Maatalous- metsätieteellinen tiedekunta


Recent Submissions

  • Nieminen, Emmi (Helsingin yliopisto, 2017)
    This thesis examines the optimal economic management of the Baltic Sea fisheries and contributes to the existing literature with its novel bioeconomic and game theoretic applications enhancing more holistic fisheries management than traditionally, and thus taking a step towards ecosystem-based management. Such management can be interpreted as integrated management of the ecosystem instead of concentrating on a single issue in isolation. This approach is fulfilled in four separate dimensions: Firstly, the thesis studies the optimal management of several species instead of focusing on only one species. Secondly, the focus is not only on management in a single country; instead, the thesis has a wider scope and analyse the prospects of cooperation among several countries. Thirdly, the problems are modelled by taking into account the long-term perspective, i.e., by maximising the resource rent over a long time period and by analysing the possible effects of climate change. Fourthly, this thesis applies a cross-sectoral approach and examines several sectors affecting the ecosystem (fisheries and energy sectors) instead of only focusing on one. This thesis highlights the importance of linking economics to biology and its significance to fisheries management. In fact, fisheries management based on society s profit maximising bioeconomic objectives with biologic constraints are often more conservative for a fish stock than management relying solely on biologic advice. The increased profitability of the fisheries industry could furthermore be improved by international coordination among fishing nations. The positive effects of bioeconomic management would be even greater when the fish stocks are weak, which may be the future in the Baltic Sea with the continuing effects of climate change. Additionally, this thesis takes into consideration the positive value of migratory fish for the recreational river anglers. When those values are included, it is often profitable from the society's point of view to enable the upstream migration even in regulated rivers producing hydropower. The optimal measures targeted to enhance the migration depend on the number of the dams in the river: the more dams, the more profitable to trap and transport fish over the dam instead of constructing fishways.
  • Pietarinen, Paavo (Helsingin yliopisto, 2017)
    The focus of medical research has steadily shifted from population-based medicine to personalized medicine in recent years. It has become clear that interindividual variability plays a big role in treatment responses. For example, CYP2D6 is involved in the metabolism of 20-25% of clinically used drugs, and the CYP2D6 mediated metabolic rate varies widely between people. Chronic myeloid leukemia (CML) is the only leukemia with highly effective targeted treatment. However, some patients become resistant or intolerant to the first-line treatment, and personalized treatment adjustment is sometimes necessary. The purpose of this thesis was to study how genetic and functional screening can be utilized in personalized-medicine research. In Study I, we genotyped 857 Finnish volunteers for 10 CYP2D6 genetic variants. We found that the frequencies of CYP2D6 variants differ from our neighboring populations. More importantly, genotype-based classification of CYP2D6 metabolic activity showed a high frequency of ultra-rapid metabolizer (UM) genotype (7.2%), which was the consequence of the high prevalence of CYP2D6 duplications. In contrast, the frequencies of poor metabolizer (PM) (2.3%) and intermediate metabolizer (IM) (3.0%) genotypes were relatively low, which indicates that Finns have a high capacity for CYP2D6 mediated metabolism in general. In Studies II and III, we explored the drug sensitivity profiles of chronic myelogenous leukemia (CML) in blast crisis (BC) and chronic phase (CP) utilizing cell line and patient primary cell samples in a high-throughput drug screening platform. The median drug responses of the BC CML cell line and patient samples correlated well. By comparing the drug responses in these samples, we were able to identify several compounds (e.g., NAMPT, VEGFR, and MEK inhibitors), which were highly effective in all samples. Testing the drug sensitivities of CP CML samples and comparing them to BC CML samples revealed CP CML cells to be clearly less sensitive in general. Most surprisingly, CP CML samples seemed to be resistant to tyrosine kinase inhibitors (TKIs). We also studied the variance of absorption, distribution, metabolism, and excretion (ADME) genes in CP CML patients with poor responses to TKI treatment. In our study population of poor responders (n=21), we discovered several gene variants significantly more frequently in poor responders than in the healthy control population. Furthermore, we identified novel ADME gene variants that have not been reported previously. Interestingly, some of these novel variants may be CML cell-specific somatic mutations. To conclude, in this thesis, we showed clinically relevant CYP2D6 variation in the Finnish population, which should be taken into consideration when prescribing drugs that are CYP2D6 substrates. We saw also that high-throughput drug screening is an effective way of studying individual drug responses in patient cells. We think that the findings of this thesis can be used to improve personalized medicine research.
