Browsing by study line "ingen studieinriktning"
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(2023)Dietamoeba fragilis is a very common human intestinal parasite in the world and also in Finland. D. fragilis causes dientamoebiasis in humans, and symptoms of infection may vary from mild bowel symptoms to prolonged diarrhoea and weight loss. Some of the infected patients are completely asymptomatic. Despite its prevalence, insufficient data exist on the life cycle and host organisms of D. fragilis. Interestingly, D. fragilis has been found in dogs in a few studies. Thus, more research is needed on the role of household pets as part of the parasite’s life cycle and choice of host organism. Comprehensive study on the role of dogs in the life cycle of D. fragilis is warranted. The purpose of this thesis was to design a study on the role of dogs in the D. fragilis parasite life cycle “The presence of Dientamoeba fragilis parasites and multiresistant ESBL-bacteria in dog owners and their pets”, to present research methods and to apply research permit from the ethics committee. The aim of the study is to analyze the prevalence of D. fragilis in dogs in Finland and the role of the dog in the spread of D. fragilis parasite within humans. In addition to D. fragilis, the study combines collection of samples for ESBL bacteria analyses, but this thesis focuses only on the part of study D. fragilis. Two different real-time PCR methods are tested in this project: an in-house method and an Amplidiag® Stool Parasites method, out of which Amplidiag® Stool Parasites method is selected to be used in the study. In the thesis documents for the ethics committee's referral are written and ethical permit to conduct the study from the HUS ethics committee is applied. A favourable opinion will allow a comprehensive study of dogs and humans to be carried out. Ethics permit is need to recruit participants for research on the basis of a laboratory-confirmed D. fragilis -discovery. The committee confirms that the study is ethically acceptable. During the thesis project, the committee gave the study a conditional favourable decision. The implementation of the study will start in the spring of 2023, when the final assent is received.
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(2022)Dietary data is essential in creating dietary guidelines and interventions, but the traditional data collection methods can be biased and costly. Wastewater metagenomes present a potential new way to collect dietary data with the utilization of microbial markers. In this study, potential microbial markers for fiber and meat intake were identified from literature. The abundances of these markers and their associations with the corresponding dietary data were analyzed using a previously published global wastewater metagenome dataset covering 58 countries. Majority of these potential markers were detected in the analysed wastewater metagenomes. Of the identified markers, Prevotella and Prevotella copri showed significant associations with whole grain intake, Alistipes and Alistipes putredinis showed significant associations with processed meat intake, and Faecalibacterium showed significant association with red meat intake. In addition, associations between dietary data and both taxonomic and functional annotations of the metagenomes were determined to identify any additional potential markers. Multiple additional species, genera and gene families showed significant associations with red meat and processed meat intakes. Future research should include finer resolution data to validify these results and further investigate the potential of these taxa and genes as markers. In conclusion, microbial markers present a promising way to collect dietary data from wastewater metagenomes.
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(2021)Poultry meat has become popular in human diet and to secure the growing demand of poultry meat, breeders have developed broilers with fast growth and high breast muscle yield. Because of this genetic selection modern broilers are suffering from various quality defects in their breast muscles, one of which is called WB myopathy. The aim of the thesis was to study whether exercise, WB status or age have effects on ultimate pH and glycolytic potential (sum of total glucose and lactic acid content, given as lactate) in M. pectoralis major of modern broilers chickens. A total of 154 post-rigor breast muscle samples of male broilers of hybrid Ross 308 were used in this study. Broilers were divided randomly into three groups (A-C). Group A birds were not subjected to any exercise during the experiment. Group B birds lived 25 days exactly like group A but after that the drinking water dispensers was elevated to a higher level. Group C birds had their drinking water dispensers elevated to a 5 cm higher level after three days, and it was risen stepwise to 25 cm during the study. Broilers were slaughtered randomly from different groups at 20, 30 or 41 days old. Group B results were disregarded due to technical problems. Initial and ultimate pH, total glucose, free and in glycogen, and lactic acid contents for glycolytic potential, were determined from the breast muscle samples. The results showed that there were no differences between groups A and C (p > 0.05). There were differences between normal and WB cases in ultimate pH (pHu; p = 0.000), total glucose content (p = 0.000), lactate content (p = 0.007) and glycolytic potential (p = 0.000), but the pH values 5 minutes after death showed no significance (pH5; p = 0.190). There were differences in pHu, total glucose and glycolytic potential (p = 0.000), and lactate (p = 0.007), between ages 20, 30 and 41 days old birds. As the severity of WB increased in the breast muscle, the pHu increased and total glucose, lactate content and glycolytic potential decreased. The correlations showed significant relationships between WB score and all the above variables (p < 0.000). The results of the current study show that exercise does not have an effect on the levels of carbohydrates in M. pectoralis major of modern broiler chickens, but WB status and increasing slaughter age result a decrease in glycolytic potential and increase in ultimate pH.
