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(2014)Enterococci is a group of gram positive bacteria part of human intestinal flora. While generally harmless, several species of the group are known to cause severe infections in humans, including bloodstream infections leading to sepsis. Since Enterococci are naturally resistant to many antibiotics, the use of glycopeptides, considered a”last resort” drugs, is common in treatment of enterococcal infections. In recent years, however, the emergence of glycopeptide resistant Enterococci (GRE) has been an increasing concern for clinics and microbiology laboratories around the world, creating a need for fast and accurate screening tests differentiating the glycopeptide resistant Enterococcus strains from the non-resistant ones. In this study, a combined PCR and microarray hybridization based method for identification of the clinically most prevalent GRE was established as a part of commercial sepsis diagnostic test called Prove-it™ Sepsis. Already identifying the most common Enterococcus species (E.faecium and E.faecalis), the detection of glycopeptide resistance causing ligase genes vanA and vanB and species level identification of intrinsically glycopeptide resistant E.gallinarum and E.casseliflavus were added as part of the the test. Primers were designed for sequencing vanA and vanB genes and multiple strains, provided by a Finnish clinical laboratory Huslab, were sequenced. Sequence regions unique to these genes were identified according to sequence alignment data containing the sequenced gene regions and other relevant sequences found in public sequence databases. Based on these data, primers were designed for the amplification of the selected gene regions. For identification of the amplified gene regions, a set of hybridization probes were designed and printed on microarray. In addition, probes for identifying E.casseliflavus and E.gallinarum were designed based on sequence aligment data gathered from Mobidiag Ltd. private biobank. The identification of these species was based on topoisomerase encoding gyrB gene amplified by the Prove-it™ Sepsis broad range PCR. Several primers for the amplification of vanA and vanB genes were designed and one primer pair for each was selected to be integrated to the Prove-it™ Sepsis multiplex-PCR. Similarily, multiple hybridization probes were designed for detecting vanA, vanB, E.casseliflavus and E. gallinarum. Four probes for each target gene region were selected to be integrated to the commercial test. With this modified test, 12 pure culture samples of clinical origin were tested and the results were compared to the ones provided by the laboratory of clinical microbiology of Hôspital de bicêtre (Paris, France). Results provided by the modified PCR and microarray test were identical to the reference results in 11 out of 12 cases.
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(2019)Jääsalaattia (Lactuca sativa var. crispa L.) tuotetaan ympärivuotisesti kasvihuoneessa ja se on kuluttajien keskuudessa suosittu lehtivihannes. Jääsalaatti kerää monien muiden lehtivihannesten tapaan nitraattia ja sen nitraattipitoisuudet voivat nousta melko suuriksikin. Jääsalaatin nitraattipitoisuuteen vaikuttavat useat eri tekijät, kuten laji, lajike, lannoitustaso ja valon intensiteetti. Tehokkailla nitraattipitoisuuden hallintakeinoilla voidaan parantaa tuottajan mahdollisuuksia vaikuttaa sadon laatuun. Valtaosa ravinnon mukana saatavasta nitraatista on peräisin lehtivihanneksista. Euroopan unioni on asettanut katteen alla kasvatetun salaatin nitraattipitoisuudelle talvi- ja kesäkauden raja-arvot. Nitraatti on ihmisen terveydelle haitallinen yhdiste, sillä osa siitä muuttuu elimistössä nitriitiksi, mikä kasvattaa etenkin pienten lasten methemoglobinemian riskiä. Glysiinibetaiini on osmolyytti ja solun metabolian kanssa yhteensopiva yhdiste. Monet viljelykasvit syntetisoivat glysiinibetaiinia vasteena abioottisille stresseille ja se parantaa kasvien stressinkestävyyttä myös eksogeenisesti annettuna. Glysiinibetaiinia saadaan ravinnon mukana esimerkiksi viljatuotteissa ja se on ihmisille turvallinen yhdiste, jota voidaan käyttää myös ravintolisänä. Glysiinibetaiinia eristetään muun muassa sokerijuurikkaan melassista ja sitä voidaan käyttää orgaanisena lannoitteena tai kasvunedistäjänä kasvintuotannossa. Tämän tutkimuksen tavoitteena oli selvittää glysiinibetaiinin käyttömahdollisuuksia jääsalaatin tuotannon edistäjänä. Kasvihuonekokeessa seitsemän vuorokautta kestänyt glysiinibetaiinikäsittely aloitettiin jääsalaattien ollessa 29 vuorokauden ikäisiä. Glysiinibetaiinikäsittelyjen pitoisuudet olivat 0, 1, 7,5 ja 15 mM. Jääsalaatin nitraattipitoisuus, glysiinibetaiinipitoisuus sekä tuore- ja kuivamassa määritettiin 24, 29, 36, 41 ja 49 vuorokauden ikäisistä kasveista. Tutkimus toteutettiin kiertovesiviljelyjärjestelmässä ja glysiinibetaiinikäsittely annettiin ravinneliuoksessa. Jääsalaatit ottivat eksogeenisesti annettua glysiinibetaiinia. Glysiinibetaiinikäsittely pienensi jääsalaatin nitraattipitoisuutta seitsemän vuorokauden käsittelyn jälkeen merkitsevästi kontrolliin verrattuna ja alenema oli suoraan verrannollinen käsittelyn pitoisuuteen. Lisäksi glysiinibetaiinikäsittely pienensi jääsalaatin tuorepainoa ja suurensi kuiva-ainepitoisuutta. Määrityksissä myös jääsalaatin glysiinibetaiinipitoisuuden havaittiin olevan suoraan verrannollinen käsittelyn pitoisuuteen.