  • Kontturi, Juha (Helsingin yliopisto, 2017)
    The type III polyketide synthases (PKSs) are a group of enzymes involved in the production of structurally diverse secondary metabolites, polyketides in plants. Compounds, such as chalcones, chromones, stilbenes and coumarins possess a variety of important biological roles for the plants, such as protection against oxidative stress, pests and diseases, herbivory and UV irradiation. From the human use perspective, polyketides or their derivatives serve as antifungal compounds, immunosuppressants, anticancer drugs, antibiotics and insecticides. Type III PKS are small (40-45 kDa) proteins functioning as homodimers. They catalyze the sequential decarboxylative condensation reaction between malonyl-CoA and a variety of CoA-linked starter molecules in a biosynthesis, which closely resembles fatty acid biosynthesis. Gerbera (Gerbera hybrida) expresses three genes encoding chalcone synthases (CHS), which are enzymes involved in the biosynthesis of flavonoids in plants. In addition, it has three genes encoding 2-pyrone synthases (G2PS1-3), which differ from the CHSs with altered substrate specificity and the amount of decarboxylative malonyl-CoA condensation reactions. It was previously shown that G2PS1 is a triketide synthase, responsible for the biosynthesis of 4-hydroxy-6-methyl-2-pyrone (triacetolactone, TAL), a putative precursor for two antimicrobial compounds, gerberin and parasorboside in gerbera. In this study, the G2PS2 and G2PS3 were functionally characterized as pentaketide synthases and their role in the biosynthesis of another antimicrobial compound, 4-hydroxy-5methylcoumarin (HMC) was demonstrated. Using protein modelling and mutagenesis studies, the structural differences in the active site cavity of gerbera 2-pyrone synthases were demonstrated. The gerbera type III PKS family was extended by characterizing two additional 2-pyrone synthases and determining their expression patterns. The newly discovered GASCL1 and GASCL2 are anther specific chalcone synthase like enzymes (ASCLs), which in many other plant species have been shown to take part to the biosynthesis of sporopollenin, the main component of a exine layer of the pollen grain. The last part of the thesis focus on glycosyltransferses (GTs), a group of enzymes that catalyze the addition of a sugar moiety to the plant secondary metabolites, including the products of the gerbera type III PKSs.
  • Reuter, Lauri (Helsingin yliopisto, 2016)
    Recombinant proteins are used as pharmaceuticals, enzymes and components of nanotechnology. The exceptional properties of fungal hydrophobins make them interesting for many of those uses. They also transfer some of their functionalities to fusion proteins enabling completely new applications. In general, plants are a potential platform for manufacturing recombinant proteins even in agricultural scale. This work explores production of hydrophobin fusion proteins in a plant cell factory: the tobacco bright yellow 2 cells (BY-2). The hydrophobin fusion technology has been mainly based on a single hydrophobin molecule the Trichoderma reesei HFBI. This work expanded the toolkit with several new molecules. When expressed in plants the hydrophobin fusion partners induced formation of protein bodies, in relation to the accumulation levels. In addition to HFBI, only HFBII and HFBIV interacted with non-ionic surfactant to selectively separate fusion proteins in surfactant based two phase separation. In Nicotiana benthamiana HFBII improved accumulation of green fluorescent protein (GFP) and Protein A in comparison to both HFBI-fused and non-fused proteins. However, HFBI, HFBII and HFBIV fusion partners all slightly reduced the yield of transferrin. Both HFBI-Protein A and transferrin-HFBIV were produced in BY-2 suspension cells with good yields. Furthermore, continuous selection resulted also in a cell line yielding 1.1 g/l GFP-HFBI. This is the first report on a plant cell culture reaching gram per litre yields. The BY-2 propagation was successfully scaled-up to 600 litre culture volume in classical stirred tank bioreactors. The aqueous two phase separation from plant cell extract was successfully scaled to 20 l volume. The fusion proteins retained functional properties from both fusion partners. The HFBI-Protein A enabled harvesting of antibodies in solution using aqueous two phase separation. The HFBIV fused transferring retained its capability to bind iron and interact with the transferrin receptor. Coating with transferrin-HFBIV resulted in uptake of the silicon nanoparticles in human cancer cells. This work builds foundation for utilization of BY-2 suspension cells in industrial manufacturing of recombinant proteins and on the other hand opens interesting new applications for bi-functional hydrophobin fusion proteins.