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(2020)Infant formulas are breast milk substitutes for 0 to 12-month-old infants. Addition of milk fat to infant formulas leads to an increase in solid fat content. Infant formulas are oil-in- water emulsions in which oil is dispersed into a continuous aqueous phase. Milk fat crystallization leads to partial coalescence and creaming which are types of instability in emulsions. Partial coalescence occurs when two droplets containing crystals collide and they partially coalesce by making contact between their oil phases. The aim of this thesis was to study if milk fat crystallization leads to partial coalescence which leads to a higher rate of creaming or the increasing density of crystallizing droplets leads to a lower rate of creaming. Also, the aim was to study the effect of interfacial layer on partial coalescence. Milk fat crystallization and emulsion stability were investigated from four series of oil-in- water emulsions containing different oils in different concentrations and either whey protein or lecithin as stabilizer. The samples were stored at 5, 20 and 40 °C and measured after 0, 7 and 28 days of storage. The crystallization of bulk fat and oil in emulsions were studied with melting enthalpies measured with differential scanning calorimetry. Emulsion stability was examined with particle size distribution, instability index and creaming velocity measurements. According to the results combining vegetable oil and butter oil, and emulsifying the fat decreases the total enthalpy change and crystallization onset temperature of oils. Mixing vegetable oil and butter oil before homogenization decreased crystallization onset temperature and total enthalpy change because the oils were in same droplet, and made the emulsions behave more like vegetable oil emulsions. Mixing the oils after homogenization made the emulsions behave similarly to butter oil emulsions. Whey protein was found to be a better stabilizer of emulsions than lecithin at 5 and 20 °C, but at 40 °C some Maillard reaction was noticed. It was suspected that the concentration of lecithin in emulsions was insufficient. Based on the results it could be stated that the increasing density due to crystallizing droplets made the emulsions more stable against creaming. Best stability of emulsions containing oil mixtures would be achieved if butter oil and vegetable oil were mixed after homogenization and whey protein used as emulsifier.
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(2024)The primary objective of this thesis was to observe the effect of fermentation of oat and faba bean flour mixture on oat β-glucan. The secondary objective was to define how fermentation conditions affect β-glucan content, pH, total titratable acidity (TTA) and viscosity in oat-faba bean matrix utilizing experimental design and response surface methodology (RSM). As fermentation is a part of manufacturing process of plant-based yoghurt alternatives, this thesis observed the fermentation process in detail to define its effect on β-glucan. The flour mixture consisted of whole grain oat flour, oat bran concentrate, faba bean flour, faba bean protein isolate and water. This mixture was fermented with a commercial yoghurt starter, consisting of Bifidobacterium sbsp., Lactobacillus acidophilus, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus paracasei and Streptococcus thermophilus species. Studied fermentation condition factors were time (7 h, 12.5 h, 18 h), temperature (30 °C, 37.5 °C, 45 °C) and inoculum ratio (0.01 %, 0.1 %, 1% w/w). The relationship between the factors and responses were analyzed with the Central Composite Face-centered (CCF) design and response surface modelling. In all tested fermentation conditions, no significant decrease in β-glucan content was observed. However, relationships between fermentation condition factors and other responses were obtained. All factors had decreasing effect on pH and increasing effect on TTA. All factors contributed to viscosity, but temperature was significantly more effective than others, having positive, non-linear effect.
