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  • Toivonen, Marjaana (Helsingin yliopisto, 2016)
    Environmental fallows are fields that aim to produce environmental benefits instead of agricultural products. In many European countries, the establishment and management of fallows is funded via agri-environmental programmes. This thesis focuses on the biodiversity benefits of environmental fallows in boreal farmland. I examined the impacts of different fallow types and landscape structure on the diversity and species composition of multiple taxa in fallows. I also aimed to evaluate what fallow types, and in what landscape context, are needed to contribute to different biodiversity objectives: the promotion of conservation concern species, overall species diversity or ecosystem services. Species richness and composition of the studied species groups differed substantially between fallow types, and landscape context further modified the value of fallows. Perennial fallows sown with meadow plants supported high plant species richness and bumblebee abundance. Old grassland fallows benefitted both butterflies in general, and butterflies and bumblebees with narrow niches and low dispersal capacities. The positive impacts were emphasized when long-term fallows were located in complex landscapes. High forest cover in the surrounding landscape increased plant species richness in perennial fallows. The breeding density of open farmland birds was highest in short-term meadow fallows in landscapes rich in perennial grasslands. Foraging edge birds preferred short-term meadow fallows in open landscapes and long-term grassland fallows in forested landscapes. Vegetation of annual fallow types game fields and landscape fields differed considerably from perennial fallows and other non-crop biotopes, thus enhancing landscape heterogeneity. My results show that the biodiversity benefits of fallows can be enhanced by adapting fallows to the landscape context and to specific conservation objectives. If the objective is to support species of conservation concern, managing long-term fallows in complex landscapes rich in perennial grasslands is probably the best strategy. Overall biodiversity can also be enhanced in short-term fallows, especially if they are sown with diverse seed mixtures of species that are not too competitive in field conditions. Depending on the sown species, short-term fallows provide good possibilities to enhance landscape heterogeneity and promote ecosystem services. Future studies should consider the specific roles of forest and perennial grasslands in driving the effectiveness of agri-environment schemes. In addition, the impacts of agri-environment schemes, including fallows, on realized ecosystem services should be investigated.
  • Mäkelä, Johanna (Helsingin yliopisto, 2016)
    Neurodegenerative diseases are characterized by the progressive loss of structure and function of neurons, but the underlying mechanisms for this are largely unknown. Disturbed cell signaling and protein metabolism as well as mitochondrial dysfunctions are thought to be involved in several neurodegenerative diseases. Mitochondria are the major source of energy in the cell, and they also regulate cell death. In brain, neurons are highly dependent on oxidative energy metabolism. Mitochondrial dysfunctions cause oxidative stress with an excess production of reactive oxygen species (ROS). In neurodegenerative diseases such as Parkinson s disease (PD), ROS are thought to contribute to the loss of dopaminergic neurons in substantia nigra pars compacta (SNpc), which leads to dopamine depletion in striatum. Peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) is a transcriptional co-activator that regulates mitochondrial biogenesis, ROS defense and respiration. The lack of PGC-1α has been shown to increase the sensitivity of neurons to oxidative stress and brain injuries. In this study we show that increasing the expression of PGC-1α protects against toxin-induced oxidative stress in dopaminergic neurons. We show that PGC-1α expression in dopaminergic neurons can be modulated by resveratrol (RSV), fibroblast growth factor 21 (FGF21) and peroxisome proliferator-activated receptor γ (PPARγ) that are known to regulate metabolism in other tissues. The increase in PGC-1α expression and activation was linked to metabolic changes mimicing low energy levels in the cell, and an increase in SIRT1, a metabolic regulator sensing changes in energy levels. PGC-1α activation was further associated with an increase in mitochondrial respiration and antioxidant levels suggesting that the neuroprotective effect of PGC-1α was due to an improved capacity to combat oxidative stress. These results show that regulation of metabolism by PGC-1α activators could be a useful tool to prevent neurodegeneration in PD. In addition to modulating PGC-1α, RSV was also found to increase the expression of dopamine transporter (DAT) in dopaminergic neurons of female mice. The increase in the level of DAT increases the uptake of dopamine, further indicating that RSV has beneficial effects in dopaminergic neurons. By affecting DAT, RSV also contributes to maintaining functional neurons, as a decline in DAT has been associated with degeneration of dopaminergic neurons. This effect on DAT expression was mediated by estrogen receptors, indicating that the effect of RSV differs between genders that should be considered if RSV is used as therapy for patients with PD.
  • Etongo Bau, Daniel (Helsingin yliopisto, 2016)
    Tropical deforestation and forest degradation (DD) contribute approximately 15% of the annual global anthropogenic greenhouse gas (GHG) emissions. However, they are considered the main emissions sources in most developing countries. Despite the potentials of forest and tree plantations to mitigate the effects of climate change through carbon sequestration, DD still remains a challenge in Africa. Globally, the forests of Africa are the most depleted of all tropical regions, with only 30% of historical forest area still remaining. In addition, Africa s complexity in terms of its geography, politics, socioculture, economy, institutions etc. is an indication of why Africa has defied all simple solutions in addressing DD: a phenomenon considered location- and situation-specific. The biophysical setting of Burkina Faso exposes the central and northern region to drought and desertification. Such conditions have caused human migration to the southwestern regions, which offer better opportunities for rain-fed agriculture, but also experiences the highest rates of deforestation. On the other hand, the ongoing regreening process in the Sahel through tree planting and assisted natural regeneration of indigenous tree species is a signal for regrowth and revegetation. This study contributes to understanding the drivers of DD in four adjacent village communities in the Ziro province, southern Burkina Faso in the light of the forest transition theory. Specifically, this study assesses the drivers of DD at the farm/forest level and also identifies options for regrowth/revegetation. This dissertation consists of four articles (studies I, II, III, and IV). Studies I and II refer to stage two of the forest transition curve (forest frontier) while studies III and IV refer to stage four of the curve (forest/plantations/agricultural mosaics). Various methods were used during data collection, including interviews with key informants, focus group discussions (FGDs), two hundred household interviews (studies I, II, and III), gathering a list of local botanical knowledge from 48 participants (study IV), and a field survey. Qualitative and quantitative methods were used in analyzing the data. Low agricultural production expressed in the sizes (areas) and ages of farms together with land tenure insecurity were found to lead to increased deforestation. Results suggested that a 10% increase in farm size would result in a 4% increase in annual deforestation (study I). Furthermore, results in study II indicated that non-poor and fairly poor farmers contributed more towards activities considered environmentally degrading, such as deforestation, overgrazing etc., than the poorest farmers. On the other hand, the adoption of sustainable land management practices was relatively low among the poorest farmers. Tree planters were mainly farmers who held large and old farm areas, were literate and relatively wealthy, held favorable attitudes towards tree planting, and had participated in a farmers group for several years (study III). Local knowledge of tree species was found to be unevenly distributed in relation to gender, age, ethnic group, and location. Plant species assigned relatively high use-values for livelihood include Adansonia digitata, Parkia biglobosa, Vitellaria paradoxa, and Balanites aegyptiaca. On the other hand, Adansonia digitata, Tamarindus indica, and Ficus thonningii were considered more important for environmental protection (study IV). The dissertation concludes that tenure insecurity and low agricultural production contribute to DD at the farm/forest level on the one hand while tree plantations, land management practices, such as fallow, zai pits (a traditional soil and water conservation technique), and assisted natural regeneration of indigenous tree species are important activities promoting regrowth/revegetation.
