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UTUPub on Turun yliopiston avoin julkaisuarkisto, joka sisältää Turun yliopiston tiedekuntien ja laitosten julkaisuja ja opinnäytteitä kuten väitöskirjoja, lisensiaatintöitä, pro gradu -tutkielmia ja niiden tiivistelmiä sekä kandidaatintöitä.

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Vapaat ryhmät, niiden toiminta puilla ja residuaalinen äärellisyys
Tuomela, Oskari (2026-07-22)
Pro gradu -tutkielma
Tässä tutkielmassa tutkitaan vapaita ryhmiä ja niiden ominaisuuksia. Erityisesti tarkastelun kohteina ovat vapaiden ryhmien toiminnat puille ja vapaiden ryhmien residuaalinen äärellisyys. Tutkielman kolmannessa luvussa määritellään vapaat ryhmät ja tutustutaan niiden konstruktioon. Tämän jälkeen määritellään vapaan ryhmän aste Cantor-Bernsteinin lauseen avulla. Lisäksi tutustutaan sanojen redusoituihin muotoihin ja esitellään Kleinin Ping-Pong lemma. Tutkielman neljännessä luvussa tutustutaan graafeihin, erityisesti puihin. Tämän jälkeen esitellään joukon S generoiman ryhmän G Cayleyn graafi Γ(G, S) ja tarkas- tellaan ryhmän toimintaa puilla. Tutkielman viimeisessä luvussa tutkitaan residuaalista äärellisyyttä ja osoitetaan, että kaikki vapaat ryhmät ovat residuaalisesti äärellisiä.
Dimeric diarylmercury-aptamer conjugates for LA-ICP-MS imaging
Zaman, Maruf (2026-07-21)
Pro gradu -tutkielma
Aptamers are synthetic single-chain DNA or RNA oligonucleotides capable of adopting stable 3D conformations and thus binding chosen targets tightly and with great specificity. Owing to the chemical tunability of their nucleic acid backbone, they can be functionalized at selected sites with small compounds, metal ions, or nanomaterial constructs for deployment in molecular imaging, diagnostics and targeted delivery applications. Aptamer based metal tagging is an emerging strategy to translate molecular recognition into spatially resolved elemental signals for mass spectrometric bioimaging. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is an elemental imaging technique that in a biological context enables quantitative, micrometer scale mapping of endogenous trace elements and exogenously introduced metal tagged biomarker species in two dimensions. The goal of this study was to synthesize a stable diarylmercurial compound which would be suitable for aptamer conjugation followed by bioimaging. Initially a diarylmercury solid support with DMTr protecting group was synthesized, but it did not survive oxidative and acidic conditions. Another, azide-linked, dimeric diarylmercury molecule was synthesized to avoid the above mentioned conditions. When separated from the analogous monoarylmercury molecule at room temperature, this compound demonstrated chemical stability. Single-stranded and double-helical oligonucleotides were utilized for conjugation, along with a recently created 76-mer DNA aptamer that is specific to GFAP. The aptamer attaches to the particular protein while bearing the metal tag when the dimeric diarylmercury-aptamer combination is administered to tissue that contains that particular protein. The presence of the protein can then be verified by using LA-ICP-MS to identify and visualize the metal tag.
NMR-based metabolomics of interspecific hybrid strawberries
Enkhkhuyag, Bilguun (2026-07-09)
Pro gradu -tutkielma | suljettu
The breeding of garden strawberries (Fragaria × ananassa) has a great significance in the food industry due to its wide cultivation. Today, allelic diversity from two wild sister species, F. chiloensis and F. virginiana, is being reintroduced to the strawberry for the purpose of enhancing agronomic traits such as fruit quality, disease resistance, and resilience to environmental change. The change in climate conditions, specifically in the Nordic region, has necessitated the development of adaptive strawberry cultivars. Consequently, newly reconstructed garden strawberries were developed through the NORDFRUIT breeding program by LUKE (National Resources Institute Finland). The aim of this research was to characterize the polar metabolic profile of the new interspecific hybrid strawberries and to help find the most potential hybrids for further breeding into commercial cultivars. Nuclear magnetic resonance (NMR) spectroscopy, known for its high reproducibility, quantitative and qualitative nature, is a robust tool widely applied in food metabolomics. NMR provides a comprehensive analysis of metabolites in organisms, with a detailed overview of the polar metabolic profile. In this study, polar metabolites (amino acids, organic acids, phenolics, and sugars) were extracted from freeze-dried strawberries and analyzed according to 1H NMR metabolomics experimental workflow. 1H NMR-based metabolomics workflow combined with multivariate statistical data analysis were used to investigate the polar metabolite composition of 163 individual hybrids from 13 progeny groups, cultivar ‘Aho’ and six commercial cultivars (‘Honeoye’, ‘Korona’, ‘Lumo’, ‘Polka’ and ‘Ria’). The results demonstrated the metabolite variation between and within progeny groups when compared to commercial cultivars. In this study, reconstructed hybrid strawberries were notably differentiated by their sugars (glucose, fructose and sucrose), organic acids (citrate and malate), and amino acids (alanine, glutamine and threonine) profiles from the commercial cultivars. Although there was variation between the commercial cultivars and the hybrids, individuals from hybrid progeny groups 2, 4 and 8 closely correlated to the commercial cultivars through their sugar and amino acid profiles, validating the potential of their commercialization. Through this study, the hybrid strawberries were identified with 38 new metabolites such as 2-heptanone, 2,3-butanediol and cis-aconitate which contributed most to the unique metabolic profile of hybrids and correlating to specific aroma properties and stress responses in strawberry metabolism.