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(2018)Tämä tutkimus selvittää Googlen roolia maatalousyrittäjän ostopäätösprosessissa. Lisäksi tutkimus keskittyy siihen, miten maatalousyrittäjä suhtautuu Googlen esittämään hakusanamainontaan. Tutkimuksen teoreettinen tausta rakentuu aikaisempaan tutkimukseen organisaatiomarkkinoista, hakukonemarkkinoinnista ja maatalousyrittäjän ostokäyttäytymismallista. Teorian tavoitteena oli muodostaa käsitys siitä, mitä aikaisempi tutkimus kertoo tutkimusongelmaan liittyvistä asiakokonaisuuksista. Tutkimuksessa Google nähdään hakukoneena. Tutkimus toteutettiin haastattelemalla seitsemää maatalousyrittäjää vuonna 2018. Tutkimus on luonteeltaan kvalitatiivinen tutkimus. Aineistonkeruumenetelminä käytettiin puolistrukturoitua haastattelua ja havainnointia. Aineiston analyysi tapahtui sisällönanalyysin keinoin. Ostopäätösprosessia tutkittiin teorialähtöisesti. Tässä vaiheessa hyödynnettiin Websterin ja Windin (1972) luomaa kuvausta ostopäätösprosessin kulusta. Hakusanamainontaan liittyvät asiat analysoitiin aineistolähtöisesti. Analyysiä tuettiin muilla lähteillä ja aineistosta nostetuilla suorilla lainauksilla. Tarpeita nähtiin syntyvän Googlen välityksellä heikosti, mutta se koettiin mahdolliseksi. Tarpeita syntyi erityisesti hakusanamainonnan kautta. Eri ratkaisujen laatiminen Googlen avulla liitettiin taustainformaation saamiseen ja kansainvälistymiseen. Googlella nähtiin olevan eniten hyötyä tilanteissa, joissa ei ole kiire. Googlen käytön koettiin vaativan omaa ymmärrystä haetusta asiasta. Vaihtoehtojen haussa korostui tunnettavuus. Tämä aiheutti ankkuroitumisen tuttuun vaihtoehtoon. Vaihtoehtojen haku keskittyi usein nimen, sijainnin ja internetosoitteen löytymiseen. Kuvahaun merkitys korostui vaihtoehtojen nimien selvittämisessä. Vaihtoehtojen arviointi Googlessa perustui aineellisiin ja aineettomiin ominaisuuksiin. Arvioinnissa keskityttiin erityisesti hintaan, sijaintiin, luotettavuuteen ja tunnettavuuteen. Uuden toimittajan valinta Googlen välityksellä nähtiin mahdollisena, mutta vaikeana. Maatalousyrittäjät pyrkivät käyttäytymismalliin, missä Googlen mainoksia ei hyödynnetä osana hakua. Googlen hakusanamainontaan suhtauduttiin negatiivisesti maatalousyrittäjien keskuudessa. Maatalousyrittäjät käyttivät kuitenkin paljon Googlen hakusanamainonnan hakutuloksia. Googlen hakusanamainonnan koettiin aiheuttavan pettymyksiä useammin kuin luonnollisten hakutulosten. Tutkimuksen johtopäätöksenä voidaan todeta, että tällä hetkellä Googlella hakukoneena on merkittävä rooli maatalousyrittäjän ostopäätösprosessissa. Maatalousyrittäjän suhtautuminen Googlen hakusanamainontaan on kielteistä, mutta he hyödyntävät sitä merkittävissä määrin.
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(2015)This thesis aims to assess the state and development of beekeeping in Uruguay. Uruguay exports more than 90% of its honey and supplies regularly to the demanding markets in the EU and the US. As marginalized actors in the global honey chain, the beekeepers' livelihoods are largely dependent on the shifts of globalization, predominantly on the patterns of global economy. Proliferation of voluntary certification schemes such as Fairtrade International and European Union Organic Farming have become evident features of these patterns. Adoption of voluntary certification schemes has impacted particularly the development trajectories of smallholders, which is why particular attention in this thesis was laid on them. It was, however, quickly understood the development is dependent on several factors on different levels. To conceptualize these levels, value chain governance and voluntary certification schemes in them were seen shaping the livelihood outcomes of the smallholders. Combining governance and horizontal livelihood approaches, which represents the main innovation of this thesis, was used to identify action points and upgrading strategies feasible for the beekeepers as actors engaged in the global honey chain. In addition, this thesis further highlights the context of beekeeping as a livelihood, honey as a commodity with certain features and market dynamics, as well as Uruguay as the main geographical scope. Research methods were qualitative. Semi-structured interviews were conducted in 2014 with four different respondent groups along the global honey chain: importers of honey in the EU; representatives of local institutions and export agencies in Uruguay; and the beekeepers themselves, which of some were organized in cooperatives. From the collected data, the development trajectories were analyzed deductively to identify the viable strategies to improve sustainable livelihood outcomes. Based on results, the global honey chain was found buyer-driven since the buyers bear the most powerful role. The structure replicates features of market and captive types of governance, suggesting there is a high degree of power asymmetry and coordination. Higher coordination, however, favors successful upgrading. By identifying the activities performed by actors in the chain, the action point was found in the production node due to the recent increase in activities. High costs of inputs and low margins throughout the chain were observed, particularly in the export node. Beekeepers' baseline conditions were determined as access to livelihood assets, which were found generally weak. State of the fundamental aspect of beekeeping, access to natural assets, was found alarming. The decreased floral resources in Uruguay are due to the rapid proliferation of changes in land use, accelerated by the main vulnerability causing shocks in production and with implications on prices: the climate variability. A key finding, however, was that the proliferation of Eucalyptus grandis in Uruguay has created a dependency by compensating the losses in production based on other flowerings. Furthermore, the emergence of pests has brought risk of losing colonies and increasing costs in treatment and prevention. Natural assets set the main constraint over sustainability of beekeeping in Uruguay, but possibilities to compensate smallholders was found among social assets, which clearly were not optimized at their current levels. This notion largely represents the main conclusion in this thesis: horizontal contractualization of the beekeepers through collective action is the only strategy with a reasonable balance between revenues and risks. In all other scenarios, the risks are likely to become unbearable, unless an external agent would be willing to guarantee the risks up to some point to initiate the process. Collective action was found as a