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Tämä Pro Gradu tutkimus on osa Helsingin yliopiston Ruralia-instituutin toteuttamaa hanketta, jossa selvitetään EU:n nimisuojan käyttöä Suomessa. Tutkimusmenetelmänä on kvalitatiivinen ja työssä on käytetty teemahaastattelua. Tutkimuksessa on haastateltu suomalaisten nimisuojatuotteiden taustatahot ja haastatteluaineistosta tutkimusteemoiksi nousivat: hakuprosessi, yhteistyö toimijoiden kesken, nimisuoja kilpailuetuna sekä nimisuojan hyödyntäminen yleisesti nyt ja tulevaisuudessa. Tutkimustulostenperusteella EU:n nimisuojajärjestelmän tuomaa lisäarvoa elintarvikkeille ei ole Suomessa hyödynnetty toistaiseksi kovin paljon. Tällä hetkellä varsin harvat tuottajat Suomessa käyttävät nimisuojaa, vaikka se olisi mahdollista. Tietoisuus järjestelmästä on puutteellista eivätkä tuottajat ole saaneet nimisuojatuotteistaan korkeampaa hintaa. Tämä voi olla osasyy tuottajien kiinnostuksen vähäisyyteen, minkä lisäksi muita laatua osoittavia pakkausmerkintöjä on paljon. Vaikka nimisuojaa käyttäville suomalaisille tuottajille ei ole ollut taloudellista hyötyä merkin käytöstä, nähdään nimisuojat kuitenkin laatumerkkinä sekä mahdollisuutena erottautua kilpailijoista. Nimisuojan käyttäminen on vähentänyt tuotenimen väärinkäyttöä, mutta tehokkaampaa ja organisoidumpaa valvontajärjestelmää toivotaan kilpailuedun vahvistamiseksi. Tuottajilla ei ole resursseja markkinoida nimisuojaa, jonka edistämiseksi kaivataan enemmän kansallista panostusta niin markkinointiin kuin suomalaisen ruokakulttuurin ja ruoan arvostuksen kohottamiseen. Tuottajien puolelta toivotaan myös sujuvampaa hakuprosessia, sillä prosessi on kestänyt kaikilla hakijoilla vähintään neljä vuotta. Tulevaisuudessa nimisuojan nähdään osaltaan rakentavan alueen symbolista arvoa ja potentiaalisia suomalaisia nimisuojatuotteita uskotaan löytyvän esimerkiksi kala- ja leipätuoteryhmistä.

Vieraslajien on todettu olevan uhka erityisesti ympäristölle, mutta niillä on myös merkittäviä yhteiskunnallisia, sosiaalisia ja taloudellisia vaikutuksia. Vieraslajien haitallisten vaikutusten ja torjuntatöihin käytettävien resurssien on ennustettu kasvavan tulevaisuudessa huomattavasti. Tämän vuoksi Euroopan unionissa tarvitaan unionin laajuista säätelyä ja toimintaa haitallisia vieraslajeja koskien. Tässä työssä arvioidaan, kuinka EU:n vieraslajiasetus tulee vaikuttamaan Suomeen yhteiskunnallisesti ja ympäristöllisesti. Arviot on tehty asiantuntijahaastatteluiden perusteella. EU:n vieraslajiasetuksen myötä EU-jäsenmaat alkavat seurata EU:n vieraslajiluettelon lajien levinneisyyttä, estää niiden leviämistä ja hävittää niitä. On odotettavissa, että luetteloon ei tule Suomessa merkittäviä lajeja, mikä merkitsisi vähäisiä vaikutuksia Suomessa nykyiselle ympäristölle tai yhteiskunnallisille toiminnoille ja