Maatalous- metsätieteellinen tiedekunta

 

Recent Submissions

  • Pokki, Heidi (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.
  • Mukrimin, Mukrimin (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
  • Saikkonen, Liisa (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.
  • Adebayo, Folasade Abiola (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.
  • Belachew, Kiflemariam Yehuala (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.
  • Wang, Jinhui (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.
  • Pavicic, Mirko (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.
  • Salih, Enass Yousif Abdelkarim (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.
  • Häyrinen, Liina (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.
  • Akenji, Lewis (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.
  • Kantola, Tuula (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.
  • Quirin, Marie Ann Christine Tania (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.
  • Junttila, Samuli (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.   .
  • Pulkkinen, Marjo (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.
  • Saarnio, Elisa (Helsingin yliopisto, 2019)
    Vitamin D is crucial for the human body and it has a significant role in bone growth and for maintenance of the skeleton throughout life. It is metabolized in the liver to the main circulating form, 25-hydroxyvitamin D (25(OH)D). Vitamin D binding protein (DBP) transports vitamin D metabolites into target tissues. A small amount of vitamin D is also free in the circulation. These free metabolites are suggested to be more active because they can enter the cells without a receptor. Genetic variation of DBP coding gene affects the protein’s ability to bind 25(OH)D, thereby influencing bound and free 25(OH)D concentrations. Furthermore, vitamin D concentrations have been reported to be lower in obese individuals than in their normal-weight peers. This study investigated the association of DBP genetic variation on vitamin D metabolism and bone traits. Study also aimed to examine whether obese individuals differ in their vitamin D metabolism from the normal-weight individuals and do these potential differences affect bone. These studies consisted of 233 Finnish children and adolescents (7–19 years) (Study I) and of 622 Finnish women and men (37–47 years) (Studies II and III). In Study III, the adults were stratified by body mass index into normal-weight, overweight, and obese. Intake of vitamin D and calcium, medications and physical activity were collected. 25(OH)D, parathyroid hormone (PTH), albumin, and bone turnover markers as well as single nucleotide polymorphisms (SNPs) rs4588 and 7041 in the GC gene (Study I and II) were determined. In addition, free 25(OH)D concentrations were calculated and in Study II adjusted with genotype specific affinity values. Bone traits were measured with Dual energy X-ray-absorptiometry and peripheral quantitative computed tomography. In Study I, 25(OH)D and PTH were lowest in genotype GC2/2. In boys, genotype was negatively associated with hip bone mineral content (BMC) and lumbar spine bone mineral density (BMD). In both girls and boys, genotype was associated with lumbar spine BMC and bone strength. In Study II, variation were found among genotypes in DBP, total, free, and bioavailable 25(OH)D, and PTH concentrations. DBP concentration was lowest in genotype GC2/2. Serum 25(OH)D concentrations were lowest in GC diplotypes 1S/2, 1S/1F, and 2/2, but adjusted free and bioavailable 25(OH)D concentrations were highest in GC2/2. PTH was also low in GC2/2. In Study III, free and bioavailable 25(OH)D concentrations were lower in obese women than in normal-weight. In men, both bound and free 25(OH)D were lower in obese than in those of normal-weight. In addition, DBP and PTH were higher in obese women and in both genders combined than in their normal weight peers. In obese women, 25(OH)D was negatively associated with distal radius trabecular density and tibial shaft cortical strength index (CSI). Furthermore, free and bioavailable 25(OH)D were negative determinants of distal radius CSI, radial shaft cortical density, and tibial shaft CSI in obese women. In conclusion, genetic variation in DBP is associated with bound and unbound forms of 25(OH)D, DBP and PTH concentrations and genetic variation of DBP can be one factor affecting bone mass accrual in adolescence. Associations of BMI with total, free and bioavailable 25(OH)D, DBP, and PTH concentrations demonstrate a difference in vitamin D metabolism between obese and normal-weight individuals. Furthermore, altered vitamin D metabolism in the obese may influence bone.
  • Rautiainen, Aapo (Helsingin yliopisto, 2019)
    Human land use affects the climate through various channels. This thesis focuses on the optimal (i.e. welfare-maximizing) regulation of land use sector climate impacts using market-based instruments, such as taxes and subsidies. The thesis consists of four articles and a summary chapter. Each article focuses on a separate aspect of land use sector climate policy. The first article outlines a comprehensive tax policy for jointly regulating carbon storage in biomass, soils and products. Considerations regarding soil carbon storage are emphasized. The second article concerns the regulation of CO2 emissions from the energy use of logging residues. The harmfulness of these emissions is compared with that of fossil emissions. A way to harmonize the carbon taxation of the both energy sources is presented. The third article regards the application of the additionality principle to forest carbon subsidies. In the stand-level context it appears that the additionality principle can be implemented without distorting the optimal rotation, by reclaiming subsidies for baseline carbon storage by a site productivity tax on forests. However, at the market-level such a tax distorts the optimal rotation and the optimal land allocation. These distortions can be avoided, if the excess subsidies are eliminated by general land taxation (which also targets other land use). The fourth article presents a new concept: the Social Cost of Forcing (SCF), which is the social cost of the marginal unit of radiative forcing at a given moment. It is a fundamental price that can be used to value different forcing agents. Forcing agents’ prices that are based on the SCF are consistent with the Social Cost of Carbon, and can therefore be consistently applied in cost-benefit analysis or utilized to harmonize the regulation of non-CO2 forcing agents. Together the four articles contribute to our understanding of land use sector climate policy design.