precondition of vertical contractualization, which could include affiliation in voluntary certification schemes. Fairtrade International was predominantly found as a more attractive scheme, but could in this context benefit only a large cooperative with already good resources. Affiliation in a certification scheme, however, would not remove the main constraints faced by the sector in Uruguay, which are the decreasing production per hive and the costs running relatively faster than the prices received, resulting in a decreasing profitability. Whereas more beekeepers are excluded from the chain, the ones remaining practice beekeeping largely based on love and tradition. Future research is suggested to take a more sophisticated approach to cost-benefit analyses to support further decision-making on the level of the beekeepers, as well as on the level of policy-makers. In addition, prospective approaches to develop and assess the potential of systems such as payments for ecosystem services in the context of beekeeping are highly recommended.
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(2020)Intercropping is an old agricultural practise to produce food and could be an interesting option to be utilized today. Use of legumes in mixtures can be a way to produce food more sustainably and minimize negative environmental impacts of current food production. Cultivation area of legumes have declined over recent years, due instability in yields and problems with pests and diseases. Intercropped systems can optimize use of land recourses and reduce issues with pest and disease. Furthermore, legumes could provide a more sustainable source for nitrogen than fossil fuels and more options for both feed and food production, especially for organic farming. Intercropping could also benefit diversity and add more options in crop rotations. In this field experiment intercropping with different mixtures of legumes and other non-legume crops were studied. This experiment by Swedish University of Agricultural Sciences was a part of the project Legumes for the agriculture of tomorrow (LEGATO). Project purpose was to promote and find solutions for increased and sustainable production of grain legumes in Europe. The main objectives of this thesis were to compare different crop mixtures and find benefits with intercropping, this thesis focused on peas and faba bean. Does intercropping add yield potential and can it have benefits for yield stability or pest damage. Results showed that intercropping did not benefit pea yields, but instead barley yields. Faba bean Gloria did benefit from intercropping, as did cereals. Yields indicate that more could be produced on the same area of land. Pest damage by pea moth (Cydia nigricana) had some statistical differences between treatments, but there were no similar effects on damage on faba bean by Broad bean weevil (Bruchus rufimanus).
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(2017)Bacteria can communicate with each other using phenomenon called quorum sensing (QS). In QS the bacteria produce and release small signaling molecules which they use to communicate. Bacteria use QS in situations where it is beneficial to act on population level. QS has an important role e.g. in the formation of virulence factors and biofilms. There are several different QS systems. Gram-negative bacteria use i.a AI-1, AI-2, AI-3, and CAI-1 systems to communicate. All QS systems are based on the accumulation of signaling molecules when the bacterial concentration increases. When the concentration of signal molecules reaches the threshold level, the system activates. The activation of the signaling system then activates the expression of the genes controlled by the QS system. AI-2 signaling is assumed to be universal. That means that bacteria can use AI-2 signaling system in interspecies communication. In AI-2 signaling bacteria produce and release 4,5-dihydroxy-2,3-pentanedione (DPD) which works as a signaling molecule in the AI-2 system. Escherichia coli and Salmonella typhimurium use an ATP binding cassette ABC-type transporter to transport DPD molecules into the cell where LsrK kinase phosphorylates the DPD molecules. The phosphorylated DPD molecules bind to the LsrR regulator protein which acts as a suppressor of the lsr operon. The binding of the phosphorylated DPD molecules releases the LsrR from the lsr promoter region enabling the expression of the lsr genes. In Vibrio harveyi the surface proteins LuxP and LuxQ form a protein complex that recognizes DPD molecules. When the DPD concentration increases, the LuxPQ complex transform from kinase to phosphatase and the reaction chain, where LuxU phosphate transfer protein transfers a phosphate group from LuxO regulator protein, activates. The dephosphorylation of of LuxO releases the LuxR transcription factor and activates the expression of QS controlled genes. The aim of this thesis was to optimize two assays which can be used to screen for compounds that disrupt AI-2 signaling. The first assay was a bioreporter based assay where V. harveyi BB120 bioreporter strain was used. The second assay was protein based LsrK assay where the LsrK activity was monitored using assay kit which measures the concentration of ATP or ADP. The concentrations of bacteria, LsrK, and DPD used in the assays were optimized. The dimethyl sulfoxide (DMSO) tolerance of both assays were tested, the stability of the kits used in the LsrK assays was tested and the reaction buffer for the LsrK assay was selected from the two tested buffer options. The selected bacterial concentration for the V. harveyi BB120 assay was 100000 CFU/ml and DPD concentration 1 µM. The selected enzyme concentration for the LsrK assay was 300 nM and DPD concentration 300 µM. The tested DMSO concentrations had no effect on the kit measuring ATP but the highest concentrations tested had a small effect on the kit measuring ADP. A buffer containing triethanolamine, magnesium chloride, and bovine serum albumin was selected as the reaction buffer for the LsrK assay. Using the optimized LsrK assay, a screening was performed for a synthesized compound library. None of the compounds showed any LsrK inhibiting activity. The optimized assay was also used to make dose-response experiment to one LsrK inhibiting compound, named FIMM000642, which was found in a separate screening. The FIMM000642 dose-response as-say was also done against glycerol kinase to see if the compound would inhibit another enzyme from the same protein family or if the compound was a specific inhibitor to LsrK. FIMM000642 inhibited also the activity of glycerol kinase.