  • Korhonen, Jaana (2016)
    International industrial competitiveness depends on many aspects. It can be based on cost advantages over international competitors, which are realized as higher market shares and increased trade flows in global markets. Competitiveness can also be improved by creating higher value through increased product quality and by means of sustainability. This places increasing strategic importance on scarcening natural resources and on how proactively environmental responsibility is perceived in the international forest sector in the future; as an additional cost or more as an opportunity of a high road to competitiveness? The goal of this dissertation is to analyze international competitiveness and its drivers from five different perspectives at the regional, country, and firm levels, with an emphasis on the pulp and paper industry. The empirical research problems of five individual research articles are approached by combining quantitative and qualitative data analyses. The time period from 1990 to 2030 was covered in the analyses. The results highlight the importance of forests, markets, and regulation in creating competitive advantages at different levels in the sector. The traditional forest sector factors such as resource availability and traditional economic factors such price competitiveness are going to play an important role also in the future. However, sustainability will become increasingly important for the value creation opportunities of industries. It is an opportunity for companies in their global value chains if the global environmental awareness and societal demand for sustainability continue to increase. Therefore, more responsible use of global forest resources can offer solutions to global sustainability challenges, and in the transition to a bioeconomy in which the forest industry plays a key role.
  • Saarinen, Ninni (Helsingin yliopisto, 2016)
    Accurate and up-to-date information concerning vegetation characteristics is needed for decision-making from individual-tree-level management activities to the strategic planning of forest resources. Outdated information may lead to unbeneficial or even wrong decisions, at least when it comes to the timing of management activities. Airborne laser scanning (ALS) has so far been successfully used for applications involving detailed vegetation mapping because of its capability to simultaneously produce accurate information on vegetation and ground surfaces. The aim of this dissertation was to develop methods for characterizing vegetation and its changes in varying environments. A method called multisource single-tree inventory (MS-STI) was developed in substudy I to update urban tree attributes. In MS-STI stem map was produced with terrestrial laser scanning (TLS) and by combining the stem map with predictors derived from ALS data it was possible to obtain improved estimates of diameter-at-breast height but also to produce new attributes such as height and crown size. Boat-based mobile laser scanning (MLS) data were employed in substudy II to map riverbank vegetation and identify changes. The overall classification accuracy of 73% was obtained, which is similar to accuracies found in other studies. With multi-temporal MLS data sets changes in vegetation were mapped year to year. In substudy III, open access ALS data were combined with multisource national forest inventory (NFI) data to investigate the drivers associated to wind damage. The special interest was in ALS-based predictors to map areas with wind disturbance and apply logistic regression to produce a continuous probability surface of wind predisposition to identify areas most likely to experience wind damage. The results demonstrated that a combination of ALS and multisource NFI in the modelling approach increased the prediction accuracy from 76% to 81%. The dissertation showed the capability of ALS and MLS for characterizing vegetation and mapping changes in varying environments. The developed applications could increase and expand the utilization of multi-temporal 3D data sets as well as increase data value. The results of this dissertation can be utilized in producing more accurate, diverse, and up-to-date information for decision-making related to natural resources.
  • Help-Rinta-Rahko, Hanna (Helsingin yliopisto, 2016)
    The interaction of auxin and cytokinin signalling regulates primary root procambial patterning, xylem cell fate and differentiation in Arabidopsis thaliana. Plants contribute to the Earth s atmosphere by binding carbon dioxide and releasing oxygen. Trees produce biomass, which is a renewable source of energy. The Arabidopsis root vasculature is a good model system for studying biomass formation, as it contains the same cell types that are also found in trees: xylem, phloem and intervening pluripotent procambial cells. In Arabidopsis thaliana roots, these cells arise from stem cells within the root meristem. The wild type root radial pattern is bisymmetric, and the regulation of xylem formation is controlled by phytohormones, especially auxin and cytokinin. Our findings show that the vascular pattern is set by a symmetry-breaking event during embryogenesis and is initiated by auxin accumulation and signalling at the cotyledon initials. As the embryo grows, the high auxin signalling promotes the expression of AHP6. Upregulation of AHP6 in specific cells leads to inhibition of cytokinin signalling and might be a key factor in symmetry breakage. Mutants with altered cotyledon numbers or altered cotyledon anatomy fail to establish the bisymmetric pattern and often show altered root symmetry. In growing roots, the bisymmetric pattern is actively reinforced by polar auxin transport and long distance cytokinin transport/translocation from the apical parts of the plant. Cytokinin movement via the phloem and unloading at the root apical meristem promotes cytokinin signalling in the procambial cells in the proximal meristem. Both cytokinin and auxin are required during root procambial patterning, and the interaction of these two phytohormones is mutually inhibitory. According to our model (described in the first part of this thesis), auxin signalling is critical for protoxylem identity formation. In turn, the results from the procambial re-patterning experiments (second part of this thesis) show that cytokinin is the key hormone in promoting cell proliferation in the proximal meristem. Epistasis experiments illustrate that a fine balance between these two hormones affects the fate of all vascular cells. We are beginning to understand the complexity and interdependencies of signalling pathway interactions during proximal meristem vascular patterning, yet the temporal aspect is still largely unexplored. In the last part of this thesis, I discuss the role ROS signalling might have in stele patterning and temporal regulation of programmed cell death. While our published GRI-MC9-PRK5 module might not be directly linked to primary root proximal meristem procambial patterning, one cannot exclude the possibility that it might be required in the final stages of protoxylem differentiation or that a similar signalling mechanism could regulate initial stele patterning and meristem growth dynamics. This thesis describes the auxin-cytokinin interaction in vascular initial patterning and the mechanism by which the hormonal signalling domains are maintained in the proximal meristem. The unpublished data demonstrate how procambial cells can be manipulated to generate new tissues by affecting the homeostasis of auxin and cytokinin signalling. The last part of the thesis describes a cell death signalling module and speculates that it (or similar module) might be involved with primary root meristem maturation.