  • Uotila, Karri (Helsingin yliopisto, 2017)
    The purpose of the work done for this thesis was to construct and develop the concept of cost-efficient Juvenile Stand Management (JSM) for planted Norway spruce (Picea abies L. Karst) stands. The principles of time based management were followed, by integrating regeneration activities as a cost-efficient value chain and by minimizing non-value-adding work with straightforward decision making based on Forest Management Plan (FMP) data. The effects of soil preparation and Early Cleaning (EC) on further development of the stands were studied in intensive field experiments. Extensive survey data from juvenile stands were used to develop methods applicable for efficient decision making in JSM. The survey data were used to model the effects of site and stand attributes on the need for EC and labor time consumption of PreCommercial Thinning (PCT). Timing of JSM had major effect on its costs; a delay in PCT increased the labor time needed to manage a stand by 8.3% annually. Moreover, 61 70% of the saplings in a typical Norway spruce stand were considered to need EC years before the need for PCT arose. EC was also found to be an effective release treatment as it subsequently increased the diameter growth of crop trees by 21 32%. However, a two-stage management regimen, which included EC and PCT, appeared to be somewhat more labor consuming than the PCT only option. The soil preparation method had a major effect on the number of trees to be removed in EC, and spot mounding led to a less labor consuming JSM program than disc trenching. Thus, spot mounding appeared to be a less costly activity overall even though it initially appeared a more expensive method than disc trenching. The results showed that interactions in regeneration chain activities are important for cost-effective wood production. Furthermore, a priori information can have practical implications in decision making for JSM. Several site or stand attributes were found to explain the need for EC or for labor consumption of PCT. However, the models developed in this study are rather inaccurate for reliable a priori estimation. The modeling data in further research should go beyond the data of traditional FMP. Big data offers promising opportunities, but data collection and storage need to include data with the relevant attributes.
  • Kokko, Pauliina (Helsingin yliopisto, 2017)
    Achieving and maintaining national self-sufficiency in milk and meat play important roles in ensuring future food security. Currently, Finland is self-sufficient in milk. However, beef production, which is strongly related to dairy production, has fallen below consumption mainly because of a decreased number of dairy cows and low profitability. Even though the efficiency and productivity in dairy herds have increased substantially during the last decades, the profitability of milk, and especially combined milk and beef production, has remained low. In addition, the environmental challenges facing the dairy cattle industry are increasing;the environmental impacts of dairy farming are of growing public concern and production is likely to be affected by new environmental legislation and constraints in the future. To meet the future challenge of safeguarding food security with more intensive use of resources, new breeding and production strategies for milk and beef production are needed. The main goal of this thesis was to investigate sustainable breeding and production strategies for increasing the productivity and efficiency in dairy herds in order to improve profitability and contribute to mitigation of the environmental impact of milk and beef production. More specific objectives were to derive economic values of feed efficiency traits along with several production and functional traits in Finnish milk production and to evaluate economic benefits of including additional feed efficiency, growth, and carcass traits in the breeding goal for combined milk and beef production systems. Moreover, the possibilities of different production strategies for increasing beef production from dairy herds and mitigating overall greenhouse gas emissions from beef production were assessed. The derivation of economic values of different traits for the Finnish Ayrshire breed using a bio-economic approach showed that milk yield with the highest relative economic value (29-40% of the sum of standardized economic values over all traits) strongly dominated the breeding goal under the Finnish production and economic conditions in 2011. However, the moderate relative economic values (given in parentheses) found for the traits not currently included in the breeding goal: daily gain of animals in the rearing and fattening periods (4-5% both), residual feed intake (RFI) trait group (6-7%) as well as mature live weight (LW) of cows (6- 11%), indicate that the inclusion of these traits in the breeding goal for Finnish milk production systems could result in economic benefits. The economic impact of including additional feed efficiency and beef production traits in the breeding goal for the combined milk and beef production systems was assessed using a deterministic approach with the derived economic values. According to the results, the inclusion of a better growth performance of fattening animals and growing replacement heifers in the breeding goal while simultaneously