  • Harju, Inka (Helsingin yliopisto, 2019)
    Streptococcus pneumoniae is one of the most significant human bacterial pathogens. It is a major causative agent of community-acquired pneumonia. It is also the most common cause of bacterial otitis media and among most common bacteria causing meningitis in children. The close relatives of S. pneumoniae, the Viridans group streptococci form a central part of the human oral microbiome, but they are also a leading cause of endocarditis. The fast and reliable identification of these bacteria from clinical specimens would therefore be of prime importance for a clinical microbiology laboratory, allowing for the laboratory to provide helpful information to clinicians for identifying the infection focus and targeting antibiotic treatment. The close relationship between S. pneumoniae and Viridans group streptococci, especially their subgroup Mitis group streptococci, complicates the reliable species level identification of these bacteria. The identification of streptococci by the traditional biochemical methods is both unreliable and time-consuming: the identification takes 1-2 days after bacterial growth has been detected on a plate or in a blood culture bottle. Even sequencing of the 16S ribosomal RNA gene commonly used as a reference method for bacterial identification cannot reliably differentiate between pneumococci and other Mitis group streptococci or identify other Mitis group streptococci to the species level. For the identification of pneumococci, detection of pneumococcal-specific genes is considered a “golden standard”. For the Viridans group streptococci, multi-locus sequence typing (MLST), based on the analysis of the sequences of several genes, is considered to be the most reliable method of identification. However, the MLST is too laborious and time-consuming for the identification of streptococci in a routine clinical microbiology laboratory. Within the last decade, MALDI-TOF mass spectrometry has enabled the fast and reliable identification of most bacterial species. However, exceptionally closely related bacterial groups pose a challenge even to the MALDI-TOF technology. This holds true even for pneumococci and Mitis group streptococci. In this study, the earlier database and algorithm versions of the commonly used MALDI-TOF systems were shown to be unable to reliably differentiate between pneumococci and Mitis group streptococci. Therefore, rapid molecular detection tests, such as GenomEra S. pneumoniae™ evaluated in this study, are still needed for rapid detection of pneumococci. However, it seems that the addition of more pneumococcal and Mitis group strains in the databases and new interpretation algorithms allow for reliable differentiation between pneumococci and the Mitis group streptococci. Altogether, the combination of rapid gene detection tests and MALDI-TOF technology with enhanced databases and identification algorithms enables fast, reliable and cost-effective differentiation between pneumococci and Mitis group streptococci and the reliable group level identification of other Mitis group streptococci. This is a sufficient level of identification in a clinical microbiology laboratory, enabling the clinician to evaluate the clinical significance of the finding and target further investigations and antibiotic treatment more specifically.
  • Kashif, Muhammad (Helsingin yliopisto, 2019)
    The fungal species complex Heterobasidion annosum sensu lato (s.l.) is considered one of the most devastating conifer pathogens in the boreal forest region. They affect European coniferous forests with root and butt rot, causing annual economic losses of €800 million. Despite several efforts in practical forestry to control the disease, the economic loss remains considerable. Therefore, it is still necessary to introduce alternate control measures for Heterobasidion infection. Heterobasidion spp. are infected by a diverse community of mycoviruses, mostly partitiviruses. Here, these viruses were studied to find potential viruses for biocontrol purposes. We described six novel Heterobasidion partitivirus (HetPV) species phylogenetically related to Helicobasidium mompa partitivirus V70 that infect four pathogenic Heterobasidion species. Interestingly, our study revealed that HetPV13-an1 causes severe phenotypic debilitation in its native and exotic fungal host. The RNA sequencing of isogenic virus infected and cured fungal strains showed that HetPV13-an1 affected the transcription of 683 genes. The RT-qPCR analysis showed that the response toward HetPV13-an1 infection varied between H. annosum and H. parviporum. Moreover, the wood colonization efficacy of H. parviporum infected by HetPV13-an1 was restricted in living Norway spruce trees. The ratio of polymerase and coat protein genome segments/transcripts of eight partitiviruses analysed was highly variable in mycelia. All the virus species had unique ratios of the genome segments, which were stable over different temperatures and hosts. The co-infection with HetPV13-an1 and HetPV15-pa1 reduced host growth up to 95%. Regarding the transmission efficacy of mycoviruses, HetPV15-pa1 transmission to a pre-infected host was elevated from zero to 50% by the presence of HetPV13-an1, and a double infection of these viruses in the donor resulted in an overall transmission rate of 90%. Altogether, the study demonstrated that the interplay between co-infecting viruses and their host is highly complex and that partitiviruses show potential for biocontrol. Keywords: Heterobasidion spp., wood decay, mycovirus, partitivirus, phylogenetics, RNA transcripts, transmission, growth rate.