  • Huovila, Janne (Helsingin yliopisto, 2016)
    Public representations of healthy eating have been shifted to value more individualistic conceptualizations. Nevertheless, it is unclear how these conceptualizations are constructed. In this doctoral thesis, the main goal is to investigate how a more individualistic understanding of healthy eating is epistemically constructed and rhetorically made credible in media publicity. The thesis contains three case analyses. The first case involves an investigation into the debate about the low-carbohydrate diet in the Helsingin Sanomat newspaper. The second case compares the argumentation of six highly popular Finnish nutrition counselling bloggers to the argumentation of two academic experts contributing to the blog of the National Institute for Health and Welfare. The third case analysed the narrative construction of diet knowledge by academically-educated experts in blogs and the Finnish Medical Journal. The main finding was to identify the rationality - termed the sense of casuistry - that put together the epistemic and rhetorical aspects about the individualization of healthy eating. The sense of casuistry defined the basis of proper diet and eating habits valuing physiological, psychological and lifestyle differences between individuals. The sense of casuistry was constructed epistemically and, especially, rhetorically in a critical relationship to the common public health thinking which argues for population-based averages and risks. The rhetorical power of the casuistry was established through old cultural resources: clinical reasoning and common sense understanding about the differences between individuals. It was also influenced, however, by new cultural shifts, especially in media publicity, which emphasize personal experience and contextual factors in nutrition science instead of consensus statements. Individualization of healthy eating in public representations does not exemplify the clear distinction between scientific and unscientific knowledge. Because of this, individualization challenge to redefine expert communication: in contemporary media publicity, it is crucial to argue not only through the epidemiological rationality about risks and probabilities, but also in relation to casuistical reasoning, or a part of it. The methodological contribution of the study brings multidisciplinary epistemological framework together with discursive analysis regarding diet knowledge. For understanding the complex basis of diet knowledge in contemporary global and networked media publicity, it is important to combine the discursive approach on diet knowledge and nutritional understanding about the generalizability and contextualization of diet knowledge.
  • Kasurinen, Ville (Finnish Society of Forest Science, 2016)
    Water and carbon cycles of the Earth are tightly linked to each other. One linkage of these cycles is through the water use efficiency of photosynthetic production its interactions with drought, and its possible changes. A second linkage between the water and carbon cycles: the transport of terrestrial carbon as dissolved organic carbon (DOC) to aquatic ecosystems has received much less attention and is, therefore, the subject of this thesis. The thesis shows that latent heat exchange in boreal and arctic biomes differs, under similar climatic conditions, between different land cover types in the boreal and arctic climatic zones. Furthermore, we found that there are large differences in the way ecosystems are exchanging water in the winter and the summer. Winter time surface resistances were much higher and the transition between the winter and summer phenological stages was slow. Similarly, stream water DOC concentrations show high temporal and spatial variability between different catchments in boreal landscapes and globally between big river systems. The model, developed here and applied to a boreal catchment simulates stream water DOC concentrations as a function of catchment water storage, soil temperature and runoff. The model is parsimonious, i.e. all parameters could be estimated statistically and it its performed better than previous models for the 18 partially nested sub-catchments of the Kryckland research area. Finally, the contribution of terrestrial DOC promoting heterotrophic food webs in coastal waters was quantified after receiving a radiation dose corresponding UV-radiation absorbed by Earth s surface in a month. Irradiation removed approximately half from the initial terrestrial chromophoric dissolved organic matter (tCDOM) suggesting that sun-light induced photochemistry is a significant sink of tCDOM in coastal waters. Tropical rainforest covered large basins of Amazon and Congo Rivers contributed the highest production of biologically labile photoproducts (BLPs) and the highest tCDOM fluxes of investigated rivers, which might be linked to large water fluxes and carbon sequestration in their basins. A strong relationship between photobleaching of tCDOM and bacterial production based on bioavailable labile photoproducts (BLPs) was found and used to estimate BLP production globally. Extrapolation of production revealed that the majority of tDOC will be mineralized to CO2 either directly or through bacterial respiration in coastal waters. In these research articles, I have investigated biogeochemical cycles of water and carbon focusing to latent heat exchange and DOC dynamics in landscapes, as well as, in coastal waters, describing their variability across space and time.
  • Niemi, Milla (Helsingin yliopisto, 2016)
    Road networks and traffic cause worldwide environmental and ecological problems, and collisions with large animals are an increasing traffic safety issue. There is thus a continuous need to improve our understanding of the factors affecting the controversial relationship between nature, traffic, and human welfare, and to develop efficient mitigation measures. In this thesis, I found that population size is the most important factor explaining the yearly variation in the number of moose-vehicle collisions (MVCs) in Finland. The monthly number of MVCs peaked in autumn with a secondary peak in early summer. This pattern differed from Sweden and Norway where the peak occurred in winter. In contrast, the relative risk of personal injuries was highest during summer in each country. Spring weather was found to affect the detailed timing of spring MVCs in Finland: collisions occurred earlier during warm springs. In addition, as the beginning of the growing season has moved to an earlier date in the last two decades, so has the spring MVC peak. In addition to MVCs, several thousand collisions involving deer species other than moose annually occur on Finnish roads. White-tailed deer was found to suffer highest traffic mortality rates in relation to population size, followed by moose, roe deer, and fallow deer. Among the studied species, moose has the largest and roe deer the smallest probability of surviving a collision. The adverse impacts of traffic on animals could be mitigated for example by constructing wildlife passages. Dry paths under road bridges proved to be an effective mitigation measure for reducing the traffic mortality of small and medium-sized terrestrial animals. The results of this thesis underline that different mitigation measures from population management and driver education to structural solutions are needed when trying to reduce the number and consequences of animal-vehicle collisions.