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(2018)The concept of ecological management can be seen tackling the relationship of agriculture and environment, not only from the perspective of limiting the negative effects of farming practices, but also promoting positive actions. This notion of managing and maintaining, rather than leaving alone, is currently in the core of biodiversity promotion in agricultural landscapes in Europe. The focus of this thesis are the perceptions Finnish agri-environmental actors have regarding ecological management innovation stemming from the grassroots. In this thesis I assess how i) Finnish agri-environmental actors perceive grassroots innovation, ii) weigh its barriers and enabling factors, as well as iii) envision further needs regarding these innovations. The study is based on a mixed-methods approach using both qualitative and quantitative data; a questionnaire and two focus group discussions conducted during a two-day seminar “Managing Nature - working together” 29.11.-30.11.2016 in Turku. The study was conducted in co-operation with the Finnish Environment Institute (SYKE), University of Helsinki Faculty of Agriculture and Forestry and a Horizon2020 project HNV-Link. I approached the research questions using an iterative approach, and my analysis is guided by Grounded Theory in constant comparative analysis and generating theory. The results indicate that Finnish agricultural actors acknowledge the heterogeneous nature of grassroots actors in agricultural areas. However, several common attributes are linked to innovation stemming from the grassroots such as practical, economic and local. Currently bureaucracy, lack of cooperation and the changes and challenges in the socio-cultural environment of grassroots hinder ecological management grassroots innovation. Finnish agri-environmental actors acknowledge that the challenges biodiversity in agricultural areas face, are of such magnitude that the need is rather to expand, not narrow down the actor-base for innovation.
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(2015)This study provides the green (the share of rain water in crop production) and blue (the share of surface and groundwater in crop production) water footprint (WF) of four annual crops in Finland and five annual crops in Iran for the growing period 2007?2012. It aims to present more recent water footprint accounting on annual crops in this study. Due to the large scale water footprint accounting (country level), the calculation for grey water footprint was omitted from this study. The green and blue water footprints of barley, maize, oilseed rape, soybeans and wheat for Iran and barley, oats, oilseed rape, and wheat for Finland were calculated over the annual growing period 2007 to 2012. Crops were selected upon the availability of crop production in each country. WF values were estimated based on crop water use (CWU) and crop yield, where CWU was estimated upon the accumulative ET over the growing season of the crops. For daily evapotranspiration values AQUACROP model was used. For running the AQUACROP model, different parameters were needed such as climatic parameters (including minimum and maximum temperature, rainfall and potential evapotranspiration), soil type, land management, irrigation practice, groundwater and initial condition for sowing, sowing and harvesting dates. This data were mined from databases. Due to the fact that crop production in Finland is rain-fed, only green WF of the selected crops were calculated for Finland. In Finland oilseed rape had the highest average green water footprint per ton of production, which was 2471 m^3 t¯¹yr¯^1 and it was followed by oats (1036 m^3 t¯¹yr¯^1), wheat (944? m?^3 t¯¹yr¯^1), and barley (838? m?^3 t¯¹yr¯^1). Considering the annual crop production, the average total green water footprint of selected crops was 3669 Mm^3 yr¯^1 in Finland. Water saving through crop trade was estimated -294 Mm^3 yr¯^1. The negative saving water amount showed the virtual water loss through crop trade of selected crops in Finland. The highest export crop in Finland was oats during 2007?2012. In Iran the major share of annual crop production comes from irrigated crop lands and that shows the importance of blue water footprint accounting beside green water footprint. The sum of green and blue water footprints of the growing crops in Iran was considered as water footprint of the crops. Water footprint per ton of crops in Iran increased from maize (696 m^3 t¯¹yr¯^1), wheat (1235 m^3 t¯¹yr¯^1), barley (1350 m^3 t¯¹yr¯^1), soybeans (2210 m^3 t¯¹yr¯^1) to oilseed rape (3503 m^3 t¯¹yr¯^1). Total average water footprint of the selected crops in Iran considering their production in the country was estimated 22816? Mm?^3 yr¯^1. Regarding the crop trade balances in Iran, the country saved 8902? Mm?^3 yr¯^1 water by importing the crops. Wheat was the major import crop during 2007?2012. WF can be a strong tool for assessing the consumptive water use of the agricultural systems in place and time according to different agricultural and water managements. It can bring a ground for comparing the production sites for certain crops or products considering the lower WF of the produced items. This study aimed at producing recent calculations of water footprint of crops in Finland and Iran, using local data.
