Faculty of Agriculture and Forestry
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(Helsingin yliopisto, 2020)Aflatoxins continue to be a food safety problem globally, especially in developing regions. Prevalent food contaminating aflatoxins are B1 (AFB1) and M1 (AFM1). These are human carcinogens and have potentially severe health impacts. Almost all (99.5 %) milk samples from Nairobi were contaminated with AFM1, highlighting the urgent need to create functional solutions to improve food safety. Based on the aflatoxin levels and milk consumption, risks were calculated: cancer risk caused by AFM1 was lower among consumers purchasing from formal markets (0.003 cases per 100,000) than for low-income consumers (0.006 cases per 100,000) purchasing from informal markets. Overall cancer risk (0.004 cases per 100,000) from AFM1 alone was low. Because of AFM1 in milk, 2.1 % of children below three years in middle-income families, and 2.4 % in low-income families, could be stunted. Overall, 2.7 % of children could hypothetically be stunted due to AFM1 exposure from milk. Based on these results AFM1 levels found in milk could contribute to an average of -0.340 height for age z-score reduction in growth. The exposure to AFM1 from milk is 46 ng/day on average, but children bear higher exposure of 3.5 ng/kg bodyweight (bw)/day compared with adults, at 0.8 ng/kg bw/day. Aflatoxins are produced by Aspergillus flavus fungus, which is prevalent in soils. Certain strains of lactic acid bacteria (LAB) have been reported inhibiting fungal growth. 171 LAB strains were tested against aflatoxin producing A. flavus fungi. The three LAB strains showing the highest antifungal activity were identified as Lactobacillus plantarum. None of the strains was able to completely inhibit fungal growth under conditions favorable for fungi and suboptimal for LAB. The three indigenous LAB Lactobacillus strains and one Lactococcus strains were tested for their AFM1 binding abilities in different conditions and after different treatments along with two reference Lactobacillus strains. The binding of AFM1 by LAB strains varied between 11 to 100 % in the biocontrol solution analysis, being approximately at the level of 40 % throughout the analysis sets. A significant amount of effort and resources have been invested in an attempt to control aflatoxins. However, these efforts have not substantially decreased the prevalence nor dietary exposure to aflatoxins in developing countries. The growth reduction of aflatoxin producing fungi with LAB could be one potential option, but there are still major issues to solve prior to any practical applications. A different approach to control aflatoxins suggesting the usage of binding agents in foods and lactic acid bacteria (LAB) have been studied extensively for this purpose. However, when assessing the results comprehensively and reviewing the practicality and ethics of use, risks are evident, and concerns arise. In conclusion, there are too many issues with using LAB for aflatoxin binding for it to be safely promoted. Arguably, using binders in human food might even worsen food safety in the longer term. A more comprehensive food safety approach has to be taken to solve this ongoing crisis.
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(Helsingin yliopisto, 2020)The thesis aimed to study the effects and mechanisms of freezing-thawing treatments on myofibrillar protein denaturation and to explore the role of myofibrillar protein denaturation in causing the formation of thaw loss. The freezing-thawing of porcine M. longissimus thoracis et lumborum (LTL) increased the free Ca2+ concentration and the subsequent chilled storage promoted an accelerated decrease of activities of calpain-1 and calpain-2, compared to unfrozen meat. Proteasome activity was observed to be around 40% lower after freezing-thawing. The observed increased purge loss and decreased water-holding capacity (WHC) of myofibrils indicated myofibrillar protein denaturation occurring during the freezing-thawing treatment. In the investigation of freezing-induced denaturation of myofibrillar and sarcoplasmic proteins of LTL in relation to freezing rate, fast frozen samples (cold metal plate/-80°C) had a characteristic freezing time of 12 min, while samples frozen at slow rate (air/-20°C) had a freezing time of around 174 min. Slow freezing led to around 30% larger thaw loss in parallel with reduced WHC and increased surface hydrophobicity of myofibrils, indicating more severe myofibrillar protein denaturation in slow compared to fast freezing. A model is proposed to explain the importance of myofibrillar protein denaturation in relation to the freezing rate in the origin of thaw loss: In slow freezing, protons are accumulated with concentrating solutes in the unfrozen water leading to a decline of pH causing denaturation of structural proteins. In fast freezing small ice crystals might trap protons inducing less decline of pH and thus less myofibrillar protein denaturation and reduced thaw loss when compared with slow freezing. Sarcoplasmic protein denaturation also was shown to occur in freezing-thawing as evaluated by differential scanning calorimetry and tryptophan fluorescence properties of drip, which was, however, independent of freezing rate. The role of decreased pH (from pH 5.5 to 5.2), combined with high ionic strength (2 M KCl), in causing myofibrillar protein denaturation was studied by exposing fresh minced meat to either high ionic strength only or to high ionic strength with decreased pH to mimic conditions estimated to be in the unfrozen water of frozen meat during freezing. Exposure to high ionic strength caused an increase of WHC of the isolated myofibrils, whereas exposure to high ionic strength combined with low pH reduced WHC and increased surface hydrophobicity of the myofibrils. These results suggest that decreased pH combined with increased ionic strength in the unfrozen water of frozen meat largely would explain myofibrillar protein denaturation and thus the thaw loss occurring in frozen-thawed meat. The storage at -3 °C of fast or slow frozen pork prior to final thawing at 2 °C diminished the impact of the freezing rate on myofibrillar protein attributes, and differences between fast and slow freezing were no longer significant for WHC and surface hydrophobicity of the isolated myofibrils when frozen samples subsequently were kept at -3 °C for 7 days. The results suggest that a marked myofibrillar protein denaturation is taking place with extended storage time at -3 °C. In conclusion, freezing-thawing increases water loss in meat and slow freezing causes a higher increase when compared to freezing at fast rate. Myofibrillar and sarcoplasmic protein denaturation occurs in freezing and thawing. The rate of freezing produces a significant effect in the myofibrillar fraction: A slow freezing will develop a more severe protein denaturation than a fast freezing. Consequently, the myofibrillar protein denaturation, related to the freezing rate, is proposed to contribute to the generation of thaw loss. However, a subsequent storage of frozen meat at -3 °C before final thawing seems to diminish the beneficial effects of fast freezing on myofibrillar protein characteristics, compared to slow freezing, due to an additional protein denaturation. Therefore, it is recommended that meat industry adjusts the thawing capacity to minimize the passage time in temperature of -3 °C in meat.
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(Helsingin yliopisto, 2020)This study analyzes the political legitimacy of forest and forest-related nature conservation policies in Finland. Legitimacy is defined here that the forest and nature conservation regimes and related political institutions are perceived as rightful among the people. The major contribution of this study is the comprehensive conceptual framework of legitimacy based on several theories, mainly from political science. The framework analyzes the objects of support, patterns of legitimacy, performance evaluations, and how these relate to one another. In this study, the objects of support refer to forest-related political institutions; these include regulations and public incentives, as well as decision-making processes, political programs, and administrative procedures. The framework is intended to be especially useful in the empirical analyses of pluralistic public political discussion and uses a methodology developed for this purpose. The study also analyses the social values of organized political actors. The empirical part of this study explores a data set from Finnish print media discourse, based on letters to editors in three newspapers and in one journal, along with comments given during the preparation of Finland's National Forest Programme 2010. Another empirical data set consists of qualitative semi-structured interviews and the writings of the organized interest groups. Many different groups of citizens were found to participate in public discussion on forests. Quite a large number of individuals shared the overall publicity, despite the fact that there were some very active writers. Nature conservation organizations, researchers, and politicians were well represented. However, the participation of governmental officials from both the forest and environmental sectors can be characterized as insufficient, considering their importance in the implementation of policies. The study of letters to editors found that groups of common social values served as patterns of legitimacy in the performance evaluations of forest policies. These include welfare and wellbeing derived from forests; values related to nature conservation; democratic values; distributive justice; good governance; core regime principles; and fair markets. Of all performance evaluations, 52% were negative while 26% were positive and 22 % were mixed. Domestic, EU-level, and international legality were commonly perceived as sources of the legitimacy of policies. Finland's good international standing and its role as a moral and economic forerunner were very common principles in the evaluations in both the forest and nature conservation policies, in all parts of data. The same idea was also found central in the national forest programs and strategies. The shared goal of the Finns seems to be that the nation would be best in the world both in forest and nature conservation policies. Keywords: forest policy, nature conservation policy, political legitimacy, democracy, justice, public discussion .