  • Hyvärinen, Antti (Helsingin yliopisto, 2016)
    The aim of this study is about the development of the capital stock on Finnish farms. Therefore the subject is closely related to investment behaviour of farmers. Due to structural change the average size of agricultural investment and capital stock have been increasing during previous decade. On the other hand, not all farms choose to enlarge, but part of them are quitting or continue as they were. Thus, large investments are concentrated to a subset of farms. The empirical goal of this study is to investigate what kind of farms do invest? (and hence are among those which shall continue production in the future). Related questions are how well investments can be forecasted by bookkeeping information and what kind of a process defines the growth of farm s capital stock. Before going into statistical modelling of farm investments, an extensive literature review is presented in the first section of the study. Topics of current economic theory that are related to investment behaviour of firms are brought up. The emphasis is on distinctive features of agriculture and in particular agriculture in Finnish operational environment. The standard derivation of demand of the capital is presented in the context of profit maximization models. These models consist of a simple static model and more complex dynamic models with adjustment costs. Furthermore, the effect of uncertainty in investment decision is analysed by using the real option model. It is pointed out that some features of agriculture may significantly restrict maximization behaviour. It is concluded that profit maximization models may describe actions of some farmers well, but may not be appropriate (in standard form) for others. The empirical part of the study utilizes statistical methods in a panel data setting. The panel data contains observations from the same farms over different years, which makes it possible to assess the development in variable values. Data are from Finnish bookkeeping farms and the period covers years 1998-2011. There are observations from 1 580 farms in total. However, some farms drop out before year 2011 and are replaced by sampling new ones from the farm population. There are 800-900 farms annually in the panel. Variables in the dataset include statistics related to the farm size, the economic state of the farm, and to human resources of the farm family. Data are first summarized by the means of exploratory analysis. Descriptive statistics show a large increase in the size of average investments and utilization of capital with respect to time. Furthermore, it is obvious that exogenous shocks have influenced on farm investments during certain years. These shocks reflect variation in profitability and the modification of investment aid scheme. Then attention is turned into analysing development paths of capital at the farm level. This reveals that investments in many cases are lumpy i.e. there are many periods of inaction followed by a large adjustment of the capital stock. This observation contradicts assumptions in a standard adjustment cost model, where smooth path of adjustment is assumed. Nevertheless, similar observations have been made with various real datasets (references are found in the text). Next section concentrates on empirical challenges with this particular study. It is shown that the distributions are highly skewed and many of the variables include plenty of possible outliers. Still, these outliers are very likely to represent real values in measured quantity (as opposed to measurement errors). In most cases outliers reflect a whole new scale of farms in Finnish agriculture as a result of structural change. Therefore, outliers contain valuable information and cannot be dropped from the data. It is also assumed that various potential explanatory variables correlate heavily with each other. This is confirmed by the results of principal component analysis (PCA), which shows that data can be significantly condensed while preserving most of the original information. Moreover, results of PCA show that main variation in the dataset is within the economic size of the farms. That is to say, farms of various sizes are operating in Finnish agriculture. The final challenge relates to the drop out of farms from the panel. If drop out mechanism is not random, it may have an effect to generalization of results. Drop out mechanism is studied by forming a Random Survival Forest model. Results show that drop out is related on past investment behaviour and the farm size. Farms with very small past investments (and small size) are most likely to drop out. This indicates that drop out from panel may be related to quitting farming altogether. The challenges above lead to choosing tree based models for analysis tool. The tree models may not offer as precise quantitative estimates as, for instance, linear regression models. However, tree models have various benefits in this particular setting. The distributional assumptions required from the data are somewhat less strict as compared to regression models. Furthermore, tree models are suitable in finding various forms of relations between dependent and explanatory variables and can handle a large number of possible covariates. Applied tree models were classification and regression trees (standard and ensemble CART trees, which forms Random Forest model). Comparison of the results was made with a newer model called GUIDE which utilizes the panel structure of the data, when the dependent variable can appear in a longitudinal form in the model. The results from tree models show that enlargement investments are most probable in farms that have sufficient size to begin with. The best predictor of various measures of the farm size turns out to be the starting capital stock. Results depend somewhat on the length of the time series from particular farm. Logically, lengthening of observation period increases the probability of observing large investment. This is problematic because the panel is unbalanced. Surely, longer time series provides more reliable picture of the development of capital stock, but there exists significant trade-off between the required length of time series and the number of farms that have such number of observations. Additionally, the results show that large past investments increase the probability of subsequent investments. That is to say, choosing expansion path results successive increases of farm size. This may be distinguishing characteristic for firms in the industry that are going through structural changes. Some authors (e.g. Nilsen and Schiantarelli (2003)) have had opposite results when studying industries in mature state. Large investments may not lead to immediate improvement in profitability. In contrast they do in many cases result poor profitability during the year the investment is made and also short period after that. This form of adjustment costs should be taken into account when testing profit maximization models empirically. In general, it seems that incentives for investments are their long term prospects. However, test data is usually available for a rather short period, which may cause profit maximization models to fail empirically. Number of issues remains to be clarified in continuation of research. One issue is whether different types of capital are substitutable or do they have to be utilized in almost constant proportions in farm production. It was shown that current theoretical models should be modified in order to obtain empirical support from the Finnish agricultural data. During the structural change the sole objective of profit maximization may not be adequate for all farms. Statistical tools in this area of research are developing rapidly and the data also allows more sophisticated analysis. Quantitative implications of differing investment aid schemes, or more precisely differing combination of investment and direct subsidies, can be studied by utilizing differences among support areas in a setting called natural experiment .
  • Ahtiainen, Heini (Helsingin yliopisto, 2016)
    Eutrophication is a major problem in both marine and freshwater areas in Europe, changing the structure and functioning of the ecosystem and reducing its ability to produce human well-being. Information on the monetary benefits of reduced eutrophication is needed to design economically efficient environmental policies. This thesis provides information on citizen s willingness to pay for reduced eutrophication in Europe, the Baltic Sea area and Finland, contributing to the literature by providing up-to-date benefit estimates to support decision-making and examining methodological issues in the economic valuation of environmental benefits. Three valuation approaches are used: meta-analysis, contingent valuation and choice experiment. The meta-analysis provides an overall understanding of the benefits of reduced eutrophication in European marine areas, the contingent valuation study investigates the benefits of reaching a specific eutrophication reduction target in the Baltic Sea, and the choice experiment reveals Finnish summer house owners preferences and values for water quality changes. The contingent valuation results are further used in a cost-benefit analysis of nutrient abatement in the Baltic Sea. The methodological issues examined include conducting a meta-analysis when only few primary valuation studies are available, preference heterogeneity and asymmetry in choice experiments, and the use of international contingent valuation studies in cost benefit analysis. The results show that substantial benefits can be gained from reduced eutrophication. In European marine areas, the annual benefits from reduced eutrophication are 5-210 euros per person, depending on the country, sea area and extent of the change. In the coastal countries of the Baltic Sea, the annual benefits range from 6 to 76 euros per person. The findings clearly indicate that the benefits differ between sea areas and countries, being greater in high-income countries. Results of the contingent valuation study in the Baltic Sea indicate that even when the sea area and the environmental change are the same, willingness to pay and its determinants differ between countries. Based on the choice experiment, deterioration in water quality results in larger welfare losses compared to the gains from an improvement of the same size, indicating that it is particularly important to prevent the deterioration of water quality. The benefit estimates can be utilized in deciding whether and how much to reduce eutrophication. The monetary benefits of reaching a good environmental status in the Baltic Sea with regard to eutrophication are estimated at 3600 million euros per year. The results also serve as justification for implementing additional nutrient abatement measures in the Baltic Sea area, as the benefits of nutrient abatement exceed the costs. In addition, identifying the differences in benefits across countries may aid international negotiations. Countries that benefit more, such as Sweden, Finland and Germany, could pay for nutrient abatement measures in Estonia, Latvia, Lithuania and Poland to reach an international agreement.