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(2017)The global trends have been guiding hotels to move to a green direction for years, and nowadays hotels are expected to maintain sustainability programs as a regular feature of their business. As the topic is receiving much more attention in hospitality, it is important to consider guests reactions to sustainable practices in hotels. In addition, customer participation is important of the implementation of green practices in hotels. The objective of this study is to investigate consumers’ general attitudes toward green hotels. Specifically, the study seeks to demonstrate how consumers evaluate green practices in hotels and how a hotel’s green image influences consumer decision- making. According to the findings of this thesis, consumers are willing to stay in green hotels and prefer green hotels. Survey study results demonstrate that respondents have positive or very positive attitudes toward green hotel image. This points out that green attributes can bring more value to the brand, and differentiate it from other hotel brands. Based on the literature review and survey study, this thesis distinguished three common green hotel marketing benefits, which are new market opportunities, green brand benefits, and competitive advantage which is achieved by product enhancement. Thus, this thesis demonstrates that there is market for green hotels and the best way to attract customers is to create green hotel brands that emphasize good and consistent value of the green hotel.
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(2017)Plenty of CO2 is commonly emitted from cultivated peat soils and substantial N2O emissions have occasionally been measured from acid sulphate soils. The factors limiting the emission of CO2 and N2O from the different layers of organic acid sulphate soil in Pärnänsuo were studied by aerobic and anaerobic incubation experiments. Two topsoil peat layers (upper and lower) and two mineral soil layers (upper and lower) were investigated. An aerobic experiment was carried out to see the emission of CO2 and N2O after application of glucose and ammonium, at two different temperatures (5o and 20o C). The water content of the soils was adjusted to 60% water- filled pore space (WFPS). Anaerobic experiment was carried out to assess the denitrification potential of different layers and the effect of glucose and nitrate alone and in combination as at 20oC using the acetylene inhibition technique. The lower peat layer exhibited more CO2 emission comparing to upper peat in the aerobic experiment. Additionally, in both peat layers and upper mineral soil layer, CO2 emission was increased exceedingly after glucose application. In the anaerobic experiment, potential denitrification from the upper peat was significantly higher than from other soil layers. Besides, the soil layers responded differently to C and N application. N2O emission from the upper peat was limited by easily available C whether it was applied as glucose alone or, in the presence of nitrate. On the contrary, N2O emission from lower peat layer was limited by nitrate with or, without glucose, but not by glucose alone. Both upper and lower mineral soil denitrification was limited by nitrate without glucose or, in combined with glucose, and not by glucose alone. Nitrogen mineralization pattern was different in upper and lower peat. A very high amount of NO3- was found in the upper peat, while there was a high amount of NH4+ in lower peat. Both the NO3- and NH4+ showed an increasing trend in lower mineral comparing to upper mineral, depicting an exceedingly high amount of mineral N at deeper layers
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(2022)Northern peatlands store approximately one-third of total global terrestrial carbon (C). These peatlands were partly drained for agriculture and forestry. In drained peatland forest, beside tree stands, ground vegetation is another relevant component concerning C fluxes between the land and the atmosphere. Thus, to explore ground vegetation gross primary production (GPPGV) dynamics, its affecting factors, and impacts of the partial harvest; forest floor net exchange (NEFF) and respiration (RFF) were measured on an hourly interval with an automated closed flux chamber method were analysed. These measurements were conducted in a forestry drained peatland before (pre-harvest, 2013 – 2015) and after (post-harvest, 2016 – 2017) the partial harvest and a control area (2015 – 2017) located in southern Finland. The results showed a similar diurnal pattern of GPPGV in all three scenarios yet, with a considerably varying magnitude between these scenarios. An 83% increase in photosynthetically active radiation (PAR) was observed in 2016 followed by the harvest event. However, a markedly higher GPPGV was obtained in the year 2017 (139.04 mg CO2 m-2 h-1) a year after the partial harvest compared to the year 2016 (42.82 mg CO2 m-2 h-1), thereby indicating a delaying effect of partial harvest induced changes on productivity. A linear mixed effect model with fixed effects of treatment (control and partial harvest) and random effects of chambers further supported this result with a significant effect of partial harvest on GPPGV in 2017 as compared to 2016. Further, a strong positive correlation was found between the daily mean GPPGV and PAR. Additionally, types of vegetation and its share of projection cover (PC) also explained GPPGV variations between flux chambers. An increase in GPPGV after the partial harvest event showed that the ground vegetation can play a considerable role in the C cycle of a managed drained peatland forest beside tree stands. As expected, after the partial harvest more lights reached the ground layer altering productivity. Besides light availability, productivity also depends on the types and phenology of inhabiting vegetation. Thus, exploration and realization of the response of ground vegetation to the partial harvest induced changes may contribute to our understanding of natural regeneration and system recovery processes.
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(2017)Bacteria are dominant members of the human gut microbiota, defined as the complex communities of microorganisms in the intestine which play an important role in regulating the health of their host, including the development of colorectal cancer (CRC). CRC is the fourth leading cancer-related mortality worldwide. Animal models are very useful in CRC research, as they allow studying molecular mechanism underlying the disease. Due to closer similarity to human beings in terms of nutrition and gastrointestinal physiology, pig models are of great value in research when compared with murine models. However, our current knowledge of the pig gut microbiome is still limited and a large number of gut bacterial species are yet to be isolated and characterised. Here, we characterised bacteria isolated from the intestine of wildtype pigs and transgenic APC1311/+ siblings (APC pigs) that develop colonic adenomas. A total of 12 novel bacteria, including 1 member of a potentially novel family, were identified from 256 strains isolated using anaerobic culturing. In addition, five other bacteria with a standing name in the nomenclature but not yet included in the pig collection were added. A draft genome was generated for four of the novel bacteria and thereby the functional potential of strains and compared their similarity. In addition, the morphology, bile salt hydrolase (BSH), 7α-dehydroxylation, carbohydrate fermentation, prevalence and abundance of all strains were analysed. The draft genome analysis confirmed the novel species status of the four bacteria. Furthermore, it also revealed the presence of genes associated with BSH, antibiotic resistance, butyrate production and carbohydrate utilization. Only two of 12 tested bacteria were positive for BSH, while none of the two bacteria selected for fermentation experiments was positive for 7α-dehydroxylation. One isolate of the species Paraclostridium benzoelyticum was found to exhibit significantly higher tolerance to NaCl than the same species described in the literature. In terms of prevalence, almost all of the bacteria (16 of 17) seem to be rare in pig, even though they appeared to be more enriched in the pig intestine when compared with other host species. Interestingly, the majority of positive samples for the bacterium representing the potentially novel family originated from the intestine of elderly human individuals. Overall, we could show that a substantial number of novel bacteria can still be isolated by classical anaerobic culture techniques using multiple rich or selective media. Even though we were able to identify most of the isolated bacteria and performed several assays to describe their properties, additional phylogenetic and taxonomic tests and development of optimal media/conditions for the novel bacteria are required in order to gain a deeper understanding of the role of these bacteria in the intestinal microbial ecosystem.
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(2020)Parkinson’s disease is a common neurodegenerative disorder that affects the movement. Although the disease has been known for a long time and intensive studies on this subject have been carried out, the cause of the disease is still unidentified. Interestingly, certain metallic molecules have been found in the neurodegenerative tissues. The metabolism of certain bacterial species has been found to be responsible for the accumulation of these molecules. In this study, we investigated the association between five specific species of gut bacteria, as well as their putative role in the accumulation of the metallic molecules and Parkinson’s disease. The methods comprised of molecular assays for detection and quantification of the bacteria, respectively, from feces samples derived from healthy individuals (n=20) and patients with the disease (n=20). The outcome of molecular assays was verified by traditional microbiological methods. The results suggested that more studies should be done to verify any role of these bacteria in Parkinson ́s disease.
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(2019)Inflammatory bowel disease (IBD) is a globally increasing chronic disease, for which the pathogenesis still is unclear. The most common subtypes of IBD are Crohn’s disease (CD) and ulcerative colitis (UC). It is widely known that, in addition to the genetics, an altered immune response against the gut microbiome plays an important role in the development of the disease. For the IBD patients, to whom conventional medication is not sufficient, the TNF-α blocker infliximab, is given. However, about one third of the patients receiving infliximab treatment, do not respond to the drug, or lose response over time. Since there to this day are no reliable diagnostic markers available, the finding of such is of great importance. The goal of this study was to investigate possible markers for drug response in the gut mycobiota composition of IBD patients. The gut mycobiota composition of 72 IBD patients receiving infliximab was studied by MiSeq sequencing of fungal DNA from fecal samples, collected during one year. The sequencing data was analyzed using the mare package in R. In addition, anti-Saccharomyces cerevisiae antibody (ASCA) concentrations were measured from baseline serum samples by ELISA. Finally, calprotectin concentrations were measured from baseline and twelve weeks post infliximab serum samples by ELISA to study whether serum samples could be used instead of fecal samples for measuring calprotectin values. Results show an increase of the Candida and Spiromyces genera in the gut mycobiota of non-responding patients at baseline. At all timepoints, the Spiromyces genus was observed at a higher abundance, compared to the group of patients responding well or partially to the medication. Interestingly, the increase of Candida was seen only in Crohn’s disease patients, when looking at the composition at all timepoints. ASCA values did not differ between the response groups. The serum calprotectin values did not correlate with fecal calprotectin, and serum calprotectin can thus not be used as a marker of gut inflammation. In conclusion, the gut mycobiota can offer predictive markers for drug response prediction to infliximab in IBD patients, which can with further studies offer a clinical diagnostic tool for prediction of drug response.
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(2017)Primary peat formation, infilling (terrestrialization) and paludification are the three main kinds of peatland formation processes. A peatland can develop over previously drier mineral soil if water table level rises or previously formed mire grows or expands. In Finland, the expansion of mires has been occasionally fast and in major part of ombrotrophic raised bogs it has occured while the mire has been in the minerotrophic fen stage. However, based on previous studies there have been different speculations whether the paludification still continues. Paludification study site at the edge of peatland and forested mineral soil was established in Häädetkeidas Strict Nature Reserve in year 1931. The study site, with a set of 4 transects, was studied in 1931, 1945, 1957 and 1997. Vegetation analysis on these permanent transects was repeated in 2016 as a part of this thesis. The aim of this study was to describe the variation of vegetation at the edge of the mire and forested mineral soil and study how the vegetation and plant species assemblies have changed between the years 1931–2016. A long-term vegetation study can reveal whether the species have changed from forest-dominated species to peatland-dominated species and does the paludification process still continue. The paludification process was studied by estimating the canopy-cover of ground layer and field layer vegetation and litter cover, measuring peat thickness, the thickness of aerated peat layer and anoxic peat layer and forest cover in four transects, consisting of 180 subplots. Non-metric multidimensional scaling (NMDS) was used to describe the data. Ground and field layer vegetation were examined by comparing the species’ average cover and frequencies. Environmental variables were studied by correlation analysis. Differences in peat thickness and in the coverage of Sphagnum-mosses between the examination years were studied with oneway variance analysis and t-test. In all four transects the coverage of Sphagnum-mosses had increased between the years 1931 and 2016. The coverage of forest mosses had decreased in two out of four transects. Succession related changes in species were observed in both vegetation layers. There was variation in the vegetation development between the transects and they seemed to be in different stages of the succession and paludification processes. In 93 percent of the study plots the thickness of peat layer had increased during the last 19 years. The changes in vegetation between the years 1931 and 2016 as well as the growth of the peat layer suggests that the paludification process still continues.
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(2014)The purpose of this thesis was to study high school student counsellors’ perceptions of university-level forest science studies and perceptions of forest sector in general. Student counsellors act as an information source when choosing a career and further studies after high school. Furthermore, this study explored the communication and student marketing implemented by the department of Forest Sciences and the Faculty of Agriculture and Forestry at the University of Helsinki. The theoretical background of this study was based on the theories of organizational communication and image forming. The aim was to clarify how the image of forest studies and forest sector is formed. The data were collected with personal theme-interviews. In addition to counsellors, personnel from the Faculty of Agriculture and Forestry were also interviewed. The data were analyzed by using thematizing. The forest sector was seen as a field of business that has been important to Finnish economy and society in the past. However, counsellors understanding of forest science studies were quite defective. Still, the employment possibilities were seen extensive, although some images of traditional positions related to the paper industry and wood trading emerged. The Internet is the main source of information to the counsellors and to the prospective students. Because of this, web-pages that are clear and up-to-date are important in student marketing. The experiences about the communication and student marketing implemented by the Faculty were few and more actions were wished. The image is that the whole Faculty offers several study possibilities. However, both counsellors, and most likely, the prospective students have very unsound conceptions of the possibilities. Both counsellors and the personnel from the Faculty described the name of the Faculty of Agriculture and Forestry challenging. The name does not define clearly what fields of study are included. Forest sector aims to improve the conspicuousness and the attractiveness of the sector among the young people. Based on this thesis, it is possible to say that the challenges with the communication and student marketing are related to the structured components of the communication, such as actions and messages. The impressiveness is low and there is a lack of resources. Even though the Faculty of Agriculture and Forestry, the Department of Forest Sciences and other members of the forest sector are investing in the communication, student counsellors are unfamiliar with the possibilities that forest sector offers as an education and as a profession. The collaboration between the university and other members of the forest sector can give the possibility to improve the communication and to accelerate student marketing.
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(2020)Tässä tutkimuksessa laadittiin haavalle (Populus tremula) puun rungon ja oksien tilavuuden käsittävä malli. Mallin luontia varten kerättiin 11 koepuun aineisto. Puista mitattiin Hyytiälän metsäasemalla erilaisia tunnuksia. Rungon ja oksien absoluuttiset tilavuudet selvitettiin käyttämällä dimensiometri-nimistä mitta-laitetta. Manuaalisesti koepuista mitattiin läpimittoja usealta eri korkeudelta rungosta ja oksista katkaisu-kohdasta. Myös oksien ja puun kokonaispituus mitattiin tarkasti puun kaadon jälkeen. Läpimittojen avul-la laskettuja pohjapinta-aloja analysoitiin korrelaatiokertoimien avulla. Koepuiden tilavuutta selitettiin lineaarisella regressioanalyysillä, jossa selittävinä tekijöinä olivat puusta mitatun rinnankorkeusläpimitan ja pituuden luonnolliset logaritmit. Lisäksi laadittiin yhdistetty malli, jossa olivat mukana kaikki aineiston koepuut. Viimeiseksi laadittiin vielä malli, jossa käytettiin vastaavia muut-tujia (neljä kappaletta) kuin Laasasenahon (1982) tilavuusmallissa. Rungon ja oksien pohjapinta-alojen välillä oli selvä korrelaatio puun suhteellisilla korkeuksilla. Korrelaa-tiokertoimet olivat rungon ja oksien yhteenlaskettujen pohjapinta-alojen osalta jopa puiden latvassa yhtä poikkeusta lukuun ottamatta yli 0,9. Pelkkää rungon pohjapinta-alaa tarkasteltaessa latvuksen korrelaa-tiokertoimet olivat hieman alhaisemmat. Koko aineiston käsittävän tilavuusmalli korjattu selitysaste oli 2 ja 4 muuttujan versioissa 0,999 ja keski-virhe vastaavasti 0,062 ja 0,066. Koepuuaineistoon perustuva haavan tilavuusmalli tuotti vain 0,56 % suurempia tilavuuksia haavan rungon ja oksien tilavuudelle verrattuna upotusmittauslaitteella tehtyihin mittauksiin. Haavan biomassan jakautuminen erikokoisten puiden välillä on tämän tutkimuksen mukaan samankal-taista. Myös runkomuodot olivat aineiston puilla samankaltaisia: niiden rungon ja oksien yhteenlasketuil-la pohjapinta-aloilla puun suhteellisilla korkeuksilla oli selvä korrelaatio. Tutkimuksessa luodulla haavan tilavuusmallilla on korkea selitysaste ja pieni keskivirhe.
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(2013)Domestic cattle grazing as a disturbance factor to the vegetation structure is investigated. It is concluded that the process of heterospecific attraction plays as important a role as vegetation structure in predicting waterfowl assemblage patterns. The study site, an estuarine wetland in an urban zone in Helsinki, is studied during one staging period. Two sets of shorelines are focused on, grazed and ungrazed. Avian assemblages are compared in both types of shorelines based on variables of community structure and habitat resource use. The two most influential variables are aquatic invertebrate biomass index as food supply, and bare shoreline proportion as habitat structure indicator. The process of competition as regulating factor in forming avian aggregations is ruled out by confirming that sufficient amounts of habitat resources, food and space are available. The co-occurrence patterns of foraging guilds are analyzed. Heterogeneous vegetation structure, combined with social attraction, influences avian distribution patterns. Niche partitioning is absent across the whole landscape as invertebrate food resource is not a limiting factor. Microhabitat use within plots is evenly distributed. The constantly popular microhabitats are sections of the grazed shorelines where resource partitioning is absent. Avian habitat preferences are shaped by extent of available bare shoreline and the presence of other waterfowl. The latter effect is confirmed both as conspecific and heterospecific attraction. It is the first time this wetland, which is also a designated Natura 2000 and Ramsar site, is being investigated for wildlife community dynamics. The site does not suffer from major environmental threats and has potential for more waterfowl consumers. In view of its international significance, this and similar research can aid urban planners in Reserve management to enhance avian diversity towards attracting species of more conservation concern.
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(2019)Boreal lakes and wetlands that are abundant in the world are vital breeding and resting areas for birds. However, a significant part of wetlands has been globally lost due to human activity. In the study area of this research, Evo, lake habitats are somewhat stable especially in landscape level, changes are mainly lake-specific. Habitat use and its stability have been studied earlier on other bird species, such as ducks (Anas spp.) but little research exists about the matter on wader or shorebird species. This study aimed to compare the patch-scale habitat use stability of two waders; Common Sandpiper (Actitis hypoleucos) and Green Sandpiper (Tringa ochropus). The comparison was also made between the pair densities of these species. Many species are known to benefit from beaver induced floods. However, previous studies have not measured the effect of beaver before, during and after beaver flooding. Therefore, this study aimed to investigate the presence and abundance of Green Sandpiper at different stages of beaver flood. This study showed that the habitat use of Common Sandpiper was more stable than that of Green Sandpiper, although both species showed variation. Pair density of Common Sandpiper was lower than Green Sandpiper’s nearly throughout the study period. Pair density of Common Sandpiper, on the contrary, showed more variation compared to Green Sandpiper’s pair density. Green Sandpipers were observed in nearly all of the beaver ponds in this study. Presence and abundance of Green Sandpiper were highest during the beaver flood, but the numbers stayed high also after the flood. It could be concluded that Common Sandpiper is a species of high site-fidelity and more prone to changes in the environment than Green Sandpiper, which seems to be able to utilize variable habitats, such as flowages regularly created by beaver in the Evo region. In previous studies, many species have been known to benefit from beaver activity, and Green Sandpiper can be seen as a species of plastic habitat use and being able to profit from surroundings altered by beaver. Therefore, this wader benefits notably from beaver floods.
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(2019)The Master's thesis was completed as part of the joint project (Haittaeläin) by the Finnish Food Authority (Ruokavirasto) and Natural Resources Institute Finland (Luke). In the project, rodents and shrews caught on farm premises were investigated for zoonotic bacterial pathogens. This thesis covers the thermophilic cam-pylobacter findings in the caught pests in autumn 2017.Rodents and shrews caught on farm premises were investigated for zoonotic bacterial pathogens. This thesis deals with the result of thermophilic campylobac-ters isolated from the pests in the autumn 2017. Thermophilic campylobacters (Campylobacter jejuni ja Cam-pylobacter coli) cause gastroenteritis called campylobacteriosis in humans, which is one of the most common cause for human gastroenteritis in the world. The literature review discusses the characteristics of thermo-philic campylobacters and their epidemiology, which focused on aspects of a public health and risk factors for campylobacteriosis and the major sources of campylobacters. Moreover, a current knowledge of campylo-bacters’ occurrence in rodents and shrews were summarized in the literature review. The presence of thermophilic campylobacters was investigated from 227 pooled samples, which comprised of a total of 442 intestinal samples collected from 12 different species. Three species (yellow-necked mouse, house mouse and bank vole) covered 81,3 % of all caught pests. The numbers of caught pests were not signif-icantly different between the farms when compared to a geographical position (south or north) or a type of farm (pig or cattle). The numbers of captured yellow-necked mice were significantly higher in farms in the south. Especially, yellow-necked mice and bank voles were detected to be campylobacter positive. Other campylobacter positive species were harvest mice, rats, field voles and southern voles. A total of 93 samples were detected as campylobacter positive and all of them were identified as C. jejuni. There was not signifi-cant difference on the numbers of campylobacter positive samples between the farms when compared the geographical position or the type of farm. 46 isolates of all 96 campylobacter positive samples were selected for a whole genome sequencing. After the raw read data was assembled, the contigs were analysed with MLST and cgMLST typing schemes by Ridom SeqSphere+. 41 isolates contained 14 new sequence types (STs). Instead, 5 isolates contained previously described STs: ST-1304, ST-2219 and ST-4791. According to MLST typing isolates obtained from voles differed from isolates from mice and rats. Moreover, cgMLST typing supported the conclusion. In the cgMLST typing scheme vole’s isolates were found to have more missing loci than isolates from mice or rats. Therefore, all isolates from voles, apart from two bank vole isolates belonging to ST-1304, contained less than 90 % loci compared to a reference genome. Furthermore, these same isolates were poorly identified in MALDI TOF analysis unlike other isolates. One interpretation to the difference between isolates could be that isolates from voles belong to a new C. jejuni subspecies.
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