preventing higher LW of cows would be the most promising option to improve the profitability of the combined milk and beef production systems. When considering the studied feed efficiency-related traits, the inclusion of smaller LW of cows in the breeding goal seems to be more beneficial than the inclusion of RFI traits in production systems where growth and carcass traits are subject to selection. This finding is also supported by the faster availability of LW of cows for selection and its lower recording costs. However, with the breeding goal that excludes growth and carcass traits, adding LW of cows alone to the breeding goal had a negative effect on the profit of the breeding program. Therefore, for production systems where growth and carcass traits are not subject to selection, selecting for RFI traits could be more profitable even with only small economic benefits. However, before any further conclusions can be made about the consequences of selection for RFI traits, more information on the genetic correlations between RFI traits and current breeding goal traits as well as on the most cost-effective selection methods for feed efficiency is needed. Finnish beef production was modeled to study the potential of different production options to enhance beef production originating from dairy operations.The most efficient way to enhance beef production, and consequently, to mitigate greenhouse gas emissions from beef production would be to increase the use of crossbreeding with beef bulls in dairy herds carrying out inseminations with Y chromosome sorted beef semen. However, in order to increase the current rate of crossbreeding, procedures that would ensure a sufficient number of replacement heifers and clear economic benefits from the production of crossbred calves to dairy farmers are needed. When considering the studied strategies that enable the increased use of crossbreeding in dairy herds, reducing the herd replacement rate showed the most potential for enhancing beef production, even though it would require substantially higher use of crossbreeding. The current global tendency towards specialized dairy and beef production systems will likely further reduce beef production from dairy herds, potentially leading to an increasing negative environmental impact of livestock production. The results of this thesis support that combined milk and beef production would likely be the most viable and sustainable way to achieve self-sufficiency in beef while maintaining sufficient milk production in Finland. Therefore, the current dairy production systems should be developed more towards systems that efficiently produce milk and beef rather than increased specialization.
  • Koskinen, Markku (Helsingin yliopisto, 2017)
    In this study, the effects of restoration of forestry-drained peatlands on the nutrient and organic carbon exports and methane dynamics of the restored sites are explored. The study consists of four sub-studies. Two of the sub-studies are concerned with the effects on water quality and export of elements of restoration and were conducted on a catchment scale. One of the studies was conducted in the laboratory, and assessed the release of elements from peat samples under anaerobic inundation simulating the effects of a rising water table after restoration or logging. The fourth study was again a field study, in which the differences in methane emissions between undrained, drained and restored spruce swamp forests were assessed. In all, 24 different pristine, drained and restored sites are featured in the study, one site being present in two of the sub-studies. The results indicate potentially large effects of restoration especially on the nutrient rich spruce-dominated sites, which had the highest restoration-induced increases in organic carbon and nutrient exports in the catchment studies, and which also exhibited high methane emissions after restoration, higher than in the undrained or drained state. The results should prompt research into the techniques applied in restoration of such sites and into the processes which lie behind these large effects.
  • Chan, Tommy (Helsingin yliopisto, 2016)
    Chan, Tommy 2016. Dynamic variations in bark hydraulics understanding whole tree processes and its linkage to bark hydraulic function and structure. University of Helsinki, Department of Forest Sciences A mature tree stem generally consists of a column of wood that is composed of a series of annual incremental layers and enclosed in a covering of bark. The dynamic variations of the bark are complex due to its structure and function: the thick outer-bark acts as a protective barrier against the abiotic and biotic environment; while the phloem is where sugar transport occurs. Much of the bark variation is due to the transport of sugars and its related processes. The xylem pathway, which transports water in the opposite direction, is connected to the phloem in parallel along the entire length of the stem. The immediate connection between these two transport pathways suggests a functional linkage. The purpose of this thesis is to study the dynamic processes that occur within the bark and its interaction with other internal tree processes and the external environment. These interactions have not been thoroughly quantified, especially on an intra-annual (e.g. daily) scale. The thesis consists of four papers, of which one