  • Heikkinen, Jaakko (Helsingin yliopisto, 2016)
    Carbon (C) that is stored in soils is the principal terrestrial C pool. The soil stores twice as much C compared to that which is stored in the atmosphere. Therefore, even a slight change in soil C stock can have a huge effect on atmospheric carbon dioxide concentration and global climate. Agricultural soils play a key role in this system: they cover about 38% of the land area world-wide and are intensively managed. The soil C also greatly contributes to sustainable food production as soil organic matter is to large extent made of C. The aim of the research carried out for this thesis was to determine the nationwide soil C stock in Finnish arable mineral soils, study historic trends of C stock in soils and examine possible factors that affect those trends. Knowing the past can also give us insights into future trends in soil C and its climatic impact. The data presented in this thesis were obtained from the Finnish national soil monitoring network and long-term field trials in Uppsala Sweden and Pushchino Russia. In addition two process-based soil C models, namely: Yasso07 and RothC, were used and their findings were compared with those of long-term field trials. Finnish arable lands were found to be rich in soil C. Mineral soils in Finland store between 41 and 67 Mg C ha-1 (0-15 cm) depending on the management, soil type and region. Nationwide the C stock in arable topsoil is about 117 Tg and although the deeper soils layers are poorly known the total soil C stock in mineral soils of Finland can be estimated to be about 300 Tg. The C stock of mineral arable soils has decreased. The decrease was found to be 0.22 Mg C ha-1 yr-1 (0-15 cm soil layer) according to the national soil inventory network of Finland and 0.29-0.36 Mg C ha-1 yr-1 (0-100 cm soil layer) according to results obtained by the Yasso07 model. The annual C emissions from agricultural mineral soils are about 0.5 Tg, which represents about 2.5% of the total greenhouse gas emissions in Finland. Process based modelling in which the past land use history was taken into account clearly indicated that the nationwide decrease can be linked to the past change in land use from forest to agricultural land, which has created the ongoing soil C loss. Finnish arable lands are relatively young and it is likely that they are still losing the soil C that had been accumulated when these lands were part of boreal forest systems. Likewise the thesis indicates that the soil C loss partly results from the intensification in cultivations that took place in the past decades and that cultivation of annual crops has become more common. Cultivation of annual crops increases the soil disturbance due to tillage and decreases the below-ground C influx into the soil. The composition of litter quality was also shown to have considerable effects on the ease of decomposition of organic matter. Previously, the Yasso07 model had been mainly tested and used in forested soils. Findings in this thesis demonstrate that this model can also be applied to agricultural mineral soils under boreal conditions. The fact that the model works equally well under various environmental conditions indicates that the accumulation of soil C is largely controlled by litter input, climate and litter chemical quality. The comparison between simulations and experimental data obtained from field trials showed that the results of Yasso07 model are comparable with those of the RothC model, which is currently one of the most widely used soil C models for agricultural applications. The decreasing trend of soil C stocks found in this thesis has undesirable ramifications for climate, environment and sustainable food production. The changes in topsoil C might reflect the condition of soil C in deeper soil layers. Therefore, it would be crucial to investigate the storage of deep soil C and the long-term effects of agricultural practices on it.
  • Viitala, Esa-Jussi (Unigrafia, 2016)
    One of the fundamental principles of natural resource economics is that nature may be treated as capital. Thus a decision-maker faces a trade-off between how much to consume of the natural capital now, and how much to save for future periods (generations) so that economic efficiency and welfare are maximized. By natural capital is meant land, forests, water, air, and all the ecosystems and natural stocks associated with them. In forestry, the most prominent manifestation of this fundamental resource economic principle is the so-called Faustmann model. It has been regarded as perhaps the oldest formal description of natural resource use that is still considered to be theoretically valid. When combined with neoclassical utility theory, the model and its underlying economic principles form a basis for determining optimal forest resource use in current and thus in all future periods. However, compared to many other forms of manufactured and natural capital, efficient allocation of forest resources is a particularly difficult task due to extended periods of production and the multitude and complexity of forest systems. This dissertation examines how the Faustmann model and the related principles that govern economic forest management emerged and developed in England and in the German states. At the same time, it shows that many of the persistent controversies in forestry not only imply insufficient understanding of the relevant domain of the Faustmann model, but also reflect the centuries-long and deeply rooted perception that land, nature and forests are distinct if not unique forms of capital and should be treated as such. The dissertation also shows how the development of forest and natural resource economic thought has for centuries been connected to broader socio-economic changes and accompanying intellectual currents.
  • Rasimus-Sahari, Stiina (Helsingin yliopisto, 2016)
    Humans are exposed to microbes and microbial compounds continuously via environmental exposure and food in addition to our own microbiome. This thesis reports new empirical findings concerning the types of mitochondrial toxins present in food and indoor air and the effects of these toxins on mammalian cells. Dust and aerosolized compounds collected from moisture-damaged buildings were shown to have mitochondriotoxic effects detectable with a boar sperm motility inhibition (BSMI) assay. Toxin-producing bacteria isolated from the dusts and aerosols included producers of the mitochondrial toxins amylosin, cereulide, and valinomycin. In addition, aerosolized valinomycin and toxic chemical compounds emitted from building materials were detected using boar spermatozoa, demonstrating that the BMSI assay could be used to screen for mitochondrial toxicity in indoor air. Amylosin, a mitochondriotoxin produced by Bacillus spp. from indoor air and food, was shown to be immunotoxic: exposure of human primary macrophages to nanomolar concentrations of amylosin stimulated the release of inflammatory cytokines interleukin 1β and interleukin 18. Amylosin is the first bacterial channel-forming ionophore toxin reported to have this effect. Low amounts of amylosin caused significant dose-dependent potassium ion efflux from human somatic cells and boar spermatozoa. Potassium efflux may be the trigger causing the observed cytokine release from macrophages after amylosin exposure. Amylosin also displayed antifungal and antibacterial activity which may give its producers a competitive advantage in mixed microbial communities. Two previously unreported food safety hazards were identified from cereal grains. A novel heat-stable mitochondrial toxin named paenilide, similar to cereulide biochemically and in mode of action, was found to be produced by Paenibacillus tundrae isolated from barley grains. This finding shows that the genus Paenibacillus cannot be considered harmless for human health. Paenilide consisted of two components with molecular masses equal to those of cereulide and homocereulide but with longer chromatographic retention times, indicating more hydrophobic structures than those of the cereulide compounds. Paenilide acted as a lipophilic potassium ionophore, causing depolarization, swelling, uncoupling of oxidative phosphorylation, and loss of respiratory control in isolated rat liver mitochondria. Paenilide accelerated glucose consumption in porcine kidney epithelial cells, causing metabolic acidosis, and was cytotoxic to porcine and murine cells. Paenilide was as toxic as cereulide at nanomolar amounts, making it a possibly potent food poisoning agent. Paenilide was produced at incubation temperatures down to +5°C, indicating potential toxin formation in chilled foods. The second novel finding connected to cereal grains was the discovery of toxin-producing Streptomyces spp. in healthy-looking grains of barley and spring wheat. The barley grain isolates, belonging to the Streptomyces albidoflavus group, produced the mitochondriotoxic macrolide antimycin A, a known disrupter of oxidative phosphorylation. The cause of the mitochondrial toxicity of the spring wheat grain isolates, most closely related to Streptomyces sedi, remained unidentified. The toxicity of the isolates and grains was detected using the BSMI assay, which was sensitive enough to detect nanomolar contamination corresponding to 2 ng of antimycin A per barley grain. Antimycin A was more toxic towards porcine kidney epithelial cells than the mycotoxin enniatin B but less toxic than cereulide or paenilide. Exposure of porcine kidney epithelial cells to these four toxins accelerated glucose consumption and caused mitochondrial depolarization, indicating upregulation of glycolysis. Pancreatic insulin-producing beta cells, however, are not able to switch to glycolytic ATP production and undergo necrotic cell death upon exposure to mitochondrial toxins. Thus, consumption of grains contaminated with mitochondrial toxins may especially affect pancreatic functions. In conlusion, the results of this thesis show that chronic exposure via indoor air or food to sub-lethal concentrations of mitochondriotoxins produced by spore-forming bacteria may be more common than known so far. This exposure may connect to the increasing worldwide incidence of western lifestyle diseases, such as diabetes, asthma, and allergies as well as cardiovascular and neurological disorders. The studied toxins are all heat-stable and produced by spore-formers able to withstand harsh environmental conditions, highlighting that preventing their presence and endurance in food and indoor environments is problematic.