toimijoille. Luettelon sisällöstä riippuen vaikutukset voivat kuitenkin olla myös erittäin merkittävät, tai ne voivat lisääntyä tulevaisuudessa esimerkiksi uusien invaasioiden myötä. EU:n vieraslajiasetuksen voimaantuloa seuraavina vuosina sen toimeenpano vaatii toimivaltaisilta viranomaisilta lisääntyvää työpanosta liittyen lajien seurantoihin ja selvityksiin. Tämän lisäksi saattaa tulla torjuntaan ja hävittämiseen liittyviä velvoitteita, jotka ovat riippuvaisia siitä, kuinka moni EU:n vieraslajiluettelon lajeista koskettaa Suomea. Toimivaltaisia viranomaisia lukuun ottamatta on todennäköistä, että asetuksella ei ole merkittäviä suoria vaikutuksia seuraavien vuosien aikana Suomessa. Vaikutukset integroituvat muihin tehtäviin ja toimintoihin. On todennäköistä, että joidenkin kasvien kasvatus ja myynti joudutaan lopettamaan, mutta vaikutus on tuottajille, myyjille ja kuluttajille kokonaisuutena pieni ja väliaikainen. Korvaavia lajeja otetaan käyttöön tarvittaessa. Kansalaiset osallistuvat enemmän vieraslajien vapaaehtoiseen torjuntaan ja hävittämiseen. Tiedotus vieraslajiasiasta lisääntyy monella tavoin, sekä virallisten kanavien että esimerkiksi elinkeinoelämän ja järjestöjen kautta. Jos EU:n vieraslajiluettelossa on Suomessa merkittäviä lajeja, vaikutuksia kohdistuu viranomaisten ohella esimerkiksi yrittäjille tai maanomistajille. Kustannuksia voi syntyä muun muassa hävittämisestä ja poikkeuslupakäsittelyistä. Hyödyt taas ovat esimerkiksi ympäristöllisiä ja taloudellisia. Suurin hyöty tulee ennaltaehkäistyjen ja torjuttujen haittojen kautta. Ympäristö (esimerkiksi elinympäristöt ja lajit) on merkittävin hyötyjä asetuksesta: haittojen ennaltaehkäisyllä torjutaan erityisesti monimuotoisuuden heikentymistä. Torjunnan avulla myös ekosysteemipalvelut säilyvät, ja kansalaiset hyötyvät torjutuista haitoista esimerkiksi elinkeinoelämän ja terveyden suhteen. Välillisesti hyödytään siitä, että muissa maissa tehdyt toimenpiteet vähentävät meihin kohdistuvia vieraslajiriskejä. Lisäksi tietoisuus ongelmasta ja valistus Suomessa ja ulkomailla vähentävät leviämisriskejä sekä lisäävät torjuntaa ja hävittämistä. Ajallisesti suurimmat varmat vaikutukset tulevat viiden vuoden sisällä EU:n vieraslajiasetuksen voimaantulosta. Nämä koostuvat valtion organisaatioiden valvonta- ja seurantatoimenpiteistä. Myös kokonaisuutena pieniä ja väliaikaisia haittoja voi kohdistua elinkeinoelämälle, erityisesti puutarha-alalle. Tämän lisäksi voi tulla vähäisiä hävittämis- ja torjuntatoimia. Suurimmat vaikutukset sekä ympäristöllisesti että yhteiskunnallisesti voidaan nähdä torjuttujen haittavaikutusten kautta. Yleensä etukäteen tehty torjunta on halvempaa ja helpompaa, minkä lisäksi lajeja ei välttämättä edes pystytä poistamaan enää leviämisen jälkeen. Näiden syiden vuoksi ennaltaehkäisty on erittäin tärkeää.

