymal tissues and at the sites of wounding. Class III peroxidases (POXs) are secreted plant oxidoreductases with implications in many physiological processes such as the polymerization of lignin and suberin and auxin catabolism. POXs are able to oxidize various substrates in the presence of hydrogen peroxide, including lignin monomers, monolignols, thus enabling the monolignol polymerization to lignin by radical coupling. Trees produce large amounts of lignin in secondary xylem of stems, branches and roots. In this study, POXs of gymnosperm and angiosperm trees were studied in order to find POXs which are able to participate in lignin polymerization in developing secondary xylem i.e. are located at the site of lignin synthesis in tree stems and have the ability to oxidize monolignol substrates. Both in the gymnosperm species, Norway spruce and Scots pine, and in the angiosperm species silver birch the monolignol oxidizing POX activities originating from multiple POX isoforms were present in lignifying secondary xylem in stems during the period of annual growth. Most of the partially purified POXs from Norway spruce and silver birch xylem had highest oxidation rate with coniferyl alcohol, the main monomer in guaiacyl-lignin in conifers. The only exception was the most anionic POX fraction from silver birch, which clearly preferred sinapyl alcohol, the lignin monomer needed in the synthesis of syringyl-guaiacyl lignin in angiosperm trees. Three full-length pox cDNAs px1, px2 and px3 were cloned from the developing xylem of Norway spruce. It was shown that px1 and px2 are expressed in developing tracheids in spruce seedlings, whereas px3 transcripts were not detected suggesting low transcription level in young trees. The amino acid sequences of PX1, PX2 and PX3 were less than 60% identical to each other but showed up to 84% identity to other known POXs. They all begin with predicted N-terminal secretion signal (SS) peptides. PX2 and PX3 contained additional putative vacuolar localization determinants (VSDs) at C-terminus. Transient expression of EGFP-fusions of the SS- and VSD-peptides in tobacco protoplasts showed SS-peptides directed EGFP to secretion in tobacco cells, whereas only the PX2 C-terminal peptide seems to be a functional VSD. According to heterologous expression of px1 in Catharanthus roseus hairy roots, PX1 is a guaicol-oxidizing POX with isoelectric point (pI) approximately 10, similar to monolignol oxidizing POXs in protein extracts from Norway spruce lignifying xylem. Hence, PX1 has characteristics for participation to monolignol dehydrogenation in lignin synthesis, whereas the other two spruce POXs seem to have some other functions. Interesting topics in future include functional characterization of syringyl compound oxidizing POXs and components of POX activity regulation in trees.

Photobiological studies of Baltic Sea phytoplankton

Phytoplankton ecology and productivity is one of the main branches of contemporary oceanographic research. Research groups in this branch have increasingly started to utilise bio-optical applications. My main research objective was to critically investigate the advantages and deficiencies of the fast repetition rate (FRR) fluorometry for studies of productivity of phytoplankton, and the responses of phytoplankton towards varying environmental stress. Second, I aimed to clarify the applicability of the FRR system to the optical environment of the Baltic Sea. The FRR system offers a highly dynamic tool for studies of phytoplankton photophysiology and productivity both in the field and in a controlled environment. The FRR metrics obtain high-frequency in situ determinations of the light-acclimative and photosynthetic parameters of intact phytoplankton communities. The measurement protocol is relatively easy to use without phases requiring analytical determinations. The most notable application of the FRR system lies in its potential for making primary productivity (PP) estimations. However, the realisation of this scheme is not straightforward. The FRR-PP, based on the photosynthetic electron flow (PEF) rate, are linearly related to the photosynthetic gas exchange (fixation of 14C) PP only in environments where the photosynthesis is light-limited. If the light limitation is not present, as is usually the case in the near-surface layers of the water column, the two PP approaches will deviate. The prompt response of the PEF rate to the short-term variability in the natural light field makes the field comparisons between the PEF-PP and the 14C-PP difficult to interpret, because this variability is averaged out in the 14C-incubations. Furthermore, the FRR based PP models are tuned to closely follow the vertical pattern of the underwater irradiance. Due to the photoacclimational plasticity of phytoplankton, this easily leads to overestimates of water column PP, if precautionary measures are not taken. Natural phytoplankton is subject to broad-waveband light. Active non-spectral bio-optical instruments, like the FRR fluorometer, emit light in a relatively narrow waveband, which by its nature does not represent the in situ light field. Thus, the spectrally-dependent parameters provided by the FRR system need to be spectrally scaled to the natural light field of the Baltic Sea. In general, the requirement of spectral scaling in the water bodies under terrestrial impact concerns all light-adaptive parameters provided by any active non-spectral bio-optical technique. The FRR system can be adopted to studies of all phytoplankton that possess efficient light harvesting in the waveband matching the bluish FRR excitation. Although these taxa cover the large bulk of all the phytoplankton taxa, one exception with a pronounced ecological significance is found in the Baltic Sea. The FRR system cannot be used to monitor the photophysiology of the cyanobacterial taxa harvesting light in the yellow-red waveband. These taxa include the ecologically-significant bloom-forming cyanobacterial taxa in the Baltic Sea.