  • Koivunen, Erja (Helsingin yliopisto, 2016)
    Four experiments were conducted to find appropriate inclusion levels of pea (Pisum sativum L.) and faba bean (Vicia faba L.) (FB) seeds as a substitute for soybean meal (SBM) in poultry diets. The inclusion levels tested for pea (cv. Karita) were 100, 200 and 300 g/kg in layer diet and 150, 300 and 450 in broiler diet and for FB (cv. Kontu) 50 and 100 g/kg in layer diet and 80, 160 and 240 g/kg in broiler diet. The effect of a specific enzyme cocktail for improving the nutritive value of wheat-pea diets was also investigated in broilers. The fifth experiment was conducted to determine the apparent metabolizable energy (AME) value and the coefficients apparent ileal digestibility (CAID) of nutrients of the seeds of two peas (cv. Karita and cv. Sohvi), two FBs (cv. Kontu and cv. Ukko), and one blue lupin (Lupinus angustifolius) (cv. Pershatsvet) in broilers. Each grain legumes contained less protein than soybean SBM did. Pea inclusion up to 300 g/kg had no effect on egg production or egg quality. Pea inclusion of 150 g/kg improved the growth of broilers, while pea inclusions 300 and 450 g/kg had no effect on growth. Feed conversion ratio (FCR) of broilers was similar between control treatment and treatment with pea inclusions 450 g/kg. The use of enzyme cocktail improves the nutritive value of wheat in the diet. FB inclusion decreased egg weight. Egg mass production decreased and FCR increased when FB proportion increased. FB inclusion had no effect on egg quality. Broilers growth and feed consumption decreased and FCR improved in a linear manner along FB inclusion. The CAID of protein was higher in peas and lupin than in FB cv. Kontu. Most of CAID values of amino acids (AA) followed the pattern shown by the CAID of protein. AAs in peas were well digested. The AAs were averagely digested in FBs with the exception of cysteine, which was poorly digested. The AAs were averagely digested in lupin. The AME for pea cv. Karita was higher than those of pea cv. Sohvi and FBs cv. Kontu and cv. Ukko. Lupin had the poorest AME. In conclusion, grain legumes can partially replace SBM in poultry diets. However, they replace also cereals in diets. Peas (cv. Karita) can be used at least up to 300 g/kg in layer diets and 450 g/kg in broiler diet. The use of FB (cv. Kontu) is recommended to be limited to the content of 50 g/kg in layer diets and 160 g/kg in broiler diets.
  • Rimhanen, Karoliina (Helsingin yliopisto, 2016)
    Sub-Saharan Africa (SSA) is one of the world´s most vulnerable regions to climate change. Even though the proportion of greenhouse gas emissions produced in SSA is low, the agricultural sector has an enormous potential for climate change mitigation. The aim here is to increase understanding of the potential of climate change mitigation to enhance food security. The focus of the study is to identify the determinants of this potential, to estimate the possibilities to increase the proportion of carbon ending up in soil and to quantify the soil carbon sequestration potential of agroecological practices in Ethiopia. Identification of the determinants of the potential of climate change mitigation to enhance food security was based on in-depth interviews and focus group discussions. The assessment of carbon flows was based on interviews and sampling. Material flow analysis and carbon balance counting was used for tracking the carbon flows and for estimating the carbon losses. Quantification of the carbon sequestration potential of the agroecological practices was based on comparison of the existing plot pairs, including a plot with an agroecological practice and an adjacent plot with a traditional practice. Soil carbon sequestration in agricultural soil was considered as the most important means to promote climate change mitigation and to enhance food security. The primary factors enhancing food security were perceived to be increasing agricultural productivity and incomes from marketed crops. On the Ethiopian farms, 8 12% of the total harvested carbon was used for soil and 9 16% for food. The largest carbon losses were due to biomass burning and livestock metabolism. The proportion of carbon used for soil could mainly be increased by reducing gaseous losses. Agroforestry led to 11.4 t ha-1, restrained grazing to 9.6 t ha-1 and terracing to 1.7 t ha-1 greater soil carbon stock than did their control plots. The estimates are higher than those based on process-modelling studies. The difference probably resulted from the development and validation of process models under conditions that differ from those in East-Africa. From the results it can be concluded that the most important means perceived as enhancing food security through climate change mitigation is improving food availability through soil carbon sequestration. The proportion of carbon used for energy determines the proportion ending up in soil. Alternative energy sources are needed to increase the flow of carbon to soil. The soil carbon sequestration potential in Ethiopian agriculture is greater than previously estimated. Climate conditions and intercropping treatment should be incorporated into process models to improve their adequacy for farming systems in East Africa.