OPTIMIZATION OF NOVEL GROUP-SPECIFIC UHPLC MS/MS METHODS INTO XEVO MRT MASS SPECTROMETER
Weerasinghe, Patalee (2026-07-17)
Pro gradu -tutkielma | suljettu
Biologically complex plant matrices often require both high sensitivity and resolution from analytical tools to reliably detect low concentrations of their specialized metabolite armory. The aim of this study was to develop a robust UHPLC-MS/MS workflow for comprehensive compound group-specific detection of a wide variety of plant specialized metabolite classes utilizing the Waters Xevo MRT (multi-reflecting time-of-flight) high-resolution mass spectrometer. This quadrupole time-of-flight mass spectrometer combines selective precursor isolation with accurate-mass MS/MS detection facilitating the separation of near-isobaric plant metabolites and reducing the spectral overlap in plant extracts containing thousands of compounds thus minimizing false positives. In this work, numerous commercial polyphenol compounds were analyzed in both positive and negative ESI modes with cone voltage (CV) ramp to capture precursor ions and fragments, and these data were compared with the group-specific MRM methods developed utilizing the Waters TQ triple quadrupole instrument. Key polyphenol classes such as gallic acid and quinic acid derivatives recorded comparable values while flavonoid glycosides and ellagitannins exhibited relatively higher CVs. In contrast, the optimized Xevo MRT workflow successfully differentiated quercetin-derivative fingerprints from HHDP-containing ellagitannin fingerprints, which can overlap at nominal m/z 301 in low-resolution Xevo TQ data and potentially lead to false-positive group assignments. The applicability and detection capability of the workflow were evaluated using a mixture of multiple plant extracts (MABA) which has also been used as a reference sample for Xevo TQ together with 23 individual plant extracts. The optimized method generated distinct group-specific fingerprints for the analyzed samples, demonstrating its potential as a rapid screening tool for qualitative profiling of several polyphenol groups.
Discovering The Impact of Different Cultivation Factors on The Phenolic Composition of Raspberries
Khan, Awais (2026-07-07)
Diplomityö | suljettu
The red raspberry (Rubus idaeus L.) fruit is a rich source of health promoting phenolic compounds, such as anthocyanins, ellagitannins, ellagic acid derivatives as well as flavonols. Genotype, cultivation environment and developmental stage are factors that influence the accumulation of these compounds. However, the effect of cultivar genotype, cultivation system and harvest time on the phenolic composition of raspberry is still poorly understood under the Nordic growing conditions. The phenolic profiles of four raspberry cultivars (Agat, Borgund, Glen Ample, and Ninni) were investigated with three different cultivation systems (open-field in-ground (A), open-field containerized (P) and tunnel containerized (T)), and at three ripeness stages (early, optimum and late ripeness). HPLC-DAD was used for analysis of phenolic compounds and LC-DAD-MS for phenolic compound identification. Principal component analysis (PCA) and three-way general linear model (GLM) analysis were performed to assess the effects of cultivar, cultivation system and harvest stage on the phenolic composition. Thirty-three phenolic compounds were tentatively identified, including 10 anthocyanins, 3 ellagitannins, 11 ellagic acid derivatives, 7 quercetin derivatives and 2 kaempferol derivatives. Anthocyanins were the most abundant phenolics for all cultivars and treatments. The GLM analysis revealed that the cultivar identity was the prominent factor affecting each of the phenolic classes (p <0.001) with the model R2 values between 0.769 and 0.961. Agat had the highest total phenolic concentration (27.9 to 34.5 mg/100 g FW) while Borgund had the lowest overall accumulation (12.3 to 18.8 mg/100 g FW). Cultivation system significantly influenced all phenolic classes (p <0.001) with generally higher levels of anthocyanins being observed in open-field compared to tunnel grown systems. The significance of harvest time on flavonols, ellagic acid derivatives and total phenol sum was observed but not the significance of harvest time on anthocyanins as an independent main effect. PCA also reinforced that cultivar is the most important structuring factor for anthocyanin variation. Results in total indicate that the phenolic quality of the raspberries grown in Finland is mostly a result of the genotype but is also influenced by the cultivation system and harvest dates in a compound basis and cultivar-specific manner.

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