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(2020)Ozone (O3) and nitrogen oxides (NOx: nitrogen monoxide NO and nitrogen dioxide NO2) are reactive gases with an important role in atmospheric chemistry. Terpenes are a reactive subgroup of BVOCs (biogenic volatile organic compounds) emitted by plants. Needle or leaf surfaces are the first point of contact between the atmosphere and a plant. Boreal forests represent a significant portion of the global land area available for atmosphere-biosphere interactions. The aim of the study was to develop methods for observing the exchange of NOx in field conditions and to explore the roles of terpenes on needle surfaces and nitrate fertilization on the fate of O3 and NOx in plant-soil-atmosphere interfaces. The methods included whole-canopy measurements, shoot-scale chamber measurements, needle sampling and laboratory analyses, utilizing both continuous observations and experimental setups. In the studied low-NOx environment, the shoot-level NOx fluxes were too small to be monitored accurately in field conditions with an automated dynamic chamber. In addition to interference, the signal to noise ratio was low, and a significant proportion of the observed fluxes were to/from chamber walls. No clear NOx fluxes from Scots pine foliage were detected, and there was no effect of nitrogen fertilization on the observed fluxes. It seems unlikely that a fertilization treatment could cause significant NOx emission from boreal pine forests. The fluxes reported in our earlier studies included compounds other than NOx. Shoot terpene emissions and needle wax extracts were both dominated by monoterpenes. There was variation in the terpene spectra of both emissions and wax extracts. The proportion of sesquiterpenes was higher in the epicuticular waxes than emissions, and the observed sesquiterpene compounds were for the most part different in the emissions and wax extracts. The role of direct transport through the cuticle from sites of terpene synthesis may be more important than has been assumed.
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(Helsingin yliopisto, 2020)This study focused on modification of rye bran to produce high fibre extruded cereal foods with a good texture and structure. Rye bran addition during extrusion is challenging due to high levels of insoluble dietary fibre, which leads to less expanded products and a hard texture. Bran modification by particle size reduction or fermentation significantly improved both the structural and textural properties of extrudates. Moreover, optimization of the processing parameters such as increasing the screw speed, lowering the water feed rate, as well as the use of in-barrel hydration regimens further improved the textural properties. The applicability of rye bran in extruded products could thus be improved by particle size reduction and fermentation. The extruded food structure and texture had a direct effect on the mastication and bolus formation process in the mouth. A hard and dense extrudate structure required more mastication effort than a crispy structure. Crispy and porous structures easily disintegrated in the mouth and produced smaller bolus particles than a hard and dense structure. A smaller particle size of the bolus was associated with increased starch hydrolysis. The bolus particle size was more effective than the matrix composition in altering the starch digestibility. Increased dietary fibre intake via appealing snack products could help reduce chronic diseases. Knowledge obtained in this thesis on cereal matrix formation and digestion and the effects of added dietary fibre on the structural and textural properties of extruded solid foams will help the food industry to develop healthy and appealing products. Understanding process-structure-digestibility relationships of high fibre extruded matrices is essential for designing health promoting foods.
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(Helsingin yliopisto, 2020)Grasslands occupy 45% of agricultural land in Finland, but in provinces characterised by grassland-based dairy production the proportion can be 67%. Phosphorus (P) loads from grasslands to inland waters have received relatively little research attention. In the Finnish climate, soils are subjected to frost in winter and snowfall comprises a considerable part of total annual precipitation. Surface runoff is generated by limited infiltration of snowmelt water into partially frozen soil in spring, which is a crucial period for dissolved nutrient and soil particle transport, especially in central and northern Finland. This thesis examined the role of perennial grass vegetation in P dynamics in the soil-plant-water continuum and quantified P losses from grasslands under boreal conditions. Potential contributions of perennial vegetation to P losses were estimated indirectly, by determining changes in nutrient content of aboveground vegetation. Susceptibility of overwintering perennial ley regrowth to deliver P was assessed in a simulated snowmelt-induced surface runoff study. These approaches were complemented with five-year monitoring of a small (3.2 km2) agricultural and forested catchment, representing grassland-based dairy production areas in east-central Finland. Amount and inter-annual variation in P losses and erosion rate were quantified. The results showed that grasslands can release substantial amounts of plant-derived P when exposed to frost, freezing and thawing. Elevated P concentrations and losses of up to 0.69 kg ha-1 were detected in simulated snowmelt-induced runoff outflow. Higher P concentrations were also occasionally measured in early spring runoff at small catchment scale. More frequent freezing/thawing will enhance plant-derived P release, especially under a reduced snow layer and lack of insulating cover. In five-year monitoring of an agricultural sub-catchment with short-terms leys, where some fields were under grassland and others under cereals, mean annual total P (TP) losses were 1.0 kg ha-1 (range 0.6−1.5 kg ha-1). The proportion of this TP load transported as dissolved reactive P (DRP) averaged 44% (range 32−56%) for the agricultural sub-catchment and 34% (28−38%) for the whole catchment area, reflecting low erosion rate under the protective grass cover. Five-year annual soil erosion rate from the agricultural sub-catchment was only 46−287 kg ha-1 (mean 115 kg ha-1 yr-1). The results also suggested that P losses were partly associated with loss of organic material. These results indicate a need for P monitoring based on chemical analysis of water samples, instead of on turbidity measurements. Grasslands are prone to DRP losses, but substantially less susceptible to erosion than arable fields during harvest years. In Finnish short-term ley rotations, grass leys are typically renovated every 3−4 years, often including autumn ploughing, which can increase erosion and particulate P losses. Thus when quantifying P loads to waters from short-term grass leys, erosion and nutrient losses within the whole ley cycle should be considered, including the ley establishment and renewal year. Keywords: phosphorus, erosion, grassland, ley rotation, nutrient loading, surface runoff, winter
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(Helsingin yliopisto, 2020)Smallholder farming is known to be highly vulnerable to climate change and climatic variability, especially in mountainous regions of the developing world, mainly due to high environmental exposure and sensitivity and low adaptive capacity to a variety of climate and non-climate stressors. Maintenance of more sustainable and resilient agricultural systems are essential for guaranteeing sustainable management of land and for securing the livelihoods of millions of rural and urban people. The aim of this study was to study the main socioeconomic and environmental parameters which influence the adaptation of smallholder farmers and their farming systems to climate change and climatic variability. The adaptation opportunities and constraints of smallholder farming systems were determined comparing their biophysical and socioeconomic sustainability (Study I) and their vulnerability to climate change and climatic variability (Study II and Study III). The data was collected by interviewing 60 households (30 agroforestry systems and 30 conventional systems) during 2015–2016. Semi-structured questionnaires were designed to collect primary biophysical, socioeconomic and sustainability data, while a modified Climate Change Questionnaire of the World Overview of Conservation Approaches and Technologies (WOCAT) was used to collect the vulnerability data. The characteristics of the farming system were analysed applying a comparative analysis approach. Qualitative variables were analysed through descriptive statistics (Crosstabs and Chi-square), while Independent Samples t test was applied for the quantitative variables. The main findings highlight the role of agroforestry systems in supporting the sustainability of the systems and farmers’ livelihoods: higher levels of agrobiodiversity, greater diversification of livelihoods, more secure land tenure, higher on-farm incomes, and greater diversification of irrigation sources. In addition, agroforesters and conventional farmers perceived climate change in the same way, as a continuing trend of rising temperatures and decreasing precipitation. Results also indicate that conventional systems had greater exposure to solar radiation, pests, weeds, disease outbreaks and droughts compared to agroforestry systems. By contrast, agroforestry systems presented greater potential to decrease exposure and sensitivity, and greater assets to support farmers’ adaptive capacity, especially in aspects related to social environment, and access to information and production infrastructure. Keywords: Andean smallholder agroforestry and conventional agricultural systems, socioeconomic and biophysical sustainability, exposure, sensitivity, adaptive capacity, traditional knowledge
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(Helsingin yliopisto, 2020)The growing conditions in northern boreal forests have remained similar for millennia. However, amplified climate change may cause higher mean annual temperatures and precipitation sums, longer growing seasons, along with increased occurrence of extreme weather events (drought, heavy rain, or summertime frost) in the region. The relationship that forest vegetation has with soil nutrients and the exchange of carbon dioxide (CO2) between the forest and atmosphere may change. This dissertation focuses on quantifying the baseline status of northern boreal forests from these aspects, to be able to predict theupcoming changes more precisely. Soil total phosphorus (P) and nitrogen (N) contents were important factors in explaining the community composition of understory vegetation in the study site. The site was located in a region near a phosphate ore, where soil nutrient contents are highly variable. The number of herb, grass, and sedge species increased with N and P contents in the humus, especially with P. The increasing P content, on the other hand, positively correlated with downy birch (Betula pubescens Ehrh.), which was the dominant tree species of the research plot. The understory vegetation had an important role in the CO2 exchange rates of a northern boreal Scots pine (Pinus sylvestris L.) forest site. The annual CO2 dynamics varied between the canopy and understory, so that when the canopy began photosynthesizing in the spring, the understory was still under snow cover. The cumulative temperature sum had a higher positive correlation with photosynthesis than the total ecosystem respiration (TER) rate of the pine site. Overall, the pine site was a weak carbon sink during the growing season, although it temporarily turned into a carbon source during a cold and rainy summer. Extreme weather events, and their effects on the CO2 dynamics of forests, were studied on a Scots pine site and a Norway spruce (Picea abies (L.) Karst.) site. Both sites had experienced extreme summers during the studied times, but the CO2 flux rates in the Norway spruce site responded more clearly to them. The TER rates of the Norway spruce forest declined when it was warm and dry. This likely happened because of decreased decomposition of organic matter. The decline was, however, only temporary, and TER returned to normal when the temperature and precipitation returned to their average levels. Thus, the studied forest sites seemed to, so far, be rather resilient towards extreme weather events. Several studies have found that N availability will increase because of warmer temperatures, which speeds up decomposition and nutrient mineralization. However, decomposition may potentially slow down in some spruce forests due to heat. Local variation may thus be high when it comes to the availability of nutrients or to the CO2 dynamics of forests. While modeling studies are important for predicting the responses of northern forests to climate change on the large scale, our research reminds that local-scale studies are also inevitable for gaining a more precise picture.
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(Helsingin yliopisto, 2020)Inbreeding increases homozygosity, which in turn increases the frequency of harmful recessive alleles and decreases advantageous heterozygosity, resulting in inbreeding depression. Inbreeding depression on fertility decreases the lifetime milk production of cows and increases the need for veterinary treatments, inseminations and involuntary cullings, which has a negative impact on the profitability, sustainability and animal welfare of the dairy sector. The main goal of this thesis was to estimate the effect of inbreeding on female fertility in Finnish Ayrshire cattle. More specifically, this study aimed to estimate inbreeding depression using different metrics based on pedigree and genomic information, and to dissect inbreeding depression to chromosomes, chromosomal segments and specific homozygous genotypes. Moreover, it identified specific ROH genotypes that had detrimental effect on female fertility and milk production traits. The data used included over 12 000 genotyped cows with corresponding phenotypic records of fertility and milk production traits. The fertility traits studied included the non-return rate at 56 days after first insemination (NRR), number of inseminations per conception (AIS), interval from calving to first insemination (ICF) and interval from first to last insemination (IFL). Milk production traits included milk, protein and fat yields. Inbreeding coefficients were estimated based on pedigree (FPED), percentage of homozygous SNPs (FPH) and runs of homozygosity (ROH; FROH). FPED was not found to be associated with inbreeding depression in any of the fertility traits. However, statistically significant inbreeding depression was observed when using genomic measures of inbreeding (FPH and FROH) in the model. For example, a 10% increase in FROH was associated with 4 and 6 days longer IFL in heifers and first-parity cows, respectively. When FROH was used to estimate inbreeding depression separately for each autosomal chromosome, a 10% increase in FROH on chromosomes 2, 18 and 22 was observed to increase IFL in heifers by 1.6, 0.9 and 0.7 days, respectively. Similarly, a 10% increase in FROH on chromosome 15 was associated with the lengthening of IFL in second-parity cows by 2.3 days. Haplotype analysis for the detected regions revealed haplotypes that, when occurring as homozygous, were associated with the lengthening of IFL of approximately 4 and 8 days in heifers and second-parity cows, respectively. Finally, an analysis of unique ROH genotypes revealed several ROHs with unfavourable effects on fertility and milk production traits. The estimated effects of ROHs with the highest statistical significance varied between parities from 13 to 38 days longer IFL, from 9 to 17 days longer ICF and from 0.3 to 1.0 more AIS. For milk production traits, the ROHs with the highest statistical significance resulted in reductions of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. In addition, this study found regions in which inbreeding is particularly harmful due to ROHs displaying unfavourable effects across multiple traits. The detrimental effects of inbreeding observed in this study highlight the importance of managing the levels of inbreeding in the Finnish Ayrshire breeding programme. The findings of this study can be utilized for more efficient control of inbreeding depression as well as investigations of the mechanisms of inbreeding depression by examining the identified regions showing inbreeding depression.
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(Helsingin yliopisto, 2020)Galactoglucomannans (GGMs) are principal hemicelluloses in softwood tissues. Spruce GGM obtained from different recovery approaches are currently studied for applications as emulsifiers and stabilizers of dispersed systems. Natural polysaccharides, owing to their origin from a complex matrix, have an intrinsic affinity for the association. Their associative properties are affected by the recovery approach since it influences purity and intrinsic characteristics (e.g., molar mass, degree of substitution). Understanding the impact of the GGM recovery approach on its associative behavior, currently limited, is essential to comprehend the stabilization mechanism of GGM in dispersed systems as well in the expansion of its functional applications. This doctoral project investigated the associative behavior of GGM at a semi-dilute concentration of 1% in an aqueous medium and its effect in an oil-in-water emulsion system, with GGM recovered from spruce sawdust/wood chips using pressurized hot water extraction, BLN process (modified pressurized hot water extraction process), and effluent of the thermo-mechanical pulping process. All studied GGM samples existed in the form of polysaccharide molecules and supramolecular fraction. It was observed that the recovery approach and sample purity affected the molar mass of the polysaccharide fraction as well as the share and structural properties of the supramolecular fraction. The supramolecular fraction was observed to be either colloidal aggregates, agglomerates, solid particles, or a combination in varying proportions. Next, these samples were studied in emulsions. Differences in the macromolecular state of samples were found to influence interfacial morphology and stability of emulsions. Following, the associative behavior of purified GGM obtained from the pressurized hot water extraction process was studied at acidic, neutral, and alkaline pH and upon addition of sodium chloride. Associative behavior of the sample displayed a positive correlation with acidic pH condition and time, improving emulsion stability. The sample exhibited an upper limit of GGM to oil ratio for efficient emulsification and stabilization ability, implying the presence of a limited amount of active emulsifying component. Currently, novel biomaterials are being developed from wood biomass. The findings of this study contributed to the characterization of colloidal properties of GGM at a nanometric scale, thereby enhancing its scope of future applications. These findings regarding the solubility of GGM would also be relevant in existing operations of paper and pulping industries, as well as for aspiring biorefineries in identifying optimal GGM recovery approach.
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Expanding the genetic and chemical biosynthetic diversity of cyanobactin family of natural products (Helsingin yliopisto, 2020)Natural products are small metabolites produced by living organisms with versatile chemical structures and diverse bioactivities. Bacteria are a rich but yet underexplored source of natural products. Natural product biosynthetic pathways encode a huge array of biosynthetic enzymes which can catalyze stereospecific and regiospecific modification of intermediates to produce complex natural products from simple precursors. The biosynthetic mechanisms underlying the production of natural products vary substantially. Cyanobactins are synthesized through the post-translational modification of precursor peptides and represent one of the most abundant natural product classes produced by cyanobacteria. Cyanobactins have a macrocyclic or linear structure with antimicrobial and cytotoxic bioactivities, although their ecological function is unclear. In this study, genome mining was used to catalog the genetic diversity of cyanobactin biosynthetic pathways from bacterial and archaeal genomes. Bioinformatic analysis of microbial genomes was used to identify cyanobactin biosynthetic pathways. New cyanobactin biosynthetic pathways were studied using a combination of bioinformatics, molecular biology, microbiology, biochemistry and structural chemistry. Bioinformatic predictions of cyanobactin biosynthetic gene clusters were performed based on DNA sequence data. Subsequently, candidate strains identified based on the predictions were grown in the laboratory and subjected to mass spectrometric analysis and heterologous expression. Novel cyanobactin natural products were discovered and the enzymes underpinning their biosynthesis were characterized. In the first part of the study, the muscoride biosynthetic gene cluster was described and a new muscoride variant was discovered. Two specific prenyltransferases from the muscoride biosynthetic gene cluster, which were biochemically characterized, catalyzed the regiospesific prenylation of the N- and C-termini of the linear polyoxazole muscorides. In the second part of the study, genome mining revealed a truncated cyanobactin biosynthetic gene cluster across the bacterial and archaeal domains for the production of structurally unusual cyanobactins. In the third part of the study, a regiospecific prenyltransferase was discovered, belonging to the anacyclamide cyanobactin pathway and catalyzing the N-prenylation of the tryptophan residue of the substrate peptide. The main aim of this work was to uncover novel cyanobactin biosynthetic gene clusters from bacteria and expand knowledge regarding the biosynthetic potential of cyanobactin pathways. The results from this thesis broaden the chemical diversity of the cyanobactin family and expand upon the biosynthetic logic underlying cyanobactin biosynthesis.
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VPg-eIF(iso)4E interaction, coat protein production and virion formation in potato virus A infection (Helsingin yliopisto, 2020)Potato Virus A (PVA), which belongs to the family Potyviridae, is a significant agricultural plant virus that causes crop loss worldwide. Most potyvirus resistance is recessive and occurs due to the loss of interaction between the viral protein genome linked (VPg) and the host eukaryotic initiation factor [eIF4E/(iso)4E]. This interaction has been demonstrated in many cultivated plants that are susceptible to potyviruses. Studies on potyvirus resistance have shown that minute changes in either eIF4E/(iso)4E or VPg can cause the interaction to fail, resulting in the development of viral resistance. However, the detailed mechanisms underlying the significant effects of this interaction during potyvirus infection remain unclear. The central domain of the PVA VPg contains an eIF(iso)4E-binding consensus motif, Tyr-X-X-X-X-Leu-phi (YXXXLΦ). The function of this motif during the VPg–eIF(iso)4E interaction, in the context of PVA infection, was investigated in the present study. The tyrosine and the leucine residues at the binding site were replaced with alanine residues in PVA infectious cDNA (icDNA, PVAVPgmut) and in a VPg expression construct (VPgmut). The results showed that PVAVPgmut was capable of replicating inside the host cell, but overall gene expression remained low, similar to the levels observed for a replication-deficient virus. Systemic infection in PVAVPgmut-infected plants only occurred upon reversion to the wild-type PVA, which occurred in 26% of PVAVPgmut-infected plants by 15 days postinfection. Although VPg typically stabilises viral RNA (vRNA) and 3’ renilla luciferase (RLUC) expression, as published previously, the VPgmut failed to perform these functions. The helper component proteinase (HCPro) induces the generation of PVA-induced granules (PGs) during infection and the assembly of vRNA within these PGs to safeguard vRNA from being silenced. Plants infected with PVAVPgmut showed an increased number of PG-like foci in infected cells as compared to the plants infected with PVAWT. However, in compare to the PVAWT the percentage of PVA RNA colocalising with PGs was significantly low in PVAVPgmut infected leaf samples. The host eIF(iso)4E is thought to bind to the PVA VPg via the YXXXLΦ motif, and this interaction is considered to be essential for PVA RNA stabilisation, the transfer of RNA to the RNA silencing suppression pathway, and RNA translocation to polysomes for viral protein synthesis. In the second study, an alternative mechanism was explored involving the production of large quantities of coat protein (CP), which is a multi-functional protein. Tight control over CP production is necessary, depending on the stage of virus infection. Increased CP concentrations have been shown to represses potyviral gene expression. Therefore, CP concentrations are maintained at low levels during active gene expression in the early infection stage through a host-mediated degradation system. During later infection stages, CP is required at high quantities for the production of a large number of stable particles. The present study showed that ectopically expressed VPg enhances reporter expression more pronouncedly from the 3' side of the genome than from the 5’ side. A similar phenomenon was observed towards the later stages of the infection, in which the 3’ CP cistron and the 3’ reporter cistron were expressed more pronouncedly than the central cylindrical inclusion (CI) cistron and the 5’ reporter cistron. The 3’CP and 3’ reporter protein showed different production/accumulation dynamics than were observed for the rest of the genome. CP expression levels were observed to increase in the presence of overexpressed VPg, during both the early infection stage and towards the later infection stage. This process could represent the mechanism through which potyviruses increase CP production for sufficient virion formation. In the third study of this thesis, whether the stabilisation of CP was necessary for successful virion formation was investigated. These results revealed the function of PVA HCPro during CP stabilisation and virion formation. HCPro was found to be unable to stabilise CP in a virus-free system. A number of additional host and viral factors are necessary to produce stable particles. CP stability by HCPro is unrelated to its capacity for silencing suppression and, therefore, cannot be complemented by other viral silencing suppressors. Together, the findings described in this dissertation revealed important mechanisms that underlie potyvirus recessive resistance and the factors that affect stable virion formation.
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(Helsingin yliopisto, 2020)The objective of the research described in this thesis was to provide new information on the ruminal biohydrogenation of long-chain n-3 polyunsaturated fatty acids (PUFA), such as 20:5n-3, 22:5n-3 and 22:6n-3, for altering bovine milk fatty acid (FA) composition, with the potential to improve human health. Emphasis was not only placed on the potential to increase milk fat n-3, but also to modulate ruminal lipid metabolism and to explore the mechanisms driving milk fat synthesis and its regulation in lactating cows in order to understand the mechanisms and metabolic pathways underlying the diet-induced changes in milk fat depression (MFD), milk FA composition and specific FA intermediates and end products associated with MFD. Experiments documented in I–IV encompassed detailed investigations of ruminal (I-III) and mammary (IV) lipid metabolism. Experiment reported in I was conducted to build up methods for the analysis of long-chain 20- to 22-carbon FA intermediates formed during ruminal biohydrogenation of n-3 PUFA. The detailed analysis of fish oil (FO) and omasal digesta of lactating cows fed FO enabled the structure identification of 27 previously unidentified 20- to 22-carbon FA intermediates, containing at least one trans double bond. No conjugated 20-carbon FA were detected in omasal digesta. Results demonstrated that the hydrogenation of 20:5n-3, 22:5n-3 and 22:6n-3 in the rumen proceeds via two principal mechanisms that involve sequential reduction or isomerisation of cis double bonds closest to carboxyl group and provided clear evidence of extensive biohydrogenation of 20:5n-3, 22:5n-3 and 22:6n-3 in cows fed FO. Experiments documented in II-IV involved two physiological studies in which, the effects of dietary FO supplements alone (II; IV) or in combination (III) with sunflower (rich in 18:2-6; SFO) or linseed (rich in 18:3n-3; LFO) oil on animal performance (II-IV), ruminal lipid metabolism (II; III), microbial ecology in the rumen (II; III) and milk fat composition (IV) were investigated in lactating cows. Dietary FO supplements increased the intakes of 20:5n-3, 22:5n-3, 22:6n-3 and total FA (II; III), whereas decreased dry matter intake (II; III). Dietary oil supplements decreased (II) or had no effect (III) on ruminal volatile FA concentrations, but FO at high amounts (II) or when supplemented with plant oils (III) promoted an increase in molar proportions of propionate (II; III) and butyrate (II) at the expense of acetate (II; III). Supplements of FO modified ruminal metabolism of 16- and 18-carbon PUFA, causing increases in trans 16:1, trans 18:1 and trans 18:2 flow and a decrease in 18:0 at the omasum, and at high amounts promoted trans-10 18:1 accumulation at the expense of trans-11 18:1. Dietary FO had no substantial influence on ruminal outflow of conjugated linoleic acid (CLA). Extensive ruminal biohydrogenation of 20:5n-3, 22:5n-3 and 22:6n-3 resulted in increases in numerous 20- and 22-carbon PUFA containing at least one trans double bond at the omasum. Relative to FO, ruminal metabolism of 22:6n-3 was more extensive on diets containing plant oils, whereas the biohydrogenation of 22:5n-3 and 20:5n-3 showed no difference between FO and diets containing plant oils (III). The inhibitory effects of FO on the reduction of 18-carbon PUFA to 18:0 were influenced by the source of 18-carbon PUFA in SFO and LFO. The ruminal outflow of 18:0 was lower and accumulation of trans 18:2 and 20- to 22-carbon FA intermediates greater for LFO than SFO. Supplements of SFO and LFO caused trans-10 and trans-11 18:1 to accumulate, trans-10 18:1 being the most abundant FA intermediate in SFO. Alterations in the ruminal metabolism of FA were not associated with substantial changes in rumen protozoal counts or analysed bacterial populations known to be capable of biohydrogenation (II; III), but lowered Butyrivibrio spp. numbers in response to increasing levels of FO (II). Supplements of FO decreased milk fat yield and content and increased 20:5n-3, 22:5n-3 and 22:6n-3 concentrations in milk fat (IV). Enrichment of milk long-chain n-3 PUFA was associated with decreases in 4- to 18-carbon saturated FA and several-fold increases in CLA, trans FA and PUFA concentrations. Dietary FO resulted in the appearance of 37 unique 20- and 22-carbon FA in milk. FO-induced MFD (up to -40.6 % reduction in milk fat synthesis) was associated with changes in the concentrations of multiple FA in milk, in particular increases in milk fat trans-10 18:1 and cis-11 18:1 concentrations, but not with changes in the amount of trans-10,cis-12 CLA in milk and omasum or estimated milk fat melting point (IV). The negative relationship between ruminal outflow of trans-10 18:1 and milk fat secretion confirmed that a shift in ruminal biohydrogenation of 18-carbon FA toward trans-10 pathway has a role in the regulation of milk fat synthesis during FO-induced MFD. A decrease in 18:0 supply in combination with increased mammary uptake of cis-11 18:1, trans-10 18:1, and trans 20- and 22-carbon FA intermediates originating from the rumen may contribute to the reduction of milk fat observed during FO-induced MFD. The dietary supplements of FO alone or in combination with plant oils increased the ruminal outflow of FA intermediates containing at least one trans double bond and enriched long-chain n-3 PUFA in bovine milk with associated changes in the abundance and distribution of FA. These changes may have implications for the host metabolism and the nutritional quality or ruminant-derived foods. Keywords: biohydrogenation, rumen, fish oil, plant oil, sunflower oil, linseed oil, lactating cow, polyunsaturated fatty acid, n-3 fatty acid, conjugated linoleic acid, milk fat, trans fatty acid, Butyrivibrio, microbial ecology, gas chromatography, mass spectrometry, silver-ion thin-layer chromatography
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(Helsingin yliopisto, 2020)Forests play a vital role in mitigating climate change, as they sequester and store large quantities of carbon. This dissertation examines how carbon storage may be increased by changing forest management at the stand level. To extend the economics of forest carbon storage beyond single-species even-aged stands, this dissertation develops a bioeconomic model framework that incorporates the size and species structure of the stand, and the optimal choice between continuous cover forestry and forestry based on clearcuts. The studies apply empirically estimated growth models for boreal conifer and broadleaf tree species. The dissertation consists of a summary section and three articles. The first article presents an analytically solvable economic model for timber production and carbon storage with optimized management regime choice between continuous cover and rotation forestry. Continuous-time optimal control theory is utilized to solve the thinning path and the potentially infinite rotation age: if no optimal finite rotation age exists, thinnings are performed indefinitely while maintaining continuous forest cover. The second article extends this model by applying a size-structured growth model for Norway spruce (Picea abies (L.) Karst.), road-side pricing of sawlog and pulpwood, variable and fixed harvesting costs, and several carbon pools. The timing and intensity of thinnings, the rotation age, and the management regime are optimized numerically. In the third article, the optimization approach of the second article is extended to mixed-species size-structured stands. Species mixtures include the commercially valuable Norway spruce and birch (Betula pendula Roth and B. pubescens Ehrh.), and other broadleaves (e.g. Eurasian aspen, Populus tremula L., and maple, Acer sp.) that have no market value. Optimal rotation age is shown to either increase or decrease with carbon price depending on interest rate and the speed of carbon release from harvested wood products. Given empirically realistic assumptions, carbon pricing increases the rotation period and eventually causes a regime shift from rotation management to continuous cover management. Hence, carbon pricing heightens the importance of determining the management regime – continuous cover or rotation forestry – through optimization. Optimal thinnings are invariably targeted to the largest size classes of each tree species. Carbon pricing postpones thinnings and increases the average size of harvested and standing trees, hence increasing mean stand volume. Without carbon pricing, commercially non-valuable other broadleaves are felled during each harvesting operation. When carbon storage is valued, some of the other broadleaves are retained standing until they are large, thus increasing tree species diversity and deadwood quantity. The results suggest that moderate carbon price levels increase timber yields, especially of sawlog that may be used for long-lived products. Increasing carbon storage through changes in forest management is shown to be relatively inexpensive, and the marginal abatement cost is the lower, the higher the number of tree species in the stand.
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(Helsingin yliopisto, 2020)The present doctoral thesis examines the epithelial host-microbe interactions of different Gram-negative commensal bacteria in the human gastrointestinal microbiota, which consists of bacteria, viruses and eukaryotic organisms. Under steady-state conditions, commensal gut bacteria are harmless symbionts co-existing with the host as part of the normal, balanced microbiota and supporting intestinal homeostasis. On the contrary, dysbiotic microbiota with reduced species richness and altered composition is associated with many intestinal and systemic diseases. Constant communication between the microbiota and the host is enabled either by direct contact or secreted effector molecules. During the last decades, the beneficial effects of commensal bacteria on intestinal mucosa, as well as the related molecular mechanisms, have been increasingly investigated. Currently, the research focus is shifting from traditional probiotics to so-called “next-generation probiotics” and their potentially health-promoting molecules, “post-biotics”. In addition to the traditional treatment strategies for intestinal diseases, novel bacteriotherapy alternatives could be utilized to increase the presence or activity of commensal species with immunoregulatory capacity and the ability to enhance the barrier function. First, the colonic mucosal microbiota of pediatric ulcerative colitis (UC) patients was compared to non-inflammatory bowel disease (IBD) controls using colonic biopsies and pyrosequencing. Microbiota richness and diversity did not differ significantly between the UC and control subjects. Compositional microbiota changes were observed in the mucosa of UC patients with increased abundance of Firmicutes and Proteobacteria, especially the family Sutterellaceae, and decreased proportion of Bacteroidetes. Furthermore, the expression of selected host genes related to the barrier function was studied in the UC subjects. Most notably, the expressions of inflammatory cytokine interleukin-8 (IL-8), inflammation marker lipocalin-2 and calcium binding proteins, forming the IBD biomarker calprotectin, were elevated supporting previous findings in the literature. Next, the abundance and prevalence of Sutterella spp., belonging to the family Sutterellaceae that displayed increased abundance in the mucosa of UC patients, were studied using biopsies from IBD, celiac disease (CeD) and non-disease controls. In addition, epithelial interactions of the genus Sutterella were assessed in vitro. A decreasing gradient from the duodenum to the rectum was observed in the abundance of Sutterella spp. in non-disease adult subjects. No difference was detected in the prevalence of Sutterella between pediatric CeD or IBD patients and controls. Sutterella wadsworthensis was able to adhere to mucus, while Sutterella parvirubra had a higher adhesion capacity to enterocytes and showed competitiveness in adhesion against S. wadsworthensis. Sutterella spp. harbor a penta-acylated, less toxic lipopolysaccharide (LPS), which caused only a mild release of proinflammatory IL-8 from the HT-29 enterocyte cell line compared to hexa-acylated Escherichia coli. S. wadsworthensis and its LPS induced a higher IL-8 response in the HT-29 enterocytes compared to the other two species, indicating differences in their proinflammatory capacity. Overall, these findings implicated Sutterella spp. as a highly prevalent, benign gut commensal with mild proinflammatory mucosal interactions. A high-throughput screening method was developed to isolate anti-inflammatory strains from a healthy volunteer who had acted as a donor for fecal microbiota transplantation. In the screening, isolates capable of attenuating inflammation in vitro, i.e. decreasing E. coli LPS-induced IL-8 levels in enterocytes as compared to the LPS control, were considered as potentially anti-inflammatory, and identified using 16S rRNA gene sequencing and finally whole genome sequencing. The majority of the isolates eliciting anti-inflammatory activity belonged to the order Bacteroidales. In vitro epithelial interaction assays studying the Bacteroidales strains revealed no correlation between attenuation capacity and adhesion, indicating that the effect was independent of cell-cell-contact. Furthermore, the culture supernatants of attenuating isolates were also effective in decreasing the LPS induced IL-8 response in enterocytes, which supported our hypothesis concerning the presence of effector molecules. Lastly, one of the Bacteroidales strains isolated from the fecal donor was Odoribacter splanchnicus, which is known as an abundant, short-chain fatty acid producing gut commensal. Bacterial-epithelial interactions of this less studied commensal were assessed in vitro. O. splanchnicus did not adhere to enterocytes or enhance epithelial monolayer integrity, yet the bacterium and its cell-free culture supernatant displayed in vitro inflammation attenuation capacity. Furthermore, the spent medium of the O. splanchnicus strain induced a higher anti-inflammatory cytokine interleukin-10 release in relation to tumor necrosis factor alpha in peripheral blood mononuclear cells compared to O. splanchnicus cells or the E. coli control. Outer membrane vesicles (OMVs) were isolated from O. splanchnicus culture medium. The treatment of enterocyte monolayer with O. splanchnicus OMVs prior to LPS stimulation caused a significant decrease in IL-8 levels. The anti-inflammatory effect was more consistent with OMVs than bacterial cells. Taken together, O. splanchnicus seems to primarily exert beneficial interaction with the host. Commensal bacteria and intestinal gut epithelium are engaged in constant cross-talk mediated by direct cell-cell contact and/or secreted bacterial effector molecules. The delicate balance of mucosal microbiota enhancing the barrier function and keeping the intestinal immune cells alerted at an appropriate level is susceptible to disturbances potentially leading to dysbiosis. In this context, the identification of gut homeostasis promoting bacteria and their metabolites, as undertaken in this study, is a vital part of novel, personalized bacteriotherapy using a defined bacterial cocktail to assist in restoring intestinal equilibrium.
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(Helsingin yliopisto, 2020)Conflicting interests in the extraction of renewable resources bring about economic trade-offs that can be quantified with the methods of natural resource economics. These methods bring economic and ecological dimensions together while providing decision-makers insight into the welfare-maximizing optimal management of natural resources. This thesis develops three bioeconomic simulation models coupled with numerical optimization to analyse the conflicting interests in the management of Baltic salmon fisheries. The interaction among protected wildlife species and resource users mirrors conflicting interests in society. In the Baltic Sea, human-wildlife conflict occurs between a high-value salmon trap net fishery and protection of the recovering grey seal population (Halichoerus grypus). In this thesis, we quantify the economic effect of grey seal conservation on the professional Finnish salmon trap net fishery. We calculate the extent of damaged and lost catch due to seals, i.e., the seal-induced damages, and model the fishers’ optimal gear adaptation in the presence of seals as well as the implications for the salmon stock (Article I). This article is the first attempt to model the economically optimal Baltic salmon fisheries management in the presence of grey seals. To avoid stock collapse and to enable the fishery’s profitability in the long term, fisheries management is needed. The EU Common Fisheries Policy sets a minimum management objective at the maximum sustainable yield yet fails to explicitly address the three pillars of sustainability: economic growth, environmental protection and social development. This thesis addresses the role of the fisheries management objectives by comparing biological and economic management objectives, namely, maximum sustainable yield and maximum economic yield (Article II), in the commercial salmon trap net fishery. Our results show that by aiming at the economic objective, society would generate more gains from fisheries while attaining a higher salmon stock size. The interactions among resource user groups affect the reproductive capacity of the fish stock as well as the utility and profits of the user groups, here commercial and recreational salmon fishers. The reciprocal negative externalities from fishing activities often give rise to conflicts among recreational and commercial fishers. This thesis addresses the economic and ecological dynamics of the commercial salmon trap net fishery and recreational angling while acknowledging the role of social norms and the heterogeneous motivations of anglers and the effects on the reproductive capacity of the salmon stock caused by the commercial and recreational fishery (Article III). This thesis consists of a summary section and three articles, which form a comprehensive picture of the bioeconomic dimensions of the Finnish Baltic salmon fisheries. The thesis contributes to the existing literature by providing novel bioeconomic tools for conflict resolution and forming a coherent, holistic view of possible improvements in Finnish salmon management. Keywords: fisheries management, trade-offs, ecosystem-based management, human-wildlife conflict, Baltic Sea, bioeconomic modelling, optimization, Common Fisheries Policy, commercial fishing, recreational fishing, maximum economic yield, maximum sustainable yield, social norms, angler motivations, Salmo salar, migratory fish, Halichoerus grypus
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(2020)Agriculture and commercial fishing are among the most hazardous occupations world- wide, also in Finland. Various efforts have been developed to prevent and mitigate the effects of occupational accidents and diseases. The process of risk management comprises two significant stages: 1) risk assessment, and 2) risk treatment. Occupational safety and health (OSH) risk assessment builds on the evolution of accident causation models and of knowledge on human behavior over several decades. Risk treatment has also evolved, ranging from limited targeted efforts to multi-faceted interventions. The aims of this thesis were to identify factors that influence the incidence and se- verity of occupational accidents (risk assessment approach) and work system related factors that affect efficacy of occupational safety interventions (risk treatment approach). Information of the identified factors, called “occupational safety determinants” in this thesis, was composed into a list of occupational safety determinant clusters with respect to their contribution to occupational safety risk assessment and risk treatment. Four original articles were used as case studies to derive occupational safety determinants. Two of the articles focused on the occupational safety of farmers while the two other articles dealt with that of commercial fishers. For both occupations, there was one article based on accident insurance claim records, and one article based on user (farmer/fisher) centered surveys. The list of occupational safety determinant clusters was used to facilitate the assessment and discussion of occupational safety determinants. The list comprises the following nine titles: Physical environment, Organization and management, Individual, Task, Tools and technologies, External, Performance, Intervention mechanisms, and Intervention drivers and barriers. Analysis of occupational accident insurance claim records with a limited set of variables yielded a narrow quantitative set of safety determinants that mainly described the immediate accident context. The result was expected, because the national and the European Statistics on Accidents at Work (ESAW) methods include sparse if any information on distal factors to the accident, such as the effect of work organization, management, or external factors of the accident etiology. The user centered surveys yielded a broader qualitative spectrum of occupational safety determinants, and provided also insight into additional, macro-ergonomic factors, such as the social and organizational context as well as contextual factors potentially influencing adoption of safety interventions. User centered research methods along with research that is based on accident claim records can assist in designing more effective occupational safety interventions. These methods contribute to understanding the individuals’ behavior in the context of work, both from accident and hazard analysis as well as from the accident prevention view- point. Multi-faceted approaches are needed to provide comprehensive information that is essential for reducing the excessive burden of injury and illness in agriculture and commercial fishing.
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(Helsingin yliopisto, 2020)In Finland, laboratory diagnostics of infectious diseases is done in clinical microbiology laboratories that are approved by the Regional State Administrative Agencies (RSAAs). The Finnish National Institute for Health and Welfare (THL) has given elaborated instructions for laboratories seeking approval. The main purpose of this licensure procedure is to ensure the reliability of diagnostics for infectious diseases regardless of the laboratory performing these investigations. The two main requirements for the approval are a sufficient number of skilled personnel and mandatory participation in external quality assessment (EQA) schemes for each test type that a laboratory offers. The licensure process for clinical microbiology laboratory is mandatory and independent of voluntary accreditation processes. This thesis focuses on three common clinical microbiological investigations: quantitative urine culture, faecal bacterial culture, and point-of care (POC) testing for infectious mononucleosis (IM) caused by the Epstein-Barr virus (EBV IM POC). External quality control (EQC) results were obtained from corresponding EQA schemes. The results of laboratory investigations will have a direct impact on patient care and in the case of infectious diseases also have epidemiological and public health implications, including a role in recognising disease outbreaks and assessing of epidemiological prevention and control measures effectiveness. For this reason, the high quality of these results is important. According to the Finnish Communicable Diseases Act laboratories have to give information on EQA schemes to THL by request. However the results from the EQC results sent to EQA provider are confidential. In this study Finnish laboratories were asked for permission to study their EQC results directly from the database provided a Finnish company specialised in producing a wide range of EQA services, Labquality Lt. Altogether 26,398 EQC results over a nine-year period (2009–2017) from 413 laboratories were collected and evaluated. Of the 413 laboratories, 335 took part in quantitative urine culture rounds, 17 in faecal bacterial pathogens rounds and 273 in EBV IM POC rounds. This study showed that the commitment to EQA was good in Finnish clinical microbiology laboratories. The laboratories typically attended all four rounds per year. The rate by which the laboratories replied to the EQA by submitting their results for the EQC samples varied from 95% to 99.5% according to the investigation studied in this thesis. This is referred as the response rate. The success rate for quantitative urine culture testing was 83%. The most common reasons for the 17% false results were due to interpreting the growth of expected pathogens as non-significant, or due to mixed growth, or no growth at all. There were differences in detecting and quantifying of the growth of Gram-negative and Gram-positive bacteria. In those EQC samples where Gram-negative rods were present, the quantitative result was correct in 91% of the results. The most common bacterial pathogen causing urinary tract infections (UTI), Escherichia coli was correctly reported in 93% of the EQC results. In those EQC samples where Gram-positive bacteria were present; the quantitative result was correct in 68% of the results. The most common Gram-positive bacterial pathogens found in urine culture samples, Enterococcus sp. and Staphylococcus saprophyticus were correctly reported in 85% of the EQC results. More untypical findings, Streptococcus agalactiae and Aerococcus urinae were reported correctly only in 23% and 31% of the EQC results, respectively. If the same sample contains several isolates, it is considered contaminated. In this study, two EQC samples containing mixed growth were correctly reported only in 66% of the results. The success rate for faecal bacterial culture testing was 92%. The common reasons for false results were improper identification of Shigella sp. and according to the collected data, the success rate was 89% for Shigella flexneri and 71% for Shigella sonnei. The success rate for the detection of Salmonella sp. was 95%. All false results with Salmonella were caused by two samples, one with low number of Salmonella Typhimurium cells, and other with Salmonella Infantis strain. The success in finding Yersinia sp. was 96% and for Campylobacter jejuni it was 98%. The overall success in the EBV IM POC rounds was 99.3%. The success varied between 94.3% for the immunofiltration method to 99.4% for the immunochromatographic method and 99.6% for latex agglutination method. The most significant factor regarding the results’ correctness was the clinical classification of the sample. The samples that represented old EBV immunity were the most difficult to interpreted with a 98.9% success rate. In order to evaluate the effect of the laboratory size on the EQC results, laboratories conducting quantitative urine culture and EBV IM POC investigations were divided according to the size, categorised by the number of named investigations they conducted per year. The laboratory type or size did not influence the success of the EQC results in this setting where all participants were licenced clinical microbiology laboratories.
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(Helsingin yliopisto, 2020)Smallholder tree growing is drawing increasing attention as population and economic growth models anticipate increasing wood demand that current natural forest or industrial forest plantations will not be able to supply without endangering sustainable development goals. Furthermore, ‘greening of economies’ calls for substitution of non-renewable materials with renewables, such as cellulose-based products. This has led to increasing attention to smallholder tree growing and it’s potential to contribute to the growing need for wood and ecosystem services from forests. Research on the motivations and drivers of smallholder tree growers and the role of smallholder tree growers in forest transition processes is available for some individual countries, and some qualitative analysis comparing countries on their enabling environments for smallholder tree growing has been done over the years. However, a systematic analysis with a global perspective is lacking. This study contributes to understanding the role and combinations of contextual and sectoral factors in establishing an enabling environment for smallholder commercial tree growing in South-East Asia and Africa, and analyses the role and importance of incentives for smallholder tree growing. The dissertation consists of three articles (papers I, II, and III). Papers I and II are in-depth case studies from Tanzania and Lao PDR, and Paper III combines the case-studies with three additional country cases for a Qualitative Comparative Analysis. Field research for the first and second paper collected data on household socioeconomic background and past, present, and future tree growing interests and practices through semi-structured interviews. Four villages in Njombe region in Tanzania, and four villages in central and northern Lao PDR were included in the study. In Tanzania, detailed information on smallholder plantation condition was collected through plantation inventories. The data collected was analysed using both qualitative and quantitative methods. For the third paper a theoretical framework was developed based on eight main factors in the enabling environment for smallholder tree growing identified in previous research. Country case-study information on these factors was collected through case studies on Tanzania and Laos, and desk studies on Indonesia, Uganda and Vietnam. Country case studies were then analysed using Qualitative Comparative Analysis applying a two-step approach and crisp set methodology. The analysis was run with Tosmana (Cronqvist, 2017) and verification of the results utilised Kirq (Reichert and Rubinson, 2014) and QCA 3.0 software (Dusa, 2019). Findings indicate that Tanzanian smallholder tree growers have strong interest to increase their tree growing area despite the weak enabling environment. In Lao PDR the smallholder teak growing area is not likely to expand as smallholders consider other land uses more attractive and the existing incentive framework fails to induce smallholder tree growing. Based on the Qualitative Comparative Analysis, secure land and forest tenure, and strong demand for timber may be sufficient to boost smallholder tree growing. However, functioning wood markets, knowledge, and direct incentives are present in the configurations in the majority of the cases, which especially seem to contribute in scaling up tree growing volumes and in building an enduring smallholder tree growing sector that is capable to maintain the tree growing activity and supply the wood markets. The role of incentives in smallholder tree growing varies in the case-study countries, but under strong market demand they may not even be necessary for plantation expansion if land tenure is clear. However, to be effective, incentives should be tailored to meet smallholder needs in a country-specific context, and adjusted according to the changing environment. Secure land tenure and wood demand are essential elements in the enabling environment for smallholder tree growing. Even though they are not necessary for the initiation of smallholder tree growing, incentives play a crucial role in establishing technical knowledge and skills among smallholders to improve the quality of the wood they produce, which over the years has remained a challenge. However, incentives are only effective if they are designed from the beginning considering the smallholder capacities, actual needs, and their other livelihood options. The findings confirm and highlight the importance of secure land and forest tenure recognized in multitudinous studies. Smallholder tree growers struggle to achieve the quality that higher value wood markets require, and their produce is sold mainly in lower value local or regional markets. This may still be a profitable business model and a way to diversify livelihoods from the smallholder perspective, but on the other hand it does not allow smallholder tree growers to reach their full production potential and profits, nor does it support the development of the wood industry. The findings also suggest that models and incentives improving smallholder access to land are an effective incentive for smallholder tree growing when the land use is defined as a condition for the allocation. If global and national policies seek increasing smallholder contributions in tree growing for wood production and climate change mitigation, the first priority is to provide them access to land and secure land and tree tenure. Smallholder tree growing schemes should either recognize and accept the capacity and financial limitations smallholders have, or support schemes should be tailored to their specific needs and to the varying socioeconomic contexts.
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(Helsingin yliopisto, 2020)The aim of this dissertation was to characterize Pectobacterium strains isolated in Finland. Pectobacterium species cause soft rot and blackleg on wide range of plants in cultivated areas worldwide. Potato is an important food crop and source of food cultivated all over the world. Pectobacterium species interfere with potato production at all stages of cultivation. Pectobacterium species belong to the Pectobacteriaceae family with the soft rot bacteria Dickeya genus. In this study, two Pectobacterium model strains, SCC3193 and SCC1, isolated in Finland during 80s and initially defined as belonging to P. carotovorum species were further examined. Biochemical tests of the strains were conducted to understand their characteristics of the bacterial strains and their differences to closely related bacterial strains. The strain SCC3193, originally determined as belonging to P. carotovorum, was redefined as P. wasabiae in the present study. However, it did not fully share the same biochemical profile with the P. wasabiae type strain and based on genome comparisons it was later placed into a novel species P. parmentieri. Furthermore, phylogenetic position of the Pectobacterium strain SCC1 was determined. Also, the strain SCC1 was originally defined as P. carotovorum, but it was observed in the phylogenetic analysis that it clustered apart from P. carotovorum type strain, and thus its taxonomical status could not be confirmed at the time of the analysis. It was later included into a novel species called Pectobacterium versatile. In addition, Pectobacterium strains isolated from diseased potato tubers in 2004, and initially classified as P. carotovorum, were characterized in this study. According to biochemical analyzes, these bacteria isolated from potato stems resembled P. carotovorum but had a low virulence on potato tuber and citrate-negative phenotype. Two genomes of these atypical Finnish stem isolates were produced to study their genome content and phylogenetic position in Pectobacterium genus. Average nucleotide identity (ANI) analysis showed that these isolates were similar to Pectobacterium polaris, a highly virulent new species recently identified in Norway. However, the Finnish isolates were most similar to atypical P. polaris isolates in ANI analysis and biochemical tests. Genome comparisons showed that the all the atypical isolates harbored similar genomic islands not present in P. polaris type strain. Alltogether, taxonomic and genomic studies placed the atypical P. polaris strains into a new subspecies, here called P. polaris subsp. parvum. One of the P. polaris subsp. parvum strains had been isolated in the Netherlands already in 1970s, but originally misidentified as P. carotovotum, which suggests that similar isolates were present in Europe also before. This study provides novel information about the taxonomy and ecology of Pectobacterium species existing in Finland. Taxonomic status of P. carotovorum isolates redefined in this and other studies show that Pectobacterium strains previously included into P. carotovorum species could be divided into several novel species with genome-based methods. The precise identification of bacterial species poses challenges for plant protection. The information from the study can be used for potato production and plant protection in the future.