  • Korkalo, Liisa (Helsingin yliopisto, 2016)
    Poor micronutrient intake and status (also called hidden hunger ) may compromise the health and work capacity of adolescent girls. In Mozambique, a low-income country with a high rate of adolescent pregnancies, girls poor micronutrient status is also an important risk factor for maternal and child mortality, adverse birth outcomes such as low birth weight, and impaired cognitive performance of the child. The main aims of this thesis were to examine the diet and micronutrient status of adolescent girls in Central Mozambique and to study whether dietary diversity is associated with biomarkers of micronutrient status. The thesis also includes a methodological study assessing the validity of using food photographs in portion size estimation in adolescent Mozambican girls. The validity study on food photographs was conducted in 2009. Two local staple foods and three sauces were selected as test foods and photographs of three different portion sizes were produced for each of them. The participants (99 Mozambican girls aged 13-18 years) were served weighted food portions, and after eating their meal, they were interviewed and asked to estimate the size of their portions with the help of the food photographs. The findings of this study indicated a tendency towards under-estimation of portion sizes. On the group level, the results were acceptable, but large variation in the accuracy of individuals estimates was found. The ZANE Study was conducted in 2010. It was a population-based cross-sectional study on the diet and nutritional status of 14- to 19-year-old girls in Zambézia Province. The study regions included one urban area and two rural districts. Two separate samples of girls were recruited: the first in January-February ( hunger season , n=283) and the second in May-June (harvest season, n=268). A 24-hour dietary recall interview and a seven-day food frequency questionnaire interview were conducted for each participant. Blood and urine samples were collected and blood haemoglobin, serum ferritin, serum zinc, serum selenium, urinary iodine, plasma retinol and serum folate concentrations were analysed. The ZANE Study revealed a low median energy intake calculated from the 24-hour recalls [5.2 MJ/day, interquartile range: 3.6, 7.4 (calculated using sampling weights); n=543]. This is in line with the findings of the validity study and is at least partly explained by under-reporting. Low intakes of several micronutrients and relatively high phytate:zinc molar ratios, typical for diets in low-income settings, were found. Marked seasonal variation was noted for vitamin A intake. According to the World Health Organization definitions, anaemia was a severe public health problem and vitamin A deficiency a moderate public health problem. The serum ferritin concentrations indicated that iron depletion was prevalent in the population. The population was also found to have a risk of zinc deficiency. Folate status was considered to be generally adequate, but an exception to this was the low serum folate concentrations in the urban area in May-June. Mild to moderate iodine deficiency was found in the rural districts, whereas the iodine status of urban girls was adequate. Selenium status was considered adequate. In the last part of the thesis, associations between dietary diversity and low concentrations of haemoglobin and serum/plasma ferritin, zinc, retinol, and folate in non-pregnant girls (n=227 in January-February and n=223 in May-June) were examined in logistic regression models using three different dietary diversity scores. First, the Women s Dietary Diversity Score (WDDS), consisting of nine food groups was calculated from the 24-hour recalls according to instructions by the Food and Agriculture Organization of the United Nations. The second score employed a minimum portion size limit of 15 g (WDDS15g), and the third was based on the seven-day food frequency questionnaires (7dWDDS). The most consistent findings of this work were the associations observed for zinc. In January-February, after adjusting for confounders, a low (≤3) WDDS and a low (≤5) 7dWDDS were each associated with higher odds of having lowserum zinc (≤25th percentile of the season-specific distribution) compared with having a higher score. These associations were not present in May-June. In conclusion, using food photographs in portion size estimation in adolescent Mozambican girls showed an acceptable level of validity. There was, however, a tendency towards under-reporting. In the future, producing and testing more comprehensive sets of locally relevant food photographs will be useful for dietary studies in Sub-Saharan African settings. Hidden hunger was found to be a public health problem among adolescent girls in Central Mozambique. Actions are needed to prevent and control hidden hunger, especially with regard to low iron, zinc, iodine, and vitamin A status. Programmes may need to be tailored according to urban-rural differences in diet and micronutrient status. Some associations between dietary diversity and micronutrient status may exist, especially in the case of zinc. However, the associations seem to be season-specific, which may limit the practical application of dietary diversity scores as tools to identify populations at risk of low micronutrient status.
  • Heikkinen, Susanna (Helsingin yliopisto, 2016)
    Cereal arabinoxylans (AXs) belong to the heterogeneous group of hemicelluloses. They are branched polysaccharides located in the plant cell wall, where they strengthen the cell wall together with cellulose and lignin. AXs vary in their molecular structure depending on the plant source from which they are extracted. Cereal AX can be extracted, for example, from the side streams of cereal processing such as bran, husks/hulls, and straw. AXs are sustainable raw materials with a film-forming ability; they can therefore be utilized more efficiently in biodegradable packaging and coatings. In this thesis, structurally different cereal-based AXs were used in the film studies. The effect of the type and amount of polyol plasticizer on the film properties as well as their storage stability during four and five months time was investigated with oat spelt arabinoxylan (OsAX). The structure function relationship of AXs in films was studied by comparing differently substituted rye and wheat flour arabinoxylan (RAX and WAX, respectively) and was further investigated by using specific arabinofuranosidases to tailor arabinose to xylose ratios and arabinose substitution patterns of RAX and WAX. The usability of crude biomass extracts in larger-scale film/sheet preparation was studied via the sheet extrusion of two wheat bran extracts (WBEs), which contained similar amounts of AX and lignin, whereas their starch and protein contents differed depending on the purification process. The film and sheet properties, such as mechanical and barrier properties as well as crystallinity and the physical state of the films, were investigated in order to evaluate the suitability of these materials for packaging. This study revealed that AX, having relatively low arabinose substitution and molar mass, such as OsAX, in general needs plasticization for cohesive film formation. It was found that the amount and type of plasticizer clearly affects the tensile and permeability properties of the films as well as their water sensitivity. In general, the sorbitol-plasticized films were stronger and had lower water vapor permeability (WVP) and oxygen gas permeability (OP) than the films plasticized with glycerol. Structure correlation studies carried out with RAX and WAX showed that the AXs fine structure affects film formation and film properties. With specific enzymatic tailoring, it was observed that the Ara/Xyl ratios of RAX and WAX did not contribute alone to the behavior of AXs in the films; instead, both the amount and distribution of arabinose side units in the xylan chain had a high impact on the results. When the number of un-substituted xylose units was high, the water solubility of AX decreased and the formed films had a semi-crystalline structure. Mild de-branching improved some film properties, for example, the tensile strength of the RAX films increased. Additionally, it was observed that the OP of the RAX and WAX films decreased along with the de-branching. A storage study showed that the polyol-plasticized OsAX film properties changed during storage; possible reasons for this were lowered plasticization caused by glycerol migration out from the film matrix and/or formation of heterogeneous structures in the film with plasticizer-rich and polymer-rich areas. The WBEs turned out to be potential raw materials in the up-scaled sheet preparation method, which was carried out with a single-screw extruder. Both of the extracts that were studied formed cohesive sheets with polyol addition. In this study, all of the AX films showed low OP properties, which were further decreased by lowering the Ara/Xyl ratio or with plasticized films by decreasing the polyol content. Thus, AX films can be thought of as a potential choice for those applications where high oxygen barrier capacity is needed to prevent the oxidative deterioration of the packaged food product. Present study on AXs fine structure gave information that can be used when various structurally different agricultural side streams are considered as raw materials for film applications. In the current study, the main challenge of the AX films and sheets was their water sensitivity, and with the plasticized films, their decreased storage stability. The sheet extrusion results proved that highly purified fractions are not essential in material production; instead, in this study, moderately purified fractions with a high starch and low protein content formed strong sheets with lowered water sensitivity.
