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(Helsingin yliopisto, 2019)Democracy as the government of the people by the people and for the people, equally represented is one of the most contested claims worldwide yet cherished by many and associated with a universal human right. The word “democracy” did not appear in the global participatory forest policy i.e., the shifting of global forest paradigm toward more participation in the 1970s. However, one of the core ideas of democracy, namely the right of local people to participate in the decision making over the use and management of their forest resources underpinned the policy proposal. Donors and international development agencies subscribed to these principles and aimed to translate them into local contexts. Likewise, central government in sub-Sahara Africa, specifically in Burkina Faso undertook political decentralization reforms and participatory forest management programmes to implement these principles of inclusion and self-determination at the local level. However, in practice, participatory forest policy and decentralization still await an effective devolution of decision-making authority to local people and the improvement of their livelihoods. In addition, the state and non-state policy translators as above continue to choose processes, plan and implement environmental projects, often in partnerships with other than the democratically elected bodies. In doing so, they risk privatizing common resources, undermine democratization, shrink the public domain and limit citizenship and the spaces available for local people’s engagement in forest management. While literature exists on those issues, it remains unclear how these three dimensions of local democracy i.e., representation, citizenship and public domain operate under environmental interventions in the context of Burkina Faso. Therefore, I ask how participatory forest policy is translated at the local level in sub-Sahara Africa, specifically in Burkina Faso. How do the translation processes influence local democracy? I adopted a policy translation perspective and the theoretical lens of the “choice and recognition” framework to assess the democracy effects of forestry interventions namely on local peoples’ representation, citizenship and the public domain. I investigated these three components of local democracy through four articles included in this dissertation using qualitative research methods. The results showed that in Burkina Faso, global forest policy was translated at the local level through political decentralization reforms and participatory forestry projects. The choices of local institutions made by the project implementers influenced the substantive representation of local people’s interests and the effectiveness of forest restoration outcomes (Article II). The forestry interventions unintentionally produced uneven forms of citizenship, turning citizens into denizens i.e., those whose citizenships was revoked (Article III). Lastly, Articles IV and I depicted the multi-layered and complex dynamics in the public domain, continually contested by both customary and post-colonial state logics. From the findings, it can be inferred that participatory forestry has the potential to strengthen local democracy through political decentralisation. However, the current policy translation processes can undermine democratisation. Thus, I recommend to more systematically pay attention and integrate indicators of local democracy when trying to apply global forest policies in a local context.
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(Helsingin yliopisto, 2019)Fungi are capable of producing an array of heterogenous toxic secondary metabolites, i.e. mycotoxins, which may acutely or chronically impact human and animal health following the consumption of contaminated agricultural commodities. Mycotoxins, like most xenobiotics, are prone to structural alterations via metabolic processes in living organisms but can also undergo changes during food manufacturing. The resulting compounds, defined as “modified mycotoxins”, possess distinct chemical properties, with potentially unique toxicological characteristics, and often coexist with their precursor forms in food- and feedstuffs. The impetus of this Ph.D. thesis largely stems from the dearth of evidence available on these compounds and aspires to contribute evidence for addressing the underlying debate: Are modified mycotoxins relevant to food/feed safety? In this context, liquid chromatography–tandem mass spectrometric methods, employing fit-for-purpose sample preparation approaches, were developed and validated for the simultaneous determination of Fusarium mycotoxins and their modified forms. At first, conventional sample preparation techniques commonly utilised in mycotoxin analyses were evaluated against automated on-line sample clean-up. On-line clean-up and the standard “extract and shoot” approach offered optimal overall performance and achieved compliance with legislative criteria. The natural occurrence of the Fusarium mycotoxins HT-2 toxin, T-2 toxin, deoxynivalenol, nivalenol, zearalenone and derivatives thereof was investigated by conducting a nationwide survey of Finnish barley, oats and wheat grains. Deoxynivalenol was the most abundant mycotoxin (in 93% of the cereal samples), and at unusually high levels compared to adjacent years, followed by the modified mycotoxin deoxynivalenol-3-glucoside (81%). All 10 additional modified mycotoxins included in the method were detectable at widely varying concentrations. The relative proportions of modified/parent mycotoxins were mostly between 15–55%. Furthermore, the metabolism of HT-2 toxin and T-2 toxin was studied in barley and wheat. Specifically, tracing of their metabolism was accomplished by untargeted metabolomics based on stable isotopic labelling and liquid chromatography–high resolution mass spectrometry. Structural elucidation of the detected compounds indicated the presence of several novel modified mycotoxins, including glucoside, malonyl-glucoside, acetyl and feruloyl conjugates of the parent toxins. Time course kinetics of the in planta metabolites revealed the HT-2 toxin-3-glucoside as the primary detoxification product, which was rapidly formed in both crops. The experiments also determined the extent of metabolism of the parent toxins, while highlighting those modified forms present at harvest. Lastly, the metabolic fate of HT-2 toxin, T-2 toxin, deoxynivalenol and deoxynivalenol-3-glucoside was investigated during a four-day beer brewing fermentation with lager yeast. Yeast tolerated high toxin levels and was able to remove 9–34% of dosed toxins from wort by adsorption and/or biotransformation. The original contribution of this work can be summarised as the discovery of several novel modified Fusarium mycotoxins and related metabolic pathways, generation of essential natural occurrence data and gaining of further insight into mycotoxin-plant/fungal interactions, all of which were facilitated by state-of-the-art analytical tools.
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(Helsingin yliopisto, 2019)Trees have various mechanisms for avoiding and mitigating biotic and abiotic stresses. Resin is one such mechanism, and it is essential for conifer trees. Conifer resin is also a large pool of monoterpenes that – similarly to other biogenic volatile organic compounds (BVOCs) produced by plants, e.g. methanol, acetone and acetaldehyde – play important roles in tree signalling and atmospheric chemistry once emitted to ambient air. BVOC emissions from various tree parts and resin dynamics depend on environmental variables, with intrinsic effects on conifer defence. This thesis aims to clarify the environmental and physiological drivers of resin dynamics and BVOC emissions from the shoots and stem of mature boreal Scots pines (Pinus sylvestris) in field conditions, with special attention given to the effect of tree water relations. Resin pressure dynamics were studied using pressure transducers and BVOC emissions using an online mass spectrometer and dynamic chamber system. Resin and monoterpene emission compositions were analysed based on gas chromatography measurements. Temperature explained resin pressures and BVOC emissions from both the shoots and stems of Scots pine in the short term. Over a longer period, resin pressures and stem monoterpene emissions decreased with decreasing soil water availability and water potential in stem. In addition, the emission dynamics of water-soluble acetaldehyde, methanol, and acetone from the shoots and stem were connected to transpiration rate and soil water content, indicating an important effect of their transport in the xylem sap. These results show that although often overlooked, tree stems are an important source of BVOCs and that even relatively small changes in water availability may alter BVOC and resin dynamics despite their strong short-term temperature control. This information may help to understand the potential susceptibility of conifer trees to biotic stresses in various environmental conditions and improve BVOC emission modelling by accounting for stem emission dynamics.