  • Gehrmann, Friederike (Helsingin yliopisto, 2019)
    Climate change will be most pronounced at high latitudes where it will affect autumn, winter and spring disproportionally more than the growing season. Increasing or decreasing precipitation as snow, rising temperature and more frequent freeze-thaw cycles raise uncertainties about how the timing of snowmelt and the length of the growing season will change for northern plants. The timing of plant developmental stages (phenophases) in relation to snowmelt timing is important for avoiding harsh weather conditions in spring and ensuring a long growing season. In this doctoral dissertation, I investigate the effect of snowmelt timing and temperature conditions on plant phenology and plant stress. The first objective was to determine the natural variation in snowmelt timing on a small spatial scale in subarctic-alpine Finland. Such variation in the microclimate is created by the landscape topography and show the range of conditions plant populations are currently adapted to. Snowmelt timing varied by up to seven weeks within a few metres distance, so that early-melting plots were exposed to more frequent and more severe spring freezing events. This implies that plant populations are already exposed to the kind of climatic conditions which would be predicted from climate change. Secondly, I studied how the physiology of Vaccinium vitis-idaea and the phenology of seven subarctic-alpine plant species are affected by this natural variation in microclimate. The higher numbers of freezing events in early-melting plots were related to a higher reduction in the quantum yield of photosystem II (ΦPSII) in V. vitis-idaea, but not to increases in frost damage. This species therefore does not suffer substantial damage from the natural climatic variation in this habitat, implying that in this location it is likely highly resistant to the predicted changes in climate. Differences in snowmelt timing also led to three distinct patterns of phenological timing in subarctic-alpine plant species along the snowmelt gradient. These patterns can raise ideas about the mechanisms underlying the rate of plant development and can help researchers classify past and future phenological responses. Lastly, I compare the effect of natural versus experimental gradients of snowmelt timing on the timing of autumn senescence in High Arctic plants. The results show that the two gradients lead to different conclusions regarding the effect of snowmelt timing on the timing of autumn senescence. Selective warming only in the beginning of autumn had a delaying effect on autumn senescence in Dryas octopetala, despite the short duration of the warming treatment. Previous studies have commonly employed a warming treatment over the entire growing season. The results of this dissertation highlight that we need to integrate different approaches to studying climate change effects on plants. Natural gradients, although often disregarded, can give additional insight into plants’ adaptation to climate variation and therefore complement experiments. Experimental treatments simulating climate change need to be very selective in which period of the plant life cycle they are applied as expected changes in climate strongly depend on the season. Due to the variable sensitivity of different phenophases and plant species to climate and the importance of plants in the ecosystem carbon balance, further detailed research is needed to understand the drivers and mechanisms underlying plant phenology.
  • Nurmi, Väinö (Finnish Meteorological Institute, 2019)
    This thesis applies cost-benefit analysis (CBA) to certain environmental questions and through its results contributes to both the theoretical literature on CBA in environmental economics and practical issues in the application of CBA to environmental problems. The work comprises an introduction and four articles, which address three common thematic areas: 1) distributional issues, 2) climate change adaptation, and 3) urban ecosystem services. Article I contributes to the literature through analyses that i) provide a connection between the income effect and distributional issues; ii) compare weighting schemes both theoretically and empirically; iii) show how weights could be incorporated into a CBA in practice; and iv) demonstrate that results are sensitive not only to whether weights are applied, but also to the choice of the inequality parameter and spatial resolution. Article II analyzes whether over-investment in disaster risk reduction and climate change adaptation is a legitimate economic concern and examines how the public reacts to major infrastructure investments. The results constitute a contribution to both the theoretical and empirical literature on the economics of climate change adaptation. Article III evaluates how potential innovations in weather services can reduce weather sensitivity and, consequently, decrease the negative effects of climate change on transport, particularly in the road transport sector. The article illustrates how innovations in the provision and use of weather and climate information can be beneficial for adapting to the changing climate and contributes to the empirical literature on the economics of climate change adaptation. Article IV presents a CBA of a relatively novel feature in the urban green portfolio: green roofs. The specific objectives of the research are i) to facilitate benefit-transfer of ecosystem services from one urban area to another by providing detailed information on valuation methods and the role of different assumptions and parameter values and ii) to include scenic values as a benefit item based on a formal and trackable analysis rather than on a guess. The article contributes to the empirical literature related to both the cost-benefit analysis of urban ecosystem services and the economics of climate change adaptation.

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