  • El Sayed Bashandy, Hany (Helsingin yliopisto, 2016)
    The flavonoid biosynthetic pathway and flavonoid metabolites have been extensively studied because of their biological roles in plant and animal kingdoms. Flavonoid metabolites are involved in plant resistance, UV-protection, pollinator attraction and have antioxidant effects. Plant species synthesise a large number of secondary metabolites, including flavonoids, carotenoids and others. Flower colour is an important feature for marketing of the ornamental model plant gerbera (Gerbera hybrida). In gerbera, flavonoid metabolites accumulate in the adaxial epidermal layer of flower petals and lead to different flower colours and patterns. These metabolites consist of three subgroups, flavones, flavonols and anthocyanins in gerbera, which have also been used to characterize different cultivars. The cultivars show variation in flower colour according to their anthocyanin type. The acyanic gerbera cultivars have flavonoid profiles comparable to the cyanic cultivars, except for the synthesis and accumulation of specific anthocyanins. Metabolite profiles indicated that all analysed acyanic cultivars have a block in a late stage of the anthocyanin pathway. Ivory, a sport of the pelargonidin-cultivar Estelle, has white flowers. Ivory has flavones and flavonols, but no anthocyanin. Gene expression of all flavonoid pathway genes was similar in Estelle and Ivory. However, both cultivars have two different alleles encoding dihydroflavonol 4-reductase and in Ivory one of them (GDFR1-2) was found to have a point mutation resulting in inactivation of the encoded enzyme. Still, Ivory expresses the second allele (GDFR1-3) and accumulates active DFR enzyme. The cyanidin cultivar President expresses only the GDFR1-3 allele, but cannot synthesize pelargonidin. Therefore, GDFR1-2 contributes specifically to pelargonidin biosynthesis and GDFR1-3 to cyanidin biosynthesis. This could be explained by a coordinated biosynthesis of anthocyanins in multi-enzyme complexes, metabolons. Gerbera chalcone synthases (GCHSs) belong to the superfamily of Type III polyketide synthase enzymes. GCHS1, 3 and 4 have different contributions to the flavonoid pathway, according to the tissue specific and post-transcriptional regulation. RNA interference of CHS encoding genes was used in different gerbera cultivars to show that GCHS1 has the main contribution to anthocyanin accumulation in petal tissues. GCHS4 was strongly expressed in petals but did not lead to anthocyanin accumulation. Still, GCHS4 is expressed and encoded a functional enzyme in the vegetative tissues.
  • Oghenekaro, Abbot (Helsingin yliopisto, 2016)
    The white rot pathogen, Rigidoporus microporus (Basidiomycota) syn. Rigidoporus lignosus is the most destructive root pathogen in rubber plantations located in South East Asia and Africa. Most management practices for the disease have been carried out without adequate knowledge of the population genetics of the pathogen. Our primary objective in the first part of this work was to characterize isolates from rubber trees (Hevea brasiliensis) in Nigeria. The lack of global studies comparing isolates from Asia and Africa where the majority of rubber plantations are located necessitated extending our molecular phylogeny studies to include isolates from other regions of the world. We compared the Nigerian isolates with isolates from South East Asia and Central/South America. Forty isolates were analyzed by sequencing four gene regions: the nuclear ribosomal DNA ITS and LSU, β-tubulin and translation elongation factor 1-α (tef1) genes. The isolates form three distinctive clades corresponding to Africa, South East Asia and South/Central America. There was high intra-species variation within each clade, but no geographic pattern was detected among the Nigerian isolates and also among the West and Central African isolates. Our multi-gene molecular phylogenetic analysis suggests the presence of two distinctive species associated with the white rot disease. Phylogenetic analysis also placed the Rigidoporus genus within the Oxyporus clade of the Hymaenochataeles. This study supports the need for a thorough revision of the Rigidoporus genera within the Polyporales/Hymaenochataeles. To gain insights on the saprotrophic abilities of Rigidoporus microporus isolates associated with the white rot disease of rubber trees, we performed wood decay tests of selected isolates on rubber wood blocks. We included a non-pathogenic endophytic South American isolate for comparative analysis. The structural alterations caused due to fungal growth in the rubber wood blocks was also studied. The pathogenic isolates associated with rubber trees significantly decayed the rubber wood blocks suggesting a capacity to switch to saprotrophic growth when the tree is killed. The non-pathogenic isolate had very low saprotrophic ability. Structural alterations of wood cell walls caused in the wood blocks were typical for white rot basidiomycetes. The fact that Rigidoporus microporus can switch to saprotrophic growth on dead cells of the tree led us to investigate the transcriptomic profiles of the fungus during growth on dead rubber wood. We performed RNA-Seq de novo transcriptomic assembly which produced 25, 880 annotated unigenes. The transcriptome expressed over 400 genes encoding lignocellulose enzymes. A number of glycoside hydrolases (GHs) were highly induced in rubber wood including all nine members of GH43 genes in the transcriptome. Twenty-four manganese peroxidase encoding genes were among a large number of oxidoreductases that were significantly up-regulated in rubber wood. Several genes involved in fatty acid and rubber latex degradation were expressed in the transcriptome. Several ABC transporters and hydrophobin genes were also expressed in the transcriptome. Finally, pathway enrichment analysis of genes related to energy metabolism revealed some genes including alcohol dehydrogenase with potential biotechnological applications. This is the first study on the transcriptomic analysis of R. microporus on rubber wood. The data generated should serve as a useful resource for future studies. Understanding how rubber tree is able to defend itself against invading Rigidoporus microporus was an additional research goal. The expression of defence-related genes; pathogenesis related proteins (PR1, PR3, PR5, PR8 and PR9), cell wall modification genes (PAL and expansin), signal transduction genes (ACC oxidase, AOC, MAPK) and a Myb transcription factor were studied in two clones (RRIM612 and PR107) of H. brasiliensis with different levels of susceptibility. Clone RRIM612 had a higher lesion size than clone PR107 after 5 weeks post inoculation with R. microporus. A class I chitinase (PR3) was up-regulated in RRIM612 in response to the pathogen while a class IV peroxidase (PR9) was highly up-regulated in PR107. Signal transduction genes involved in ethylene and jasmonic acid signaling as well as Phenylalanine ammonia-lyase (PAL) were up-regulated almost equally in both clones. The predicted expansin like protein was up-regulated 40 fold in RRIM612 in response to the pathogen. The results obtained demonstrate the variability in defence responses in the two clones studied and provides the first set of defence genes expression profiles of the host-pathogen interaction of the white rot disease of rubber trees. This study sheds light on the phylogeny of pathogenic Rigidoporus microporus isolates associated with the white rot disease as well as evidence showing its ability to switch to saprotrophic growth. The transcriptome of the fungus during saprotrophic growth was also de novo assembled revealing a vast number of lignocellulose degrading enzymes. Finally, this work provides an overview of potential candidate defence genes in H. brasiliensis in response to infection by R. microporus.