is a modelling paper and three are experimental studies. Growth is estimated with the model by separating the water-related influences from measured inner-bark, revealing a growth signal proxy for cambial stem growth. Using this signal, a correlation study to microclimate variables is examined in one paper; and to assumed growth respiration in a second paper. The remaining two papers explore the seasonality of photosynthesis and respiration, and bark stem dynamics during the spring recovery period. As a conclusion of this thesis, these papers show how inextricably linked individual tree processes and the environmental are to the changes within the bark. The culmination of this thesis opens new opportunities to further understand the dynamics of bark hydraulics and ecophysiological processes by implementing field measurements and state-of-the-art modelling. Keywords: xylem, phloem, growth, respiration, photosynthesis, spring recovery
  • Chamlagain, Bhawani (Helsingin yliopisto, 2016)
    Vitamin B12 (later B12) intake is insufficient in developing countries, and globally, vegetarians and vegans are also at risk of B12 deficiency. Occurring naturally only in foods of animal origin, new affordable and sustainable dietary sources of B12 are needed to ensure sufficient intake. The only known food-grade producers of active B12, Propionibacterium freudenreichii strains, however, are yet to be exploited to enrich plant-based foods with B12. The B12 production capacity of P. freudenreichii depends on the strain, and the availability of the B12 lower ligand (5,6-dimethylbenzimidazole, DMBI) is a key factor for the production of active B12. Bread can be considered as a potential food for B12 fortification; yet the stability of in situ-produced B12 incorporated during breadmaking processes is not known. Current analytical methods such as the microbiological assay (MBA) lack the required specificity and the existing high-performance liquid chromatography (HPLC) methods are only capable of measuring higher B12 levels in fortified foods and supplements. The determination of active B12 in fermented foods, however, needs sensitive and selective methods. An ultra-HPLC (UHPLC) method was developed and validated to measure the active B12 contents. The identity of the B12 form was confirmed with an ion-trap or quadrupole time-of-flight mass spectrometry (MS). The B12 production capacity of 27 P. freudenreichii and 3 Propionibacterium acidipropionici strains was first studied in whey-based medium (WBM), and three of these P. freudenreichii strains were chosen to study B12 production in three aqueous cereal matrices prepared from malted barley (BM; 33% w/v), barley flour (BF; 6% w/v) and wheat aleurone (AM). Riboflavin (RF) and nicotinamide (NAM) as food-grade replacements for DMBI were investigated in WBM and cereal matrices. The stability of in situ-produced B12 and added cyanocobalamin (CNCbl) and hydroxocobalamin (OHCbl) during straight-dough, sponge-dough and sourdough breadmaking was studied. The developed UHPLC method employing an Acquity high-strength silica (HSS) T3 column showed excellent separation of active B12 from its analogues. A low limit of detection (0.075 ng/inj) enabled the measurement of the B12 levels in cell extracts directly and following immunoaffinity purification in extracts of fermented cereal matrices and B12-fortified baking samples. Analysis with UHPLC MS confirmed the production of active B12 by all 27 P. freudenreichii strains in WBM and 3 P. freudenreichii strains in cereal matrices. P. acidipropionici strains, however, produced an inactive form (pseudovitamin B12), thus making them unsuitable for active B12 fortification in foods. The level of B12 production in WBM varied considerably between the strains (0.45‒3.35 µg/mL), which increased up to 4-fold in 12 of the 27 P. freudenreichii strains following supplementation with RF and NAM. In many of these strains, the B12 yield was higher with RF and NAM co-supplementation than with DMBI. In cereal matrices without supplementation, the produced levels of active B12 (9‒37 ng/g) with P. freudenreichii strains were nutritionally significant. The B12 production increased many-fold, reaching up to 430 ng/g in BM, 39 ng/g in BF and 114 ng/g by adding cobalt (Co) and reached 712 ng/g in BM and 180 ng/g in AM with RF and NAM co-supplementation with Co. The incorporated in situ-produced B12 was retained during straight-dough breadmaking and the loss of 29% during sourdough baking was similar to the losses observed for relatively stable CNCbl. However, the added OHCbl decreased by 21%, 31% and 44% respectively in straight-dough, sponge-dough and sourdough breadmaking. These results showed that B12 produced in situ and incorporated during breadmaking was well retained in the bread prepared by the conventional breadmaking processes. This thesis shows that UHPLC combined with MS allows for the accurate identification and quantitation of low levels of active B12 in fermented food matrices (≥1 ng/g). P. freudenreichii strains could be utilised for in situ production of active B12 in cereal matrices and WBM. The availability of RF and NAM could considerably improve B12 production. The produced levels could easily fulfil the recommended dietary allowance set for B12 (e.g. 2‒2.4 µg/day for adults), and could be well retained in bread in the commonly used breadmaking processes.