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(2023)Sorghum (Sorghum bicolor L. Moench) has high contents of phenolic compounds which have both beneficial and antinutritional health effects, including forming insoluble complexes with proteins. This is significant because sorghum has low protein digestibility. Lactic acid bacteria (LAB) fermentation has been found to decrease and modify sorghum phenolic compounds and condensed tannins. The aim of this thesis was to evaluate the effects of LAB fermentation on the phenolic compounds in white and red sorghum using a metabolomics approach. The hypothesis was that fermentation would degrade phenolic compounds into smaller metabolites. Free phenolic compounds were extracted from sorghum using 80% ethanol. The samples were analysed using ultra-performance liquid chromatography coupled with a photodiode-array detector and quadrupole time-of-flight mass spectrometry (UPLC-PDA-Q-TOF). In order to identify phenolic compounds, both targeted and untargeted metabolomics approaches were used. Multivariate analysis was employed to determine compounds with different abundances between sample groups. The study confirmed the identification of 40 compounds, 37 of which were phenolic compounds, and 23 were distinct between sample groups. Red sorghum contained more flavonoids and condensed tannins compared to white sorghum. Native samples were statistically different from fermented samples, with most changes involving the release of phenolic acids from their conjugated forms and an increase in phenolamines. The metabolomics approach effectively covered the wide range of phenolic compound analysis in sorghum.
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(2022)Herbs are valued for culinary and health purposes and their metabolism and chemical composition can be influenced with LED lighting. This Master’s Thesis aimed to study how different spectra (green, blue, and white light) affect the sensory properties of hydroponically grown dill (Anethum graveolens L.) and coriander (Coriandrum sativum). The hypothesis was that green light produces more soapy and musty flavours in coriander, whereas blue light produces more citrus and typical coriander-like flavours. For dill the hypothesis was that blue and green light treatments produce stronger flavours compared to white light. A generic descriptive analysis method was chosen, and trained panels created sensory profiles for three light treatment and one commercial coriander and dill samples. Intensities of smell, taste and flavour attributes were evaluated using a line scale (0 = not at all to 10 = extremely) in three replicates. Study was conducted during the COVID-19 pandemic in the sensory laboratory conditions (ISO 8589). One-way ANOVA showed that light treatments had only slight impact on the sensory profiles of coriander and dill. In coriander blue light produced significantly lower lemon odour intensity compared to green light treatment. In dill total odour intensity was significantly lower in blue light sample compared to white light and commercial samples. Otherwise, one-way ANOVA did not show significant differences between samples. However, principal component analysis (PCA) implied that samples differed. Two-way ANOVA results showed that neither panel worked uniformly and deviation among intensity scores was observed. Herb samples proved to be rather difficult to evaluate and more extensive training could have improved panel’s performance. In future consumer study could be performed to study if spectrum affects the hedonic response to these herbs.
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(2024)Elintarviketurvallisuus on ensiarvoisen tärkeää kansanterveyden ja kuluttajansuojan näkökulmasta. Euroopan unionin sisämarkkinat edellyttävät tiukkojen elintarviketurvallisuusstandardien noudattamista kaikilta toimijoilta. Tämä näkyy mm. salmonellan torjunnassa ja valvonnassa. Salmonellan merkitys elintarviketurvallisuudelle on monialainen ja vaikuttaa yksilöiden turvallisuuteen, mutta myös yhteiskuntaan. Useat salmonellatapaukset voivat aiheuttaa terveydellistä vaaraa yksilöille ja samalla nostaa yhteiskunnan terveydenhuollon kustannuksia. Salmonellan merkitys elintarviketurvallisuudelle näkyy erityisesti eläinperäisissä tuotteissa. Tutkimuksen tavoitteena oli selvittää eläinperäisten elintarvikkeiden sisämarkkinatuonnin toimijoiden lainsäädännön tuntemista ja selvittää, minkälaista on näiden käytännön osaamisen sekä toiveet valvojien ohjeistukselle. Tarkoitus oli saada käsitys siitä, minkälaiseksi toimijat kokivat oman osaamisensa harjoittamansa sektorin lainsäädäntöön. Tutkimus koostui toimijoiden haastattelusta puolistandardoidulla teemahaastattelulla, jonka avoimista kentistä selvitettiin toimijoiden hankaluuksia vastaanottotarkastuksien suorittamisessa ja jäljitettävyyden hallinnassa. Lisäksi selvitettiin, mitä asioita toimijat itse pitävät hankalina liittyen elintarvikkeiden tuontiin Suomeen. Tutkimuksessa havaittiin, että osa toimijoista kokee Suomeen vaadittavan byrokratian jopa epäreiluksi, sillä salmonellaerityistakuiden ulkopuolella olevat maat eivät läheskään aina tunnista, mitä asiakirjoja tulisi toimittaa Suomeen, sillä samoja asiakirjoja ei tarvita muualle. Tutkimuksen tuloksista havaittiin, että toimijat kaipaