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Faculty of Agriculture and Forestry

 

Recent Submissions

  • Ahlqvist, Kati (2022)
    Common sexually transmitted pathogens like human papillomavirus (HPV) and Chlamydia trachomatis have profound effects on sexual health of women ranging from acute genital tract infections to cancer and infertility. These infections are often asymptomatic, increasing the risk of being left untreated and thus increasing the probability of complications. Most cervical cancer cases are caused by persistent HPV infection and would be preventable by timely HPV detection. Cervical cancer screening using HPV nucleic acid detection has proven efficient and is used in many European countries, including Finland. Chlamydia trachomatis and Neisseria gonorrhoeae infections can lead to upper genital tract infection and increased risk of ectopic pregnancy and infertility. C. trachomatis infections are also associated to increased risk of epithelial ovarian cancer. Due to lack of national screening program and often asymptomatic nature of these infections, many of them are left untreated. In order to streamline cervical cancer screening and to include C. trachomatis and N. gonorrhoeae analysis in the same package with HPV, a liquid-based cytology sample medium, BD SurePath™ was validated for use with cobas® 4800 HPV and CT/NG nucleic acid detection tests. Work presented here shows that HPV and CT/NG tests and cytological analysis can all be done from a single sample in an efficient, reliable and cost-beneficial way. Based on the results, Vita Laboratoriot will be able to offer the package analysis to their customers.
  • Jokelainen, Liisa (2022)
    Lähivuosina turvetuotannosta vapautuu suuria määriä suonpohjia jälkikäyttöön. Suomessa metsittäminen on ollut yleisin suonpohjan jälkikäyttömuoto, mutta metsittämisen ilmastovaikutuksia tutkittu vain vähän. LULUCF-sektorilla pyritään lisää-mään hiilinieluja ja hiilen varastoja muun muassa metsittämällä joutoalueita, kuten suonpohjia, kasvihuonekaasupäästöjen vähentämiseksi. Tämän tutkimuksen tarkoituksena on tutkia ja tuottaa tietoa metsittämisen vaikutuksesta suonpohjan maa-hengitykseen, eli hiilidioksidivuohon maasta ilmaan, sekä metaanivuohon. Metsittämisen vaikutusta tutkittiin viidellä eri suonpohjalla Pirkanmaan ja Etelä-Pohjanmaan alueella. Yhteensä 14 koealalla mitattiin CO2- ja CH4-voiden lisäksi pohjavedenpinnan tasoa (WT) sekä maan lämpötilaa 5 cm:n (T5) ja 30 cm:n (T30) syvyyk-siltä kesällä ja syksyllä 2021. Kasvihuonekaasumittaukset tehtiin kammiomittausmenetelmällä kasvillisilta (Rtot) ja kasvittomil-ta (Rhet) mittauspisteiltä. Kokonaismaahengitystä mitattiin kasvillisilta pisteiltä ja heterotrofista hengitystä mitattiin kasvittomilta pisteiltä, joista oli katkottu juuriyhteydet sekä poistettu maanpäällinen kasvillisuus. Lisäksi koealoilta selvitettiin puuston ikä sekä turvekerroksen paksuus. Puuston iän sekä turvekerroksen paksuuden vaihtelu oli melko hyvin edustettuna valituilla koealoilla (0-57 v. ja 10-100+ cm). Kokonaismaahengityksen hetkelliset vuot vaihtelivat -39–1662 mg m-2 h-1 välillä ja koealakohtaiset keskiarvot olivat 58–694 mg m-2 h-1. Heterotrofisen hengityksen hetkelliset vuot vaihtelivat -39–836 mg m-2 h-1 välillä ja koealakohtaiset keskiarvot olivat 58–366 mg m-2 h-1. Maahengityksen määrä oli samankaltainen kuin aiemmissa suonpohjilta tehdyissä tutkimuksissa. Metsä-ojitettuihin soihin verrattuna suonpohjien maahengitys oli hieman pienempää. Maan lämpötilat vaihtelivat mittausjakson aikana 0–25 ˚C:n välillä. Maan lämpötila vaikutti sekä kokonaismaahengitykseen että heterotrofiseen hengitykseen. Maan lämmetessä maahengityksen määrä kasvoi, mutta tietyn rajan jälkeen maahengitys väheni huomattavasti. Puuston ikä selitti parhaiten sekä kokonaismaahengitystä että heterotrofista hengitystä usean selittäjän regressiomallilla. Myös turpeen paksuus vaikutti maahengitykseen. Pohjavedenpinnan tasolla (WT) ei puolestaan ollut mallin mukaan vaiku-tusta suonpohjan maahengitykseen. Puuston ikä korreloi positiivisesti maahengityksen kanssa eli puuston ollessa iäkkääm-pää maahengitys oli suurempaa. Turpeen paksuus korreloi negatiivisesti eli paksuturpeisilla koealoilla maahengitys oli pie-nempää. Kasvillisilta (Rtot) pisteiltä mitatut metaanin hetkelliset vuot vaihtelivat -0,148–1,206 mg m-2 h-1 välillä ja koealakohtaiset kes-kiarvot olivat -0,056–0,111 mg m-2 h-1. Kasvittomilta (Rhet) pisteiltä mitatut metaanin hetkelliset vuot vaihtelivat -0,077–0,111 mg m-2 h-1 ja koealakohtaiset keskiarvot olivat -0,34–0,111 mg m-2 h-1. Metsittämättömällä suonpohjalla avonaiset ojat aiheutti-vat metaanipäästöjä. Ojien kasvihuonekaasupäästöjä mitattiin vain tällä yhdellä suonpohjalla. Puuston ikä ja turvekerroksen paksuus selittivät parhaiten myös suonpohjan metaanivuota usean selittäjän regressiomallilla. Pohjavedenpinnan tasolla (WT) ei ollut vaikutusta metaanivuohon. Metsittämättömät koealat toimivat metaanin lähteinä ja koealat, joilla oli varttunutta puustoa toimivat pääosin metaanin nieluina. Tämän tutkimuksen perusteella suonpohjan metsittäminen kasvattaa suonpohjan maahengitystä ja vähentää metaanipäästö-jä. Metsittämisen kannattavuutta jälkikäyttömuotona ilmaston kannalta ei kuitenkaan voi päätellä näiden tulosten pohjalta. Lisää ekosysteemitason tutkimusta tarvitaan ilmastovaikutusten tarkempaa arviointia varten.
  • Paananen, Saana (2022)
    This master thesis aimed to develop a calibration model of the whipping cream for FTIR spectrophotometer MilkoScanTM FT3 and identify the effects of disruptive factors on whipping cream measurement. In the previous calibration model of whipping cream, there could be improvements in the level of the results, especially for lactose. The experimental part of this research included the development of a calibration model, calibration of lactose, total solids assay, and calculation of measurement uncertainty. The calibration model was developed utilizing the statistical methods PCA and PLS in the FossCalibrator program. Lactose calibration was carried out with the LactoSens method, utilizing whipping cream and α-D-lactose, and the results from the reference laboratory were used as reference. The accuracy and functionality of the calibration of total solids wanted to verify, which was why the experimental part included the total solid assay. Total solids were determined by a gravimetric method, and the results were compared with those of the reference laboratory. The measurement uncertainty of the calibration model was calculated with the results of the whipping cream sample reproducibility, repeatability, and accuracy. The new calibration model of whipping cream was verified utilizing validation samples, and the check results were at the expected level. The result of lactose calibration was considerably more accurate than the previous model. The total solids result from the gravimetric method varied slightly with the FT3 results, which, however, did not affect practically. The measurement uncertainty was relatively good, but the calculation will be improved as the number of reference results increases. The main subject of this research was achieved, i.e., the development of the calibration model was successful. The research on the disruptive factors was less than initially intended.
  • Juvonen, Siri (2022)
    Coffee is one of the most traded goods in the world, and Finns are the ones consuming the beverage the most on a per capita basis. In terms of sustainability, the value chain of coffee is of interest from an environmental, social and economic perspective. Being a global value chain, coffee production, processing and trade is affected by regulation and therefore several certification schemes and voluntary sustainability standards are trying to address multiple sustainability issues in the coffee industry. The aim of this thesis is to explore which stakeholder groups effect the decisions related to sustainability practices of organization’s operating in the Finnish coffee business, and to understand to what extent the choice of different voluntary sustainability standards by coffee value chain (VC) stakeholders is a function of "legitimacy trade-offs", in terms of balancing an organization’s internal expectations and norms with external expectations and norms. The overall research question is as follows: To what extent is the choice of different voluntary sustainability standards by coffee value chain (VC) stakeholders a function of "legitimacy trade-offs", in terms of balancing an organization’s internal expectations and norms with external expectations and norms? This is studied first through a short literature review on stakeholder theory, institutional theory and a recourse-based theory. The subsequent empirical study part was based on survey research, which was executed through a self-administrative web questionnaire. The questionnaire was sent out to Finnish companies in the coffee business. The results of the empirical study highlighted that there is pressure from both internal stakeholders (employees and shareholders) and from some external stakeholders (including domestic customers) to adopt or not to adopt different standards, confirming that coffee businesses in Finland (roasters/ processors) must indeed be balancing the needs and wishes of different stakeholders in the coffee value chain. The results also suggest why different organizations adopt different certification schemes while some did not use any. In sum, the views on the usefulness and stakeholder expectations regarding certifications varied, and some organizations hope that certifications contribute to improved coordination and cost savings.
  • Nyhamar, Ellisiv (2022)
    S. aureus infections are prominent worldwide, and with the rapid increase in antimicrobial resistant variants such as methicillin-resistant MRSA, the need for new treatment alternatives is imminent (Monaco et al., 2017). Lytic bacteriophages are continually evolving new methods for the destruction of bacterial cells while avoiding their defence mechanisms. Screening hypothetical proteins of unknown function (HPUFs) from bacteriophages for toxic activity against bacteria may provide new and potentially life-saving approaches to combat bacterial infections (Liu et al., 2004, Singh et al., 2019). The Stab21 phage of Staphylococcus is a recently described lytic phage with over 85 % of its open reading frames annotated as HPUFs (Oduor et al., 2019). The successful identification of potentially toxic gene products could facilitate the discovery of novel bacterial targets for the development of new antimicrobials. It could also provide treatment options to multi-drug resistant S. aureus caused infections where no effective drugs are currently available. To reduce unnecessary screening of phage particle associated yet poorly annotated proteins, total proteins of phage particle were previously identified by LC-MS. Similar studies have previously been performed with Yersinia phage fR1-RT and Klebsiella phage fHe-Kpn01, where a handful of toxic proteins were discovered (Mohanraj et al., 2019, Spruit et al., 2020). To accelerate the screening process, a next-generation sequencing (NGS) high-throughput screening method was further developed by Kasurinen et al. (2021). In this study, 96 true HPUFs were selected and screened for their bactericidal activity in E. coli using the NGS-based approach. Fourteen potentially bacteriotoxic Stab-21 gene products were identified through toxicity screening in E. coli. Of these, three had a particularly low ratio of isolated plasmid after transformation while having a significant number of reads over each joint sequence, indicating their potentially high toxicity. The three most promising candidates were the gene products of g008, g081c and g175 of the Stab21 bacteriophage.