  • Tanhuanpää, Topi (Helsingin yliopisto, 2016)
    Urban forests provide various ecosystem services. However, they also require fairly intensive management, which can be supported with up-to-date tree-level data. Until recently, the data have been collected using traditional field measurements. Laser scanning (LS) techniques provide efficient means for acquiring detailed three-dimensional (3D) data from the vegetation. The objective of this dissertation was to develop methods for mapping and monitoring urban forests at tree level. In substudy I, a method (MS-STI) utilizing multiple data sources was developed for extracting tree-level attributes. The method combined airborne laser scanning (ALS), field measurements, and tree locations. The field sample was generalized using the non-parametric nearest neighbor (NN) approach. The relative root mean square error (RMSE) of diameter at breast height (DBH) varied between 18.8 33.8%. The performance of MS-STI was assessed in substudy II by applying it to an existing tree register. 88.8% of the trees were successfully detected, and the relative RMSE of DBH for the most common diameter classes varied between 21.7 24.3%. In substudy III, downed trees were mapped from a recreational forest area by detecting changes in the canopy. 97.7% of the downed trees were detected and the commission error was 10%. Species group, DBH, and volume were estimated for all downed trees using ALS metrics and existing allometric models. For the DBH, the relative RMSE was 20.8% and 34.1% for conifers and deciduous trees respectively. Finally, in substudy IV, a method utilizing terrestrial laser scanning (TLS) and tree basic density was developed for estimating tree-level stem biomass for urban trees. The relative RMSE of the stem biomass estimates varied between 8.4 10.5%. The dissertation demonstrates the applicability of LS data in assessing tree-level attributes for urban forests. The methods developed show potential in providing the planning and management of urban forests with cost-efficient and up-to-date tree-level data.
  • Riikonen, Anu (Helsingin yliopisto, 2016)
    In urban forestry, the assessment and valuation of ecosystem services provided by urban trees are increasingly important both for the rationale of planting new trees and for retaining and managing existing tree populations. To support the field of practical urban forestry, research is needed on the net effects of ecosystem services and costs. The aim of this thesis was to analyse the ecosystem service potential of young street tree plantings. To this end, transplanting recovery, tree growth and carbon and water exchange were studied on two case study streets, one planted with Tilia × vulgaris Hayne and the other with Alnus glutinosa (L.) Gaertn. f. pyramidalis Sakari . The relationships between tree growth, tree and soil water and carbon exchange, environmental variables and tree properties were examined. Transplanting recovery of Tilia trees was delayed due to excess soil water, while Alnus trees recovered within the first few years. Alnus shoot growth responded positively and Tilia negatively to an increase in soil water content. Branch leaf area in relation to branch basal area varied, showing effects of transplanting and subsequent adaptation of the trees to the new growing sites. The studied trees accumulated carbon in their woody biomass during the first decade after transplanting, but the sequestration was small relative to carbon loss from the man-made tree soils. Several additional decades of tree growth were estimated to be needed to attain net carbon sequestration in these street tree plantings if peat originating C and/or renewable C lost from tree soils was counted as C loss. Biomass equations developed in traditional forests predicted total aboveground street tree biomass fairly well, but performed unsatisfactorily in estimating specific aboveground biomass compartments. The biomass distribution and litter production of street trees also require further study to gain insights into the role of tree litter in urban biogeochemical cycles. The annual variation in tree water use of the studied trees was high, but within one year, a Penman-Monteith-based evapotranspiration model with added stomatal conductance and leaf area dynamics description, together with soil water status, explained the variation in tree transpiration quite well. Using a single parameterization over all four years examined did not produce reliable tree water use estimates however. Scaling tree transpiration to different canopy cover percentages implied that especially the columnar Alnus trees could transpire a considerable proportion of annual rainfall with attainable canopy cover, potentially contributing to stormwater management.