The European spruce bark beetle (Ips typographus L.) is one of the most concerning forest pest to Norway spruce (Picea abies Karst) forests in Central and Northern Europe. The species has been fairly well studied, especially after the storm Gudrun in Sweden in 2005 and some widespread damages in spruce forests in Central Europe in the recent years. I. typographus is a highly opportunistic species and a population can expand drastically if favorable conditions, mainly weakened or windthrown trees and suitable temperatures, are met. After reproducing on these favorable conditions, the species may have reached a population size so large that it is capable of infesting and killing even standing, healthy trees in the nearby areas. Damages caused to standing trees are the most problematic as there losses in economic revenue, carbon storage and, in some cases, ecosystem services. In Finland, the problems caused by I. typographus have fortunately been localized, but with climate change increasing extreme weather patterns, the problems are likely to increase in the future, which is why the species, as well as other potentially problematic species should be studied as intensively as possible, so that informed decisions can be made in case of a windthrown or other pest inducing event was to occur. After the Asta-storm in 2010, some 9000 cubic meters of wood had fallen in Ruokolahti municipality. Quickly after the storm, two areas (Viitalampi and Paajasensalo) were conserved under METSO-program and no commercial harvests were done in the sites, and permissions for bark beetle studies were given to increase knowledge especially on I. typographus. The two sites were mostly harvest-ready or mature Norway spruce dominated forests. Field work began in 2011 in Viitalampi, and new study plots were established in Viitalampi and Paajasensalo in subsequent years. To study bark beetle population dynamics, a total of 140 fallen trees were studied. From each tree diameters were measured at base (d0), breast-height (d1.3) and ten meters (d10), as well as full height of the tree. An entomological analysis was done in two-meter intervals (from 0m to 10m) to establish changes of bark beetle activity on a stem. A 25cmx50cm piece of bark was analyzed on each height, from which new and old entry and exit holes and different bark beetle maternal galleries were calculated. This was done on a different tree each year on a plot, although it was done only to trees which had root connections to the soil and were thus deemed alive and potential breeding and feeding ground for bark beetles. In addition, National Land Survey of Finland provided high resolution aerial images from the study sites so that the surrounding areas and conditions could be taken into account in studying bark beetle population dynamics. From the aerial images, a number of fallen and standing trees were calculated on a 25-meter zone around the center of a plot, as well as the size of the closest windthrown gap and the plot’s distance to that gap. The analysis of each measured factors’ significance to I. typographus maternal gallery density (m²) were calculated with Generalized Linear Models. Yearly changes in I. typographus occurrence were expectedly high and complied with observations in previous studies. In addition, there was a significance found in gap size and distance to gap in 2013, which could be explained with population behavior in previous years and with the exhaustion of larger and more nearby resources in the beginning of population build-up. Extensive field work combined with aerial images and other spatial tools are important in understanding the complexity of bark beetle, or any other forest pest, population dynamics. As extreme weather patterns increase, so do the damages caused by biotic agents, such as the European spruce bark beetle. Future studies are needed to educate and prepare forest owners for forest disturbances, be it from the viewpoint of commercial forestry, carbon storage or biodiversity conservation.

As an alternative to complex 3D-modelling of structure, the canopy spectral invariants are a novel concept to describe the average behavior of photons in a vegetated canopy. The probabilities of canopy absorption and scattering can be summarized with only three parameters (?L, p and R): The green leaf single scattering albedo (?L) describes the wavelength-dependent probabilities of absorption for each time a photon interacts with a leaf. In the event of scattering, a photon’s probabilities of reinteraction (photon recollision probability p) and exiting the canopy in a given direction (directional escape factor R) can be described as independent of wavelength; as the size of the scattering elements is considerably larger than wavelengths in the shortwave radiation budget, p and R depend only upon the structural arrangement of the scattering elements. In this work, a recently published (2011) approach to infer remotely sensed (spaceborne) hyperspectral imagery (also referred to as imaging spectroscopy data) based on the canopy spectral invariants was tested in a case study on southern boreal forests at full leaf development. An atmospherically corrected image taken with the Hyperion imaging spectrometer aboard the National Aeronautics and Space Administration’s (NASA) Earth Observing-1 (EO-1) spacecraft was interpreted with a single reference transformed green leaf scattering albedo. Transforming of a traditionally defined leaf albedo means correcting the measurements for the effect of surface reflectance, resulting in probabilities of leaf scattering and absorption given a photon interacts with the leaf internal constituents. Utilizing such transformed albedo as reference results in reference (canopy) spectral invariants describing the relative difference between the reference and the scattering properties of (theoretical) mean leaves at the scale of inference (pixel). The results of the study are parallel to those of previously published and ongoing research: In essence, even while the individual parameters p and R depend on the reference, the ratio R/(1–p) (directional escape factor to total escape probability) was found practically independent of the selection of the reference, thus implicating a possibility to develop a physically-based algorithm to infer hyperspectral imagery in vegetated areas. Moreover, the reference (canopy) spectral invariants were found as highly applicable in retrieval of forest structural properties such as dominant forest type (broadleaved, coniferous, mixed) and a quantitative estimate of the broadleaf fraction of a forest area.

Urban development can generate substantial greenhouse gas emissions through deforestation and land-use change. This underscores the urgency for effective climate change mitigation strategies. This thesis scrutinizes the feasibility of local forest conservation, specifically at a municipal level, as a strategy to compensate for losses in carbon storage and reductions in carbon sequestration linked to land-use changes. The study uses a case study approach, focusing on a proposed development of a data centre in Espoo's Hepokorvenkallio area in Finland. The proposed construction site spans 19 hectares and consists mainly of a forest earmarked for clearance. As a possible countermeasure, the city is considering conserving the nearby Hynkänlampi forest, covering an area of 79 hectares. The study leverages empirical modelling via long-term forest simulations to assess carbon storage and sequestration dynamics for these two sites under different scenarios. For Hepokorvenkallio, the analysis compares a construction scenario with continued forest management. The findings suggest that land clearing necessary for construction could result in a carbon storage loss of 15,820 tCO2 over a century, thereby indicating a need for compensatory measures. For Hynkänlampi, the modelled forecasts propose that a conserved forest could theoretically offset these losses. However, the offset capacity is notably influenced by the chosen discount rates applied to the carbon storage values. While simulation results for Hynkänlampi indicate a buffer capacity exceeding 10,000 tCO2 with a 0% discount rate, this buffer decreases to approximately 5,800 tCO2 with a 1% discount rate. Beyond the numerical aspects of carbon accounting, the thesis also addresses existing uncertainties and the prevailing regulatory landscape for carbon accounting procedures. Considering Finland's current legal and regulatory framework, the interpretation of this study posits that Espoo could view forest conservation at Hynkänlampi as a viable carbon offsetting measure to mitigate the impacts of land clearing at Hepokorvenkallio.

The intensification of milk production has increased the size of farms and reduced the use of pastures in recent decades worldwide. The interest in farm animal welfare and the climate impact of dairy products is growing. Offering dairy cows full-time pasture access has declined, but there are other possibilities to provide outdoor access for dairy cows. The aim of this study was to evaluate the effects of two outdoor management systems on the feeding behaviors and productivity of lactating dairy cows. This study was conducted at the University of Helsinki research barn’s freestall and adjacent pastureland in Viikki. The experimental design was a replicated 3x3 Latin square. Twenty-seven Ayrshire cows were divided into nine squares. During the experiment, cows went through three 21-day periods. Cows in squares were assigned to the following treatments: partial access to pasture with sufficient forage for grazing (pasture), partial access to pasture without grazeable forage (paddock), and indoor confinement. Milk yield and ECM were greater in the paddock than in the pasture treatment. Part-time grazing led to an energy deficit because pasture cows had the lowest milk yield. Outdoor access reduced the content of saturated fatty acids and increased the content of monounsaturated fatty acids in milk. Pasture cows spent 30% of their outdoor time eating and paddock cows 27%. Paddock cows used 15% of their total eating time eating TMR and 12% attempting to graze. Pasture cows ruminated the most between 12:00 a.m. and 6:00 p.m., and indoor cows ruminated more than outdoor cows between 7:00 a.m. and 5:00 p.m. Outdoor cows ruminated more than indoor cows from 6:00 p.m. to 11:00 p.m. The cows on the pasture produced less methane per day than the paddock cows. However, methane production in g/kg ECM was not different among groups. According to this study, grazing seems to be a motivating activity for dairy cows. Providing TMR outdoors can be beneficial for the welfare of dairy cows because it enables a choice between feeds and helps to maintain milk yields. Partial outdoor access changed the diurnal pattern of rumination but not the total time used for rumination. There were no differences in milk’s polyunsaturated fatty acid contents between treatments, but eating fresh grass modified the cow’s milk to be healthier.

Field work is needed to obtain reliable estimates when forest inventories are carried out. Field measurements traditionally have been the main source of information for inventories. But nowadays, also remotely sensed data collected using active or passive sensors mounted on satellite and aerial platforms are used to help in the estimation of forest parameters. Although the use of remotely sensed data is of great help in forest inventories, field data still plays a very important role as reference data, for results calibration and accuracy assessments. Considering that time and budget required for field work are generally some of the main concerns in forest inventory planning, the development of faster, cheaper, simpler, more accurate or more reliable field inventory methods and tools is a topic of great interest. TrestimaTM is a forest inventory system based in the interpretation of images taken with a mobilephone. Its accuracy and efficiency in estimating forest parameters was studied using sample plots in Russian. A total of 156 field plots were measured. The forest parameters measured were: the plot basal area and sample trees’ diameters and heights. The data collected with Trestima was meant to replicate a typical relascope sample plot inventory (variable radius plot inventory). Measurements obtained using traditional tools were used as reference data. The data collected for the inventory included plots at forest stands with different structures: from young to mature stands; and mixed stands to stands dominated by different species (most often Norway Spruce, Picea abies, (L.) H. Karst). The plots’ basal areas ranged from 7 to 62 m2/ha, the tree diameters from 3 to 60 cm and the tree heights from 3 to 35 m. The time used to measure the plots with the Trestima and the reference methods were collected. The data for each forest variable and the time invested in taking the measurements were organized as paired samples and compared using the statistic estimators of bias and RMSE, as the paired Student's t-test. Compared to the reference measurements, Trestima underestimated the basal area with a bias of 1.2 m2/ha (3.7%), but the differences were not statistically significant. In mixed stands, Trestima overestimated spruce basal area (bias of 13.9%), but for spruce dominated stands underestimated it (bias of 4.9%). Trestima overestimated tree diameters with a root mean squared error (RMSE) from 5.5 to 7.9%, depending on the tree species. but underestimated tree heights with an average RMSE of 3.7m (17.5%). The Trestima sample plot measurements were done faster than with traditional tools. Trestima measurements were in average 1.6 minutes (14.8%) faster. The Trestima system provided results comparable to the reference method for all the measured forest parameters. The worse results were obtained for the measurement of the tree heights. The interpretation of the results for the basal area, indicated that the system could benefit from taking into consideration stand structure, especially for species specific estimations. Trestima provided faster measurements of the forest parameters. One important advantage, is that Trestima produces automatically geographically referenced data, which can be used during later analysis, for example, interpretation of remotely sensed data or forest planning.

Late blight, caused by Phytophthora infestans (Mont.) de Bary, is considered the most devastating disease in potato (Solanum tuberosum L.) production worldwide. Control methods involve mostly the use of fungicides, which are costly and are under political pressure for reduction in Europe. Potatoes from the major potato cultivar in Sweden, King Edward, previously stacked with three resistance (R) genes (RB, Rpi-blb2 and Rpi-vnt1.1) were tested in a local Swedish field, with spontaneous P. infestans infection over three seasons to evaluate the effectiveness and stability of the resistance on leaves. In addition, testing of resistance was done in both in leaves and tubers. Field results demonstrated that the 3R stacked into the cultivar King Edward, showed practically full resistance to infections of P. infestans, with no difference to fungicide use. Moreover, the resistance was effective in both leaves and tubers. The results reveal the 3R potatoes offer a functional field resistance, that could, alone, reduce the total use of fungicides in agriculture by several percent in Sweden, in an event of modifications in the EU legislation.

The Oxford Nanopore MinION is a third generation sequencer utilizing nanopore sequencing technology. The nanopore sequencing method allows sequencing of either DNA or RNA strands as they pass through the membrane-embedded nanopores. By measuring the corresponding fluctuations in the ion flow passing through the nanopore the passing strands can be sequenced directly without additional second-hand reactions or measurements. The MinION sequencing has very distinctly different characteristics compared to the market leaders of the sequencing field. The small form factor of the device further helps it to separate itself from the other alternatives. However, the technology has only been on the market for a very short time and thus very little golden standards regarding its capabilities or usage have been established. This thesis describes our experiences testing the capabilities of the MinION sequencer both before its commercial release as a part of a special early access program, as well as our continued experiments with the device following its commercial launch. The main results of this study include successfully sequencing and aligning E.coli and human gDNA samples to their respective reference genomes. Using our sequencing and analysis pipeline specifically tuned to the MinION we were able to sequence the entire E.coli genome on a single MinION flow cell with an average depth of around 180. Over the course of the thesis project the MinION sequencing protocol was evaluated and optimized in order to determine whether it has the potential to achieve our ultimate goal of reliably sequencing the previously inaccessible genomic regions of the human genome. The possibility of augmenting the sequencing protocol by adding the pre-sequencing target enrichment was also explored. Ultimately we were able to confirm that the MinION sequencer can be used to sequence long DNA fragments from a multitude of sample types. The majority of the produced reads could successfully be aligned against a reference genome. However, the limited yield and sequencing quality of a single experiment does limit the applicability of the method for more complicated genomic studies. These issues can be addressed with various techniques, chiefly target enrichment, but adapting such methods into the sequencing pipeline has its own challenges.