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(Helsingin yliopisto, 2019)Because of the pace and magnitude of land cover change, terrestrial ecosystems across the globe are under unprecedented pressure. Industrial production of wood in large-scale tree plantations is one of the drivers of this change. The development of funds of natural capital on private lands for marketable commodities, however, often comes at the expense of other non-marketable benefits that people derive from ecosystems. The disturbances to existing ecosystems and social systems caused by the establishment of plantations can be drastic. Identifying factors that foster and impede actors and institutions to solve problems and address injustices thus becomes crucial for advancing sustainability through changes in policies and practices. This dissertation synthesises findings from four articles. It takes on the task of filling two gaps in the previous scholarly literature: the first concerning the human impacts of large-scale tree plantations (articles I and II); the second concerning the different institutions that shape their governance (articles III and IV). It also brings these contributions together under a framework for empirical analysis, which combines and structures key concepts of environmental social sciences ranging from systems ecology to sociology. Both qualitative and quantitative research methods have been used in the four articles. Article I presents the findings from a systematic review of the impacts of large-scale tree plantations for local communities. The review shows that impacts are frequently grounded in the process of land acquisition for plantations and the subsequent loss of livelihoods. Plantations have often caused more losses of livelihoods than created jobs. Article I also identifies gaps in the evidence base. Article II applies the concept of resilience and qualitative content analysis to analyse the Uruguayan beekeepers’ experiences of and responses to land cover change to plantations. The results show that the community faces this change as multiple interlinked challenges (e.g., lower honey yields and higher costs), to which they generally have a limited capacity to adapt. Both articles III and IV use data from the domain of South African tree plantation policy. Based on an analysis of policy beliefs, the former identifies two competing coalitions: a dominant business-as-usual coalition, of which ideas a minority justice and change coalition challenges. Article III also clarifies the role that beliefs concerning specific policy instruments play in coalition formation. Article IV focuses on policy learning – the acquisition and dissemination of information between actors with diverse knowledge. It tests hypotheses concerning actors’ information exchange behaviour and finds that actors tend to exchange information and build trust with those who think alike. However, its findings support the idea that co-participation in policy forums enables policy learning. Large-scale tree plantations have often caused negative impacts for local communities. The unfolding of impacts, however, also depends on the context (e.g., land use rights). The impacts are in many ways rooted in the governance of plantations, the dynamics of which can be better understood through coalition formation and policy learning.
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(Helsingin yliopisto, 2019)Role of lipid-modifying enzymes in oat and faba bean Increasing utilization of plant materials and especially their proteins is a global trend. One of the challenges in using grains and legumes as sources of protein is the off-flavour that is associated with them. Many of the undesirable flavour compounds are formed from lipids as a result of complex enzymatic and chemical reactions. To understand and control lipid-modifying enzymes is essential to prolong the shelf life of cereal and legume ingredients and products, and raise consumer acceptance towards them. The aim of this thesis was to study the role of lipid-modifying enzymes in oat and faba bean. To reach this aim, the levels of and variations in the lipid-modifying enzyme activities present in oat and faba bean seeds from selected cultivars and cultivation years were studied (Study I). In addition, the formation of non-volatile oxidised fatty acids (NVOFAs) by lipid-modifying enzymes in oat was investigated (Study II). Finally, the role of lipid-modifying enzymes in the formation of volatile off-flavour compounds in faba bean foods was studied (Study III). The results of Study I showed the presence of marked lipase and peroxygenase activities oat, while lipase and lipoxygenase (LOX) activities occurred in faba bean. The enzyme activities were affected by sample cultivars and cultivation years. Lipase activity in faba bean was surprisingly high, and it could effectively start lipid-derived off-flavour formation as soon as the seed structure is broken and it has access to inherent or added lipids as substrates. Study II showed that NVOFAs occurred in the flours of non-heat treated oat grains, and their amounts increased remarkably during the storage of oat samples. The formation of NVOFAs was in line with the release of free fatty acids by oat lipase. In addition, the formation of NVOFAs in the flour of heat-treated oat grains was quite small. In the third study, the optimum pH of faba bean lipase was found at 7.5-8, and for LOX the optimum pH was at 6. The LOX pathway produced various types and amounts of volatile lipid oxidation products using different substrates. In addition, adding rapeseed oil in emulsions increased the formation of volatile lipid oxidation products, and adding rapeseed oil fatty acids increased it even more. This study also showed that the pH levels greatly affected the extent of the reactions. Overall, this thesis evaluated the role of reactions catalysed by lipid-modifying enzymes together with chemical lipid oxidation for their potential to form lipid-derived off-flavours in oat and faba bean. The lipid-modifying enzymes should be properly inactivated to prevent the causing of potential problems. By studying comprehensively the lipid modifying enzymes, we are able to produce knowledge which assists in developing high-quality oat and faba bean based foods.
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(Helsingin yliopisto, 2019)Wheat is the world’s most important staple food, providing one-fifth of the daily protein consumed globally. However, the majority of wheat is used as refined flour, in which the nutritionally superior bran layers and germ are removed during milling, thus producing yearly a massive amount of underutilised food side streams. Better exploitation of the side streams and development of new plant-based protein ingredients are required to ensure the future global demand for food protein. This study aimed to examine hydrolytic enzymes and lactic acid fermentation as tools to improve the bioavailability, nutritional quality and technological properties of wheat bran proteins for food applications. The study showed that proteolytic activity, either by endogenous or exogenous enzymes, was crucial for increasing protein liberation and solubilisation from wheat bran, whereas microbial activity was required for improving the nutritional quality of the proteins. The application of commercial carbohydrases or proteases was able to either solubilise the bran cell walls or the proteins from the residues of endosperm in bran but was not effective in liberating proteins within aleurone cells. The endogenous enzymes of wheat bran, activated by chemical acidification, increased the protein solubilisation up to 75% with a simultaneous increase in in vitro protein digestibility (from 14% to 20%). However, bioprocessing by lactic acid bacteria (LAB), yeast and cell wall-degrading enzymes (Depol 761P and Viscoferm) was found as the most beneficial and microbiologically safe method to improve the solubilisation and nutritional quality of bran proteins. This bioprocessing meth-od resulted in a protein solubilisation of 52% and significantly improved the in vitro protein digestibility to 39%. In this work, the bioprocessing of wheat bran by LAB and yeast, with and without cell wall-degrading enzymes and phytase prior to the production of protein isolates, was found to influence the biochemical and technological properties of the bran proteins. The bioprocessed protein isolates had significantly higher protein content (80%), presumably due to the degradation of starch and soluble arabinoxylans during the bioprocessing. In general, the bioprocessing of bran resulted in a lower protein solubilisation of the protein isolates and had no influence on the emulsifying properties of the isolates in oil-in-water emulsions. However, bioprocessing by lactic acid fermentation together with cell wall-degrading enzymes almost doubled the foaming stability. Furthermore, wheat breads were made by substituting 20% of the total energy by proteins from the isolates. Wheat breads enriched with the lactic acid fermented bran protein isolate was found to have the most optimal technological characteristics, showing delayed staling and lower firmness during four days’ storage in comparison to bread enriched with a protein isolate produced without bioprocessing. In conclusion, by utilising lactic acid fermentation in combination with selected hydrolytic enzymes, the aleurone cell walls can be degraded and the proteins liberated for microbial modification, leading to improved protein bioavailability, nutritional quality and technological functionality. This study is the first to show the potential of using bioprocessing for the development of new wheat bran-based protein ingredient for food applications.
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(2019)Fish stocks in the Baltic Sea are an important natural resource for Finland; targeted by both commercial and recreational fishermen. Fisheries managers require data on the economic value of commercial and recreational fisheries for decision making and to assess the economic sustainability of fisheries. The volume of recreational catch of salmon in Finland is greater than the volume of commercial catch. However, there is marginally information available on the recreational value of salmon angling. These data deficiencies hinder the possibility of fishery managers to make optimal regulatory decisions concerning fish stocks. Additionally, the angler preferences and related angler profiles should be consid-ered in the decision making process as the reaction to different management measures can vary considerably depending on the angler type. This thesis contributes to the alleviation of the existing data deficiencies by contributing knowledge on the economic state of marine commercial fisheries and on the economic value of salmon angling. Defining an economic value is often ambiguous as the valuation methods involve inaccuracies which affect the reliability of the estimates. Therefore, it would be benefi-cial for the data end users to understand the consequences of the choices made in the estimation process in order to interpret the results correctly for decision making. In this thesis, the application of two different valuation methods: the perpetual in-ventory method and the travel cost method is described for defining the value of capital and recreational fishing in Finland. The perpetual inventory method is applied for estimating the capital value of the marine commercial fishing fleet of Finland. The thesis describes the justification for the choices made in the estimation process and how these choices affect the results. In addition, the differences between economic and financial analysis are discussed. Moreover, the thesis describes the value estimation of salmon angling in the River Teno and the River Tornionjoki employing the travel cost method. The studies use a two-step estimation procedure, which considers the potential endogeneity of on-site time per fishing trip. The case study of salmon angling in the River Tornionjoki explores the influence of angler profiles on the fishing behavior; the length of a fishing trip and the number of trips taken. The results show that the importance of increasing catch rate for the recreational benefit obtained by the angler is smaller than expected and the importance of salmon catch differs between the Teno and Tornionjoki rivers. In the River Teno, the experience of catching salmon in the previous season increased, on average, the number of fishing trips during the following season. In the River Tornionjoki the higher catch rate reduced the average number of fishing trips and the length of a trip during the season. The results presented in this thesis can be utilized for e.g. bio-economic modeling, assessing the sustainability of commercial fisheries of Finland, evaluating the implementation of EU common fisheries policy, and defining river specific fishing regulations.
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Heterobasidion – conifer pathosystem: Host mycobiome and evaluation of potential resistance markers (Helsingin yliopisto, 2019)Forests are the hotspots of Earth’s biodiversity, providing habitats to animals and resources to humans, protecting watersheds, preventing soil degradation, and mitigating climate change. In fact, forest disturbance is mainly caused by biotic and abiotic stresses, which affect both the primary metabolic components required for growth, development, and reproduction and secondary metabolites (defense-related chemical compounds) of trees. In the Northern Hemisphere, including Finland, members of the fungal group Heterobasidion annosum species complex are the most important pathogens of conifer trees causing serious economic losses for forest industries. The existing control and management strategies against this pathogen do not lead to 100% protection. To gain better insights and knowledge of Heterobasidion–conifer tree interactions, I investigated the impact of pathogen infection on the resident mycobiota in naturally infected trees as well as performed an analysis of fungal community structure under field conditions. Fourier transform infrared spectroscopy (FT-IR) analysis was also performed to discriminate between asymptomatic and symptomatic trees. In a parallel study, I investigated the genetic variants that could be associated with the control of necrotic lesions caused by H. parviporum inoculation among selected clonal lines of Norway spruce. Additionally, the expression level of a subset of selected genes involved in terpene, stilbene and flavonoid biosynthesis and programmed cell death in Scots pine trees with varying levels of resistance was further assessed. Mycobiome analysis demonstrated significant differences in the structure of fungal communities residing within symptomatic and asymptomatic Norway spruce trees. The results provided novel insight into the interactions between fungal plant pathogens and resident plant mycobiota. The FT-IR spectroscopy analysis was able to discriminate between symptomatic and asymptomatic Heterobasidion-infected Norway spruce trees. Other findings in terms of genetic and chemical markers revealed ten single nucleotide polymorphisms (SNPs) associated with eight genes. The identified SNPs were significantly associated with larger lesions in response to H. parviporum inoculation in Norway spruce saplings. In Scots pine, genes with higher expression levels predicted to encode α-pinene synthase, geranyl diphosphate synthase (GPPS), and metacaspase 5 (MC5) were associated with trees exhibiting high levels of necrotic lesion formation in response to fungal inoculation. Concentrations of two terpenoid compounds (β-caryophyllene and α-humulene) were significantly negatively correlated with lesion size. These results can be used in further studies to elucidate potential biomarkers in conifer tree genetic resistance research. Keywords: Heterobasidion, Norway spruce, Scots pine, tree-pathogen interactions, mycobiome analysis, FT-IR spectroscopy, gene expression, terpenoid, chemical markers
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(Helsingin yliopisto, 2019)This dissertation examines the economics of agricultural production and related environmental externalities. In the context of this study, environmental externalities are market failures caused by unintentional outputs of agricultural production. These outputs may be characterized as public goods/bads and they are approached using a joint production framework. The examined externalities are biodiversity benefits, nutrient runoff damages, and costs related to greenhouse gas (henceforth GHG) emissions and climate change. The main objective of this thesis is to study the welfare impacts of the production of different agricultural commodities, especially bioenergy, and agricultural production methods, when environmental externalities are taken into account. Also the costs of increasing or decreasing the unintended environmental public goods or bads causing the externalities are examined. The dissertation consists of an introductory article and four separate studies. In the first three studies, the focus is both on optimization of agricultural joint production systems, and on studying the welfare and environmental impacts of different policies. The last paper examines a case where a public environmental bad,namely climate change, of other anthropocentric/economic activities impacts agricultural production and thus it serves as an input factor of agricultural production. The dissertation shows that the scope of an agricultural externality often depends on local characteristics and underlying assumptions, such as those related to land use, the existence of adaptation measures, and the utility and damage functions. The studies also indicate that policies targeted to agri-environmental externalities should be designed holistically for example by taking into account entire landscapes or sectors, but at thesame time by relying on heterogenous policies within these entities.
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(Helsingin yliopisto, 2019)Diet is an indicator of health and chronic disease. Food consumption patterns of a particular population may define their nutrient intake, including vitamin D, revealing their health profiles. The food consumption patterns among immigrants often differ from those of the host population, and health inequalities exist between these two groups. Vitamin D insufficiency (S-25(OH)D <50 nmol/L), which has been associated with bone disorders, such as osteoporosis, and risk for cancers and other chronic diseases, is a public health problem among populations at northern latitudes, especially during winter because of low ultraviolet B irradiation and reduced skin synthesis of vitamin D. Nevertheless, the risk of vitamin D insufficiency is higher among non-Western immigrants, particularly dark-skinned ones, living in these regions. In the Nordic countries, vitamin D status in the majority of the host populations seems to be better than that of immigrants. This study seeks insights into immigrants’ nutrition with the aims of examining food consumption and vitamin D status among immigrants of Russian, Somali, and Kurdish background. The study also aimed to investigate whether ethnic differences exist in the response of serum 25-hydroxyvitamin D (S-25(OH)D) to vitamin D3 supplementation between Somali and Finnish women. The thesis was based on three datasets: i) a cross-sectional population-based Migrant Health and Wellbeing Study (Maamu Study), ii) the nationally representative Finnish Health 2011 Survey (Health 2011), and iii) the randomized controlled trial Marwo-D intervention study. Study I (n=1372) comprised immigrant participants aged 18-64 years from the Maamu Study. Healthy food consumption frequencies were evaluated among 527 Russian, 337 Somali, and 508 Kurdish men and women, through dietary questions in interviews. Data on socio-demographic factors were obtained from a sampling frame and through interviews. Potential socio-demographic determinants of healthy food consumption were assessed by logistic regression. Immigrants of Russian background more frequently consumed healthy foods, especially rye bread, vegetables, fruits, and berries, than Kurds and Somalis. Female sex, older age, and higher education were positively associated with healthy food consumption. Low consumption of fresh vegetables, fruits and berries was observed among Somali immigrants. In Study II, the S-25(OH)D concentrations of 1310 immigrants (446 Russians, 364 Somalis, and 500 Kurds) aged 18-64 years from the Maamu Study and a Finnish reference group aged 30-64 years from the Health 2011 Survey (n=798) were standardized according to the Vitamin D Standardization Program (VDSP) by liquid chromatography-tandem mass spectrometry. Data on socio-demographic, lifestyle, and dietary habits were obtained from a sampling frame and through structured interviews or through a self-administered health questionnaire. Vitamin D status (S-25(OH)D) of the immigrant groups was analysed relative to the Finnish reference group through linear regression. The consumption of dietary vitamin D sources and the potential socio-demographic, lifestyle, and dietary determinants of low vitamin D status i.e. deficiency (S-25(OH)D <30 nmol/L) and insufficiency (<50 nmol/L), were evaluated with logistic regression analyses. The prevalence of vitamin D deficiency and insufficiency was higher among the immigrants, especially Somalis and Kurds, than among the Finns (p<0.001). Consumption of vitamin D-rich foods differed between the immigrant groups; vitamin D-fortified fat spread was commonly used by a higher proportion of Somalis than Russians and Kurds; fish consumption was less frequent among Kurds than among Russians and Somalis; and higher proportions of Russians and Kurds consumed vitamin D-fortified dairy daily than Somalis (p<0.001 for all). The main determinants of low S-25(OH)D concentration were daily smoking, alcohol consumption, obesity, and winter blood sampling (p≤0.04). Older age, physical activity, consumption of fish, vitamin D-fortified fat spread, and dairy products, and use of vitamin D supplements were associated with reduced odds of low S-25(OH)D concentration (p≤0.04). In Study III, 191 subjects were screened and 147 women (Somali n=72, Finns n=75) aged 21-64 years were randomized to receive placebo or 10 or 20 µg vitamin D3/d in a 5-month trial during winter in the Helsinki area (60oN). S-25(OH)D concentrations were assessed by liquid chromatography-tandem mass spectrometry. Background and dietary data were collected through a detailed questionnaire and a validated semi-quantitative interview-administered food frequency questionnaire. Response of S-25(OH)D to vitamin D3 supplementation was assessed with repeated-measures analysis of covariance. Vitamin D status (S-25(OH)D) and vitamin D intake from diet and supplements were analysed. High prevalence of vitamin D insufficiency was observed among Somali women at screening. Interestingly, total vitamin D intake was higher among Somalis, but their baseline mean S-25(OH)D concentrations were lower than among Finns (p<0.001 and p=0.001, respectively). Moderate vitamin D3 supplementation at doses of 10 µg and 20 µg effectively increased mean S-25(OH)D in both Somali and Finnish women, without ethnic differences in the response to supplementation (p>0.05). In conclusion, food consumption patterns among immigrants with Russian, Somali, and Kurdish background were not similar. Healthy foods, particularly rye bread, vegetables, fruits, and berries, were consumed more by Russian immigrants than by participants with Kurdish and Somali background. Frequent consumption of fresh vegetables and fruits and berries was uncommon among Somalis. Higher consumption frequency of the healthy foods was associated with some socio-demographic factors, namely female sex, older age, and higher education. Likewise, differences existed in the consumption of vitamin D-rich foods between the immigrant groups. Use of vitamin D-fortified fat spread was more frequent among Somalis than among Russians and Kurds; fish consumption frequency was lower among Kurds than among Russians and Somalis; and vitamin D-fortified dairy was more frequently consumed daily by Russians and Kurds than by Somalis. The extent of the risk of low vitamin D status also differed between immigrant groups; higher prevalence of vitamin D deficiency and insufficiency was observed among Somalis and Kurds than among Russians. Hence, the immigrant groups cannot be considered a homogeneous group. In addition, non-fair-skinned immigrants are at higher risk of deficiency/insufficiency than their host populations. This thesis demonstrated that moderate vitamin D3 supplementation was effective in increasing S-25(OH)D in both Somali and Finnish women, and supports previous findings that ethnicity has no effect on the response of S-25(OH)D to vitamin D supplementation. Promotion of healthy food consumption patterns, including fruits, vegetables, whole-grains, and vitamin D-rich foods, is essential among immigrant groups to improve overall health.
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(Helsingin yliopisto, 2019)Background. Abiotic stresses affect the productivity and the evolutionary pathway of adaptation in crops in different agricultural regions. Soil acidity and drought are two major abiotic stresses, when severe, reduce the suitability of fertile lands for crop production, and when moderate, reduce yield and often quality. Faba bean (Vicia faba L.) is sensitive to acidity, aluminium toxicity and limitation of soil moisture, and these stresses greatly reduce the yield potential and stability of the crop. The overall objectives of this study were to investigate complementarity in shoot and root morphological and physiological phenotypic markers to acid soil and drought adaptation in pre-flowering faba bean plants, and to identify sources of tolerance for further breeding work. These objectives were tested in light of four hypotheses: acid zone germplasm would have higher acid and Al3+ tolerance index than other germplasm (publication I); dry-zone germplasm would have more prolific root systems than wet-zone germplasm (publication II); dry-zone germplasm would maintain its root system growth better in drought than wet-zone germplasm would (publication II); and drought avoidance is based on a combination of leaf gas exchange and exploitation of soil water (publication III). Materials and Methods. Multiple sets of faba bean accessions were chosen based on their expected exposure to acidity, aluminium, or drought stresses in their regions of provenance, and based on previous research data and reports. Experiments were established in aquaponic, peat and perlite media in controlled/environment growth chambers, greenhouses and a robotic phenotyping facility to evaluate the performance of a range of faba bean accessions in acid, aluminium, and watering treatments. Key root and shoot data were collected and analysed. Results and Discussion. Acidity and Al3+-toxicity treatments were sufficiently strong to initiate detectable variation in root length, stain score and Al3+ tolerance index, SPAD value, stomatal conductance, biomass and leaf area in solution culture, peat, and perlite experiments. Roots behaved differently in response to pH and Al3+ treatment differences. Al-tolerant accessions showed contrasting shoot Al content, indicating multiple Al tolerance mechanisms in faba bean. The results of acid tolerance index in aquaponic and perlite media experiments were positively correlated. Trait expression complementarity and variability were observed across the experiments owing to differences in growth media. Accessions differed in root regrowth length in solution culture and in SPAD values and taproot length in perlite medium to changing pH and Al3+ concentrations as shown by accession by treatment interactions. Root tolerance index, root regrowth length, and SPAD values were found to be largely informative traits in solution culture, and peat and perlite pot experiments. In aquaponics experiment, 41 µmol/l Al3+ was not informative, 82 µmol/l Al3+ was informative, 123 µmol/l Al3+ was severe. As a result, 82 µmol/l Al3+ was used in the next peat and perlite experiments. However, 82 µmol/l Al3+ was found to be less informative in peat experiment, hence 123 µmol/l Al3+ could be recommended for selection of outstanding accessions in solid media. Overall, accessions responded to acid and Al3+ treatments independently. Cultivars Aurora and Messay were found to be Al3+ tolerant but acid sensitive; Kassa and GLA 1103 acid tolerant, but Al3+-sensitive; NC 58 and Dosha were tolerant to both Al3+ and acidity, while Babylon was sensitive to both. Aquaponic media for mass screening and perlite media for verification experiments were found to be convenient (publication I). Screening of germplasm for drought was successfully conducted in a perlite-based pot experiment, which allowed quicker screening of a large set of materials and enabled detection of variation in constitutive traits among accessions. Use of the GROWSCREEN Rhizo phenotyping facility allowed detection of useful differences between treatments and among accessions. In both the screening and phenotyping drought experiments, accessions originating from the drier regions of the world showed drought avoidance behaviour thereby confirming FIGS as a valuable strategy (publication II and III). In germplasm screening, root and shoot dry mass and their fractions, along with SPAD value provided useful information in discriminating accessions with potential drought-avoidance characteristics. In the phenotyping experiment, root traits were strongly and positively correlated with each other and with shoot traits, but these correlations indicated specific plasticity of traits with watering treatments (publication III). In the well watered treatment, total dry mass was correlated with root length traits, whereas in the water-limited treatment, it was correlated with root width and convex hull area. Apparent root length density was positively correlated with second order lateral root length in the well watered treatment and with apparent specific root length in water limited treatment, indicating high surface area to volume ratio to maximize water absorption is a key strategy in droughted condition. In the water-limited treatment, root traits contributing to drought avoidance such as lateral root length and root system depth, convex hull area and root system width, and apparent root length density (publication II and III) were positively associated with shoot traits such as total dry mass, leaf number, and leaf mass fraction reported in publication III. Accession DS70622 exhibited deeper and wider growing roots that filled the root system volume with long and thin laterals. The larger root system combined with moderately high total dry mass and stomatal conductance endorsed this accession as a potential drought-avoiding candidate by effective use of water suitable in transient droughts. Accessions such as DS11320 and ILB938/2 that combined a large and thick root system with low root length density, low specific root length and low stomatal conductance can be recommended as potential sources of drought-avoiding traits by improved water use efficiency suitable in terminal droughts. Future research directions on the development of multiple abiotic stress tolerant cultivars enables climate change resilience in crops. Most acid soils are subject to Al3+-toxicity, and drought can occur on this soils as it occurs in others. Hence, multiple stress tolerance traits, mechanisms and QTLs need to be investigated in faba bean to identify host accessions with multiple tolerance to Al3+ and drought stresses for breeding of high yielding materials.
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(Helsingin yliopisto, 2019)The phloem-limited bacterial pathogen ‘Candidatus Liberibacter solanacearum’ is known to cause several economically important plant diseases. Among the distinct haplotypes in ‘Ca. Liberibacter solanacearum’, haplotypes A and B are associated with zebra chip disease in potato, haplotype C is associated with carrot yellowing disease, and haplotypes D and E are associated with disease in carrot and celery. However, the vector-transmitted and unculturable nature of ‘Ca. Liberibacter solanacearum’ has limited the use of many conventional microbiological methods and advanced molecular biological techniques. Current understanding of the pathogenesis of ‘Ca. Liberibacter solanacearum’ and the pathophysiology of infected host plants is still very limited. In this study, a series of experiments were designed and implemented to improve our understanding of those aspects. Multi-omic approaches, high-throughput sequencing technologies and bioinformatic analysis were fully integrated in this research. Metagenomic sequencing was applied to obtain the genome sequence of ‘Ca. Liberibacter solanacearum’ haplotype C in Finland. Two draft genome sequences of haplotype C, FIN114 (1.24 Mbp) and FIN111 (1.20 Mbp), were obtained from carrot psyllids (Trioza apicalis) harbouring ‘Ca. Liberibacter solanacearum’. Genome comparison between haplotypes A, B and C revealed that prophages were involved in most of the genome rearrangement events. Comparison of the gene content between haplotypes revealed that the core and pan-genomes of ‘Ca. Liberibacter solanacearum’ consisted of 885 and 1327 orthologue groups, respectively. Orthologue groups putatively involved in host specificity associated with a certain haplotype were also identified. Twenty-seven orthologue groups were only present in haplotype C, while 11 orthologue groups shared by haplotypes A and B were absent from haplotype C. Based on the obtained genomic sequences, a finer genotyping system was designed and applied to the study of genetic variations of ‘Ca. Liberibacter solanacearum’ in Finland. Two sub-clades of haplotype C were characterized through the MLST approach. One sub-clade was associated with T. anthrisci and its primary host, Anthriscus sylvestris, and the other sub-clade was associated with T. apicalis and carrot. A novel haplotype was identified in the psyllid T. urticae and the stinging nettle Urtica dioica in Finland, named haplotype U. This was the first study to identify the presence of ‘Ca. Liberibacter solanacearum’ in the family Urticaceae. Phylogenetic analysis suggested that haplotype U was closely related to A and D and haplotype D was more closely related to A than to C. Dual RNA-Seq was applied to study the interaction between ‘Ca. Liberibacter solanacearum’ haplotype C and carrot plants at 4, 5 and 9 weeks after inoculation. ‘Ca. Liberibacter solanacearum’ infection significantly suppressed many genes involved in photosynthesis and chloroplast function, while genes related to defence response and phenolic compounds were up-regulated. A gene encoding the master regulator HY5 was constantly down-regulated in all the infected samples. Many genes involved in jasmonate biosynthesis were up-regulated in the infected samples, while genes related to the biosynthesis of other plant hormones showed complex differential expression at different time points. However, ‘Ca. Liberibacter solanacearum’ infection seemed to have a sustained impact on the expression of the key regulators of plant hormone signalling. Key regulators such as JAZs in jasmonate signalling, CTR1 in ethylene signalling and PP2Cs in abscisic acid signalling were all significantly altered by the infection. The bacterial gene encoding salicylate hydroxylase showed stable expression in ‘Ca. Liberibacter solanacearum’ at all the time points, which suggests that the bacteria were able to reduce the concentration of salicyclic acid in the host carrot plants. The proliferation of ‘Ca. Liberibacter solanacearum’ was very active at the early time point, as indicated by the high expression levels of genes related to the basic bacterial cell cycle, including replication, transcription and translation. ‘Ca. Liberibacter solanacearum’ appeared to have reduced mobility and increased adherence at the late time point examined, as the Flp pilus genes were expressed at high levels. A major change in the use of energy sources was identified between the early and late time points in ‘Ca. Liberibacter solanacearum’. A gene involved in the uptake of ATP was more actively expressed at the early time point, whereas genes related to the uptake and metabolism of C4-dicarboxylate were more actively expressed at the late time point, suggesting an adjustment in the acquisition and utilization of energy and carbon sources. This study provides novel information about the genome structure and genetic differences of ‘Ca. Liberibacter solanacearum’ and its interactions with its host plant.
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(Helsingin yliopisto, 2019)Ubiquitin proteasome system (UPS) is an ATP dependent pathway for targeted protein degradation. The role of UPS is to maintain a healthy protein balance in the cell and to mediate activation and repression of plant developmental processes, hormones and other signalling cascades as well as responses to environmental perturbations. The UPS is composed of several actors, the most important of them being the ubiquitin E3 ligases, which are responsible for providing the specificity for substrate recognition. About 5% of Arabidopsis thaliana genome encodes for ubiquitin E3 ligase genes (~1.400), classified in seven different subgroups, among which the second most abundant group is the RING-type ubiquitin E3 ligase family with nearly 500 members. More than half of the RING-type ubiquitin E3 ligase genes are uncharacterised. Those that are characterized demonstrate their multi-target ability which implies additional roles and cross-reactivity with other pathways. With the emergence of high throughput sequencing, improved Arabidopsis genome assemblies are available and there is a constantly growing amount of transcriptomics data available for the RING-type ubiquitin E3 ligase genes that link them to different developmental stages and perturbations. However, only few of these genes have been associated phenotypically with these processes. Our first aim was to use reverse genetics approach to rescreen Arabidopsis genome in order to update the number of annotated RING-type ubiquitin E3 ligase genes. We further aimed to develop a set of image-based phenotyping methods to systematically assign them in their signalling cascades and developmental pathways, and to functionally characterize the identified molecular networks of the RING-type ubiquitin E3 ligases and their substrates. This study revealed 50 new RING-type ubiquitin E3 ligases genes, while 31 earlier annotated genes were excluded, giving a total new count of 509 RING-type ubiquitin E3 ligases genes. RING-type ubiquitin E3 ligases were then assigned to different developmental, hormonal and/or perturbation related pathways, based on their gene expression profiles. To allow systematic and efficient functional confirmation of these associations in plants, protocols for image-based high throughput phenotypic assays were established. In these assays, the associated knockout lines were studied for rosette shape and growth, cotyledon emergence as a proxy for germination analysis, and Botrytis cinerea symptom progression. These phenotypic screens confirmed 36 flower enriched RING-type ubiquitin E3 ligases, 11 of which were associated to flowering, three rosette and one sepal development. Four of them responded negatively and one positively to ABA treatment at germination. Furthermore, ten RING-type ubiquitin E3 ligases were associated with Botrytis responses, with one characterised at molecular level. Collectively, the results of this study demonstrated the versatility and pleiotropy of RING-type ubiquitin E3 ligases and set the foundation for a systematic screening of phenotypes regulated by UPS components.
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(Helsingin yliopisto, 2019)A variety of tree species, belonging to the genera Combretum, Anogeissus and Terminalia (Combretaceae) are well known for their uses in African traditional medicine for the treatment of infectious diseases and wounds. In this study, Anogeissus leiocarpus, Terminalia brownii and Terminalia laxiflora were selected based on ethnopharmacological information for in-depth studies on their antimicrobial effects and phytochemical constituents. The mentioned species were collected from the Blue Nile and Kordofan regions in Sudan. The main objectives of this research were (1) to perform ethnobotanical and ethnopharmacological documentation of the medicinal plants found in the study areas in Sudan, (2) to study the in vitro antibacterial and antifungal effects of extracts, obtained from A. leiocarpus, T. brownii and T. laxiflora, (3) to elucidate the chemical structures of compounds in extracts with promising antimicrobial activity and to (4) isolate fractions with antibacterial activity using preparative TLC and column chromatography. Ethnopharmacological and ethnobotanical information was collected from seven villages during three expeditions. According to this information species belonging to the family Combretaceae could be especially prospective as sources for antimicrobial extracts and compounds. Therefore various parts of the studied plants were subjected to antimicrobial testing using Staphylococcus aureus ATCC 25923, S. epidermidis ATCC 12228, Micrococcus luteus ATCC 4698 and Mycobacterium smegmatis ATCC 14468. In addition the plant pathogenic fungi, Aspergillus niger ATCC 9763, Aspergillus flavus ATCC 9763, Nattrassia mangiferae ATCC 96293 and Fusarium verticilloides (syn. F. moniliformis) ATCC 24378 were used. Compounds in the active extracts were characterised using HPLC-DAD, GC-MS, UHPLC/QTOF-MS and LC-MSn Tandem Mass Spectrometry. In studies I, II and III the ethnopharmacological data of the uses of Terminalia brownii, T. laxiflora and Anogeissus leiocarpus in traditional medicine in the villages in Sudan against diarrhoea and cough and for wound inflammation, could be verified. Our results demonstrate that especially extracts of the studied plants are active in vitro against the growth of human pathogenic bacteria, including a model bacterium for tuberculosis, with the lowest MIC values of 39 µg/ml. Pure compounds, such as punicalagin and corilagin, present in these active extracts, did not give as low MIC values and demonstrate that the antimicrobial compounds in the studied plants could act in concert. However, purification using Sephadex LH-20 of a root extract of T. brownii resulted in a significant reduction of the MIC against M. smegmatis from 5000 to 62,5 µg/ml. The chemical profiling of the most active extracts demonstrated the presence of a high variety of chemical classes, including ellagitannins, gallotannins, condensed tannins, flavonoids, stilbenes and fatty compounds. Methyl-(S)-flavogallonate was characterized for the first time from the roots of T. brownii and corilagin and its isomer, sanguiin H-4, and punicalagin have not been found before in the roots of T. laxiflora. Among the compounds in the studied species both antibiotic scaffolds and adjuvants could be found. Moreover, our in vitro results against phytopathogenic fungi demonstrate that T. brownii could be used for the protection of crop plants against fungal contamination.
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(Suomen Metsätieteellinen Seura, 2019)Non-industrial private forest (NIPF) owners are important forest ecosystem service providers and users. Along with the structural and general lifestyle changes of owners, their forest ownership objectives have become more diverse, strongly emphasizing intangible forest values alongside timber production. Therefore, NIPF owners and their versatile forest ownership objectives are a potential source of information for exploring the untapped future potential that could help the forest sector to retain its future viability on the road towards a bioeconomy. This doctoral thesis aims to understand the drivers of demand for new forestry services and forest-based business opportunities from the perspective of NIPF owner objectives and forest meanings. Objectives and forest meanings are examined from methodological, socio-demographic and NIPF owner sustainable lifestyle perspectives, leading to more general examination of NIPF owner perceptions of future utilization prospects of forests and the forest sector. Thus, the objective of the thesis is to build a more in-depth understanding of NIPF owner objectives and to examine how this information could be used in the development and marketing of forestry services and other forest-related products and services. The findings present a way to systematically analyse the objectives of forest ownership and also illustrate how certain segments of forest owners value aesthetics and biodiversity conservation over a traditional monetary value orientation. The results also indicate that the owners with the highest sustainable consumption orientation place a greater emphasis on multiple benefits of forests than owners who have a lower such orientation. The findings show that the future value creation of forests will be based on multiple aspects, and the widening of perspective beyond raw material dominance in the utilization of forests is important. Thus, recognizing customer pressure towards more diversified forestry services would be essential in meeting the versatile needs of forest owners but also from the perspective of developing new forest-based businesses.
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(Helsingin yliopisto, 2019)Transitioning to sustainable living is a complex, conflicting, and highly contested issue. As part of this push, governments and businesses have focused on promoting green consumerism - framing people as primarily consumers with “a utility function” and seeking to solve the consumerism problem by paradoxically building consumer capacity to purchase more energy and material efficient products. The now-debunked assumption is that a critical mass of informed, ecologically conscious consumers can, through the market mechanism, apply pressure on producers and thus transform the economic system into a sustainable one. In this thesis I argue that this approach, which is driven by economistic thinking, is consumer scapegoatism, and is both simplistic and flawed. In light of the magnitude and urgency of the unsustainability problem, green consumerism could even be dangerous as it delays deployment of effective solutions. Consumer scapegoatism occurs when ecological imbalance is examined primarily through an economic-growth lens, and the critical role of addressing these systemic flaws is ascribed to the consumer without proper regard for whether he or she has the power to influence other more salient actors in the system. This thesis argues for the need to develop an explicit political economy approach to sustainable living research, policy and practice. Political economy asks questions about power, institutions and agency. For sustainable living, these would be questions such as: who benefits or loses from current patterns of consumption, what are the drivers and structures that propagate unsustainable consumption, where are the meaningful points of intervention that can have desired effects. Critical to finding solutions is in understanding the power dynamics around the issue. I analyse sustainable living as an issue of heterogeneous claims and conflicting interests. The means and practical implications of achieving sustainable living threaten the interests of powerful actors such as national governments, large transnational corporations, and institutions that together shape contemporary politics, policy, and markets. Such actors are also responsible for the systems of provisioning and choice architecture that largely predetermine how individuals and communities pursue and meet their needs. As heterogeneity and conflict of interests are essential to political economy, this approach is well situated as the organizing frame of the field of sustainable living. I discuss the main tensions embodied in the pursuit of sustainable living, and juxtapose these with characteristics of the political economy approach that make it a suitable research framing. Political economy characteristics include: understanding of social transition; interdisciplinarity in research design; use of a moral perspective; and praxis, or practice orientation. I emphasize the element of power as vital in the articulation of social transformation, and highlight the need for sustainable living research to undertake a systemic analysis of power. To apply this, I develop the In-Power framework for analysing power dynamics within a system. The in-power framework has four components: institutions, interests, instruments, and influence. Institutions set the conditions or “rules of the game” for how actors operate in the production-consumption system; Interests identify stakes, showing heterogeneity or homogeneity of those interests in the sustainable living issue; Instruments refer to sources of power and tools available to each stakeholder to support its objectives; and Influence refers to activities stakeholders undertake and reflects agency. I use the framework to analyse the global value chain of consumer goods with a view to understanding drivers of consumption, how power is wielded by stakeholders, and potential points of effective intervention that can enable sustainable living. Dismantling the architecture of unsustainability would invariably call for a questioning of corporate architechture, not only due to the environmental impact resulting from its mode of operation, but also its lock-in effect on institutions and other actors of society. By extension, understanding unsustainable consumption and approaching sustainable living has at its core the need to address the balance – or imbalance – in power dynamics between consumption patterns and corporate power. Using the in-power framework to analyse power flows in a value chain leads to identifying the nexus of influence and the lead actor. The nexus of influece is the concentration of stakeholders who act interdependently and who have a combined decisive influence on the final product and also on the eco-system around it. The lead actor is the main actor in the system with a critical marketing, technological, or financial edge that permits it to set the standards or specifications for other actors in the value chain, and the characteristics that determine its production and use. Thus I argue that consumer scapegoatism, assigning full responsibility to the consumer, is ineffective; a more effective approach to addressing the systemic flaws causing or caused by unsustainable consumption is to target the nexus of influence and the lead actors in order to reform the choice architecture and systems of provision upon which people depend for meeting their needs and wants. Finally, I discuss two points not addressed in this thesis but which are essential to the political economy of sustainable living. They are: the need to define parameters for a sustainable consumption space; and to move research on sustainable living out of the shadows of economics.
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(Finnish Society of Forest Science, 2019)Climate change is amplifying forest disturbances, especially those by insect pests. In addition to native species, alien insects are threatening forest health, ecosystem sustainability, and economic return. Uncertainties related to insect pest infestations are increasing along the risk of high impacts. There is a high demand of accurate and cost-effective methods for forest health monitoring to prevent, control, and mitigate the various negative impacts, as well as to support decision-making. Current needs for information for efficient forest management are complex and extensive. The required quality cannot be met with traditional forest inventory methods. Forest information should be up-to date and available across spatial and temporal scales. The developing field of remote sensing and geographical information systems provide new means for various forest monitoring. However, disturbance monitoring, especially by insect pests, gives an extra challenge and increased uncertainties compared to other forest monitoring tasks. With new approaches, valuable information on disturbances can be derived for evaluation of insect-induced forest disturbance at reasonable high accuracy and reduced amount of fieldwork. This dissertation aims towards improved forest health monitoring. Insect-induced disturbances from tree level to larger areas were evaluated in six sub-studies. Different remote sensing sensors and approaches, and ecological niche modeling were employed in disturbance evaluation. Study species include native and invasive insect pests. In context of recent research, issues specific to insect disturbance monitoring are discussed. Pattern, frequency, scale, and intensity of insect infestations vary depending on the pest and landscapes in question affecting disturbance detection and impact evaluation. Sensors, platform, and/or modeling methods have to be chosen accordingly. Environmental features, such as topography, and level of landscape fragmentation give restrictions to the method selection, as well as to the appropriate spatial resolution. Importance of varying information is also affected by the scale and resolution of investigation. Timing of data acquisition is crucial. Early detection and timely management operations are often the only way to mitigate insect outbreaks. Moreover, amount and accuracy of auxiliary information, including forest inventory data, and disturbance history, differ between countries and continents. Forest policies and practices differ between regions affecting selection of usable data sets and methods. Forest health monitoring should be included into forest monitoring systems for timely disturbance detection, accurate monitoring, and impact evaluation. Higher and lower spatial resolution remote sensing should be combined over varying spatial ranges and modeling techniques incorporated for flexible and cost-efficient monitoring over a gradient of different forest ecosystems, climatic conditions, and forest inventory and management practices. Open access remote sensing archives with high temporal resolution could facilitate continuous monitoring of wide forest areas. Developing satellite technology may respond to these needs. Plenty of valuable research on forest health monitoring exist. However, considerably more research is still needed before comprehensive monitoring systems can be adopted at the operational level. Development of remote sensing and modeling techniques, as well as improving computational power and databases facilitate continuous improvement of forest health management practices.