  • Nyholm, Outi (Helsingin yliopisto, 2016)
    Diarrheagenic Escherichia coli (DEC) strains cause diarrheal diseases and related sequelae in humans. They are important foodborne pathogens that cause significant public health problems worldwide, especially in developing countries, due to poor hygiene and inadequate health care. DEC can be divided into five pathogroups based on their distinctive virulence factors: Shigatoxigenic E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC) and enteroaggregative E. coli (EAEC). The virulence traits of different DEC pathogroups are responsible for diverse intestinal infection symptoms ranging from mild diarrhea to more severe disease such as hemorrhagic colitis and hemolytic uremic syndrome. STEC is considered to be the most dangerous pathogroup because of the severe disease it may cause. E. coli are able to acquire virulence genes through horizontal gene transfer. This originally established the different pathogroups. However, it can also lead to the emergence of novel hybrid strains that possess a mixture of the pathogroup-specific virulence factors. The aim of this thesis was to study the variety of virulence genes of DEC and hybrids of STEC and other DEC. The occurrence and characteristics of hybrid pathogroups of STEC and other DEC were studied in Finland in human and non-human (animal, food, environmental) STEC strain collections. Burkina Faso in West Africa was observed as a model country for DEC occurrence in the developing world. Raw meats sold at local markets in Burkina Faso were screened for the presence of virulence markers for DEC. STEC strains and hybrid strains in raw meats were subsequently isolated, characterized, and compared with the strains appearing in other countries. Genetic background and the virulence combination of hybrid DEC strains was further investigated using whole genome sequencing (WGS) and comparative genomics. Furthermore, the usefulness of WGS as a novel tool for STEC typing was evaluated. Hybrids of STEC and ETEC pathogroups were found both in Finland and Burkina Faso from two climatically and socioeconomically distant countries. Among Finnish human patients and food production animals, STEC/ETEC hybrids were present. In Burkina Faso, STEC/ETEC hybrids were found in raw meat products. In addition, Burkinabe retail meats were found to be heavily contaminated with STEC and other DEC, reflecting poor food hygiene and the common occurrence of potential human pathogens in Burkina Faso. STEC isolated in Burkina Faso were diverse according to their virulence characteristics and serotypes, with similar being associated with human disease. Genomic comparison of the Finnish and Burkinabe STEC/ETEC hybrid strains indicated several virulence genes and that the strains originate from different phylogenetic lineages among E. coli, suggesting their independent emergence. The study indicated that WGS can be used to replace the phenotype-based and gene-based typing methods in STEC typing. The multiple virulence factors, especially the ability to produce several cytotoxins and to adhere to intestinal epithelial cells, may increase the virulence of hybrid E. coli for humans. This may result in more severe disease in a patient and increased spreading potential. Hybrid E. coli should be considered as emerging pathogens, which may have serious consequences for public health. Hybrids of STEC and other DEC should be taken into account in surveillance, and suitable diagnostic methods for their detection and typing should be developed. By applying modern food protection practices, such as the cold chain and decent meat processing hygiene, the common occurrence of DEC may be decreased in retail meats in Burkina Faso as it has been in Finland and other industrialized countries.
  • Hotti, Hannu (2016)
    Coniine, a piperidine alkaloid, is known from poison hemlock (Conium maculatum L.), twelve Aloe species and Sarracenia flava L. Its biosynthesis is not well understood, although a possible route starts with a polyketide formed by a polyketide synthase (PKS). This study focused on identification and characterization of PKS-genes involved in coniine formation, induction of callus from plants containing hemlock alkaloids and investigation of the possibility to elicitate the alkaloid pathway in cell culture in order to understand coniine biosynthesis. Plant materials involved in different stages of this study were investigated for their alkaloid content using gas chromatography-mass spectrometry. A novel type of PKS, CPKS5, was identified as the starter candidate for the initiation of coniine biosynthesis by catalysing the synthesis of the carbon backbone from one butyryl-CoA and two malonyl-CoA moieties. When elicitated, poison hemlock cell cultures produced furanocoumarins but no piperidine alkaloids. The hemlock alkaloids are wider distributed than previously has been thought among Sarracenia, and Aloe spp. contain a new alkaloid for the genus. These results together pave the way towards possible utilization of hemlock alkaloids.