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(Helsingin yliopisto, 2019)My doctoral thesis examines the prerequisites of replication for three positive-strand RNA viruses, Chikungunya virus (CHIKV - alphavirus), Semliki Forest virus (SFV - alphavirus) and Flock House virus (FHV - nodavirus). Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes high fever, rashes and joint pain. Semliki Forest virus (SFV) has been extensively studied as a model to comprehend the replication strategies of alphaviruses because of its low pathogenicity. A characteristic feature of alphavirus replication is the formation of membranous invaginations termed spherules, associated with the plasma membrane. Spherules act as genome factories as they are the sites of active viral replication and release nascent viral RNA strands into the cytoplasm through a bottleneck-like structure. We created a trans-replication system specific for CHIKV that would be flexible and presents no danger to the scientist. In this system, the viral replicase proteins are expressed from a DNA plasmid while the RNA template is produced from a second plasmid, in mammalian cells. This allowed for the study of viral replication without generating infectious particles. It also enabled the visualisation of spherules and labelling of all viral replicase proteins with fluorescent or small immunological tags while preserving their function. Various mutations associated with noncytotoxic phenotypes were analysed and the results showed no correlation between the level of RNA replication and cytotoxicity. Moreover, the trans-replication system was used to elucidate that the cysteine residue of CHIKV nsP2 at position 478 is responsible for its protease activity and essential for replicase polyprotein processing. Trp479 of nsP2 also plays a vital role in RNA replication. The insect nodavirus, FHV, verges upon the properties of a ‘universal virus’ as it can replicate in a wide range of hosts. Only the replicase protein A is required for its replication. An efficient FHV trans-replication system was established in mammalian cells. The outer surface of mitochondria displayed pouch-like invaginations with a ‘neck’ structure opening towards the cytoplasm. High-level synthesis of both genomic and subgenomic RNA was detected in vitro using mitochondrial pellets isolated from transfected cells. The newly synthesized RNA was found to be of positive polarity. This system was used to investigate the capping enzyme domain of protein A, both in cells and in vitro. Mutating the most conserved amino acids of the capping domain abolished or reduced viral RNA synthesis. Surprisingly, transfection of capped RNA template did not rescue the replication activity of the mutants. FHV and alphaviruses show evolutionarily intriguing similarities in their replication complexes and RNA capping enzymes. The biological systems presented in this study offer valuable knowledge that could be exploited to understand the replication of other RNA viruses and also open up new avenues for the elucidation of key virus-host interactions.
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(Helsingin yliopisto, 2019)The World’s forests are facing novel stress due to climate change. Pest insects and pathogens are shifting towards new latitudes and heat stress is resulting in increased tree mortality and more frequent forest fires globally. Uncertainty in estimating the magnitude of climate change induced forest and tree decline requires new methods for unbiased estimation of tree decline. The development of remote sensing methods to detect early tree decline has been a major challenge due to the subtle nature of the early changes caused by different stressors. Multispectral lidar technology has the potential of detecting early tree decline by providing accurate three-dimensional and spectral information of tree structure simultaneously. The main objective of this thesis was to investigate the capabilities of multispectral terrestrial lidar in the detection and assessment of tree decline caused by different stressors. This was done by investigating the estimation of a remotely detectable indicator of tree decline, leaf water content (LWC). Specifically, new methods for measuring LWC using multispectral lidar intensity were developed from the leaf to the canopy scale in various environments and the relationship between LWC and tree decline induced by various stressors was investigated. Furthermore, the developed methods were tested in a forest environment to assess the applicability of multispectral lidar in the detection of bark beetle infestation in the field. Studies I-III focused on investigating the relationship between LWC and lidar intensity at multiple wavelengths. First, a hyperspectral lidar instrument was used to detect significant changes between fresh and drought-treated Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies L.) trees (study I). Then, a leaf-scale study (II) with Scots pine, Norway spruce, Small-leaved lime (Tilia cordata L.), Norway maple (Acer platanoides L.) and Silver birch (Betula pendula L.) was conducted and a strong relationship (R2=0.93) between a normalized difference index (NDI) calculated from 1550 nm and 690 nm wavelengths and LWC was found. This was followed by a study (III) where LWC estimation and pathogen- and drought-induced variation in LWC was studied with Norway spruce seedlings. Blue-stain fungi (Endoconidiophora polonica) inoculated seedlings expressed a rapid decrease in LWC while drought-treated seedlings showed more stable LWC until a very severe drought. LWC of the seedlings was predicted with an R2 of 0.89 using an NDI with 1550 nm and 905 nm wavelengths. In study IV, the developed method and the relationship between LWC and tree decline was investigated in the field with European spruce bark beetle (Ips typographus L.) infested trees. It was found that of the LWC metrics studied, gravimetric water content showed significant differences in the early stages of infestation and was more sensitive to bark beetle induced tree decline than equivalent water thickness (i.e. amount of water per leaf area). Linear discriminant models that were developed between infestation severity and lidar intensity metrics from 1550 nm and 905 nm wavelengths showed that green attack stage of the infestation could classified with an overall accuracy of 90%. This dissertation contributes both to the development of an objective and automatable method for detecting and measuring tree decline in the field, and to the understanding of the relationship between LWC and tree decline with implications to remote sensing. The dissertation will be published and popularized as a music video here: http://bit.ly/idanproffa. .
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(Helsingin yliopisto, 2019)Legumes are a sustainable source of plant protein, and their production could be increased in Europe. The use of faba bean (Vicia faba L.) is limited in part due to the presence of the pyrimidine glycosides vicine and convicine. Vicine and convicine, and particularly their aglycones, can cause a form of haemolytic anaemia called favism in individuals who have genetic deficiency in the glucose-6-phosphate dehydrogenase (G6PD) enzyme. Different processing methods have reduced the vicine and convicine contents to varying levels, but the formation of the aglycones have not been studied. Practical processing methods for removal of vicine, convicine and their aglycones are still required. The main aim of this study was to implement methods for the total elimination of vicine and convicine, with a focus on the aglycones. The compounds of interest were quantified using reversed phase high performance liquid chromatography (RP-HPLC) with ultraviolet (UV) detection against an internal standard uridine. The contents of vicine and convicine were determined in cultivars grown in Finland, and the contents were compared within a selected growing year and among three growing years. Vicine and convicine were hydrolysed in faba bean extracts, in vicine and convicine fractions and in faba bean suspensions by using β-glucosidase to study the formation and stability of the aglycones. Finally, the formation and stability reactions were studied under selected model conditions and in sourdoughs and breads. The performance of the HPLC method was suitable for the analysis of vicine and convicine. The levels in the studied cultivars varied from 5.2–7.6 mg/g dry matter (DM) and 2.1–3.6 mg/g DM within one growing year for vicine and convicine, respectively. Cultivar comparison showed that the cultivar ‘Kontu’, the commonly grown cultivar in Finland, contained high amounts of vicine and convicine. No extensive variation was noted among three studied growing years, even though the weather conditions varied markedly. The aglycones were detected and monitored with the HPLC method used for vicine and convicine analysis. The aglycones formed in the vicine and convicine fractions decreased in amount and finally lost their UV absorptivity after 2 h at pH 5 at 37 °C. The need for an external enzyme source was confirmed, as losses of vicine and convicine were rather small in faba bean suspensions. Selected lactic acid bacteria (LAB) strains were able to hydrolyse vicine and convicine in faba bean sourdoughs at 25 °C, 24 h; the hydrolysis depended on the fermentation temperature. Sourdoughs lost up to 82–85% of the vicine and up to 34–47% of the convicine. The amounts of vicine and convicine in wheat breads, containing 30% faba bean, were comparable to the amounts that were in sourdoughs after 24 h of fermentation. The aglycones were measured from sourdoughs fermented at 25 °C and from the corresponding doughs, but not from the breads. This study showed that vicine and convicine can be analysed simultaneously with their aglycones with an RP-HPLC-UV method, which provides the benefit of estimation of the total elimination of these compounds. The aglycones were found to disappear in all the studied matrices. Fermentation can induce losses of vicine and convicine, but the efficiency of hydrolysis depends on the selection of strains and the fermentation conditions. Furthermore, controlled acidification is necessary for maintain acceptable sensory quality.