  • Jokiniemi, Tapani (Helsingin yliopisto, 2016)
    Energy saving objectives have arisen recently in all sectors of life due to the climate change sce-narios and depletion of fossil energy resources. In boreal and northern temperate climate zone countries one of the most energy intensive operations in arable farming is grain preservation, which in most cases means drying. This work focused on examining the energy use and energy saving possibilities in grain drying, and grain preservation in general, from several aspects. The main focus was in Finnish conditions, but the results can be applied also in other areas, when applicable. In addition to the energy aspect, some economic considerations were conducted, since economic profit is the ultimate decision making factor for farmers. The principal method for grain preservation in Finland is hot-air drying. Energy use and energy savings in drying hence constituted the major part of the research work included herein. The aim of the work was to produce information that could be easily utilized in current farming practices. Therefore all the experiments and measurements were conducted in grain recirculat-ing mixed-flow hot-air dryer, which is the most common grain dryer type in Finland. The energy utilization in dryer was first examined and energy losses identified, and three energy saving methods were chosen for closer consideration: 1) controlling the air flow rate and temperature of the drying air (publications I and II), 2) heat insulation of the dryer device (III) and 3) heat recovery from the dryer exhaust air (IV). The aim of the method 1) was to improve the utilization of the supplied heat energy by increasing the humidity of the dryer exhaust air and thus reducing the energy losses via sensible heat in the exhaust air. Method 2) aimed to eliminate the heat losses from the dryer surfaces by the heat insulation. Method 3) focused on recovering the sensible as well as latent heat from the dryer exhaust air with a passive parallel plate heat exchanger. In addition to the energy saving potential in drying, also the possibilities for enhanced use of alternative moist grain preservation methods and their effects on the energy consump-tion in grain preservation were examined (publication V). While drying is practically the only suit-able preservation method for market quality grain in Finnish conditions, moist grain preservation methods could be applied basically for all home-grown grain used for animal feeding, which rep-resents roughly one third of the total annual grain yield in Finland. The examined moist grain preservation methods were airtight preservation, acid preservation of whole grains and grain crimping (ensiling). The energy saving possibilities with these methods, compared to the current situation, were evaluated by theoretical calculations. The results indicated that considerable energy savings could be achieved by the methods examined in publications I to V. The drying process control method produced energy savings of 5 15%, depending on the grain species, compared to conventional drying method. The energy savings achieved by the heat insulation were 16 21% in the examined dryer. Heat recovery method saved on average 18% energy compared to the conventional system, and energy sav-ings up to 40% were suggested for passive heat recovery by the theoretical model developed in the publication IV. Moist grain preservation methods for preserving home-grown feed grain provided energy savings of 50 90% compared to drying. The combined energy saving potential of the examined methods was 20 43% of the total energy consumption in grain preservation at the present situation, when the realizable potential was considered. It was concluded that significant energy saving possibilities exist in current grain preser-vation practices and their utilization could aid to reduce the energy consumption in the agricul-tural sector and thus to achieve the energy saving objectives set by authorities. Energy savings of 5 11% of the total direct energy use in arable the farming sector could be achieved. However, even the relatively large energy savings would have quite a modest effect on the economy of farming with the current energy prices, which indicates that the direct energy inputs are still relatively cheap, compared to other inputs. While energy prices are expected to rise in the long term, energy saving measures will become more viable for the economy of farms in the future, which is the ultimate incentive for more energy efficient production.
  • Huang, Xin (Helsingin yliopisto, 2016)
    Gluten-free foods are defined by their lack of prolamins that trigger coeliac disease. In order for foods derived from Triticeae grains to be considered as gluten-free, the prolamins need to be eliminated. Previously, enzymatic degradation of cereal prolamins has been intensively studied. In the present work, another method is investigated, namely the metal-catalysed oxidation of prolamins. The aim was to modify prolamin peptides and proteins, and to examine the modifications, in order to reduce their immunological activities. The metal-catalysed oxidation was first examined on model peptides, including repetitive sequences of prolamin peptides and a model coeliac-toxic peptide (33-mer), and then tested on C-hordein, a model monomeric barley prolamin, and finally on whole hordein, thus covering the range from peptides to a whole protein. The fragmentation of prolamin peptides and proteins was observed to be a consequence, partly due to proline oxidation. On the other hand, aggregation also occurred, through dityrosine formation, disulfide bridges or carbonyl interactions. The amino acid profile and protein structure affected the oxidation behaviours and resulted in various modifications that were compared after metal-catalysed oxidation treatments. The immunoreactivity of oxidised peptides, C-hordein or whole hordein decreased in R5 antibody-based measurements that are used in gluten-free detection. The present study demonstrated that cereal prolamins can be modified by metal-catalysed oxidation, and their immunoreactivities against R5 antibody were reduced. The information of their oxidative modifications offers a new alternative to be utilised in the elimination of prolamins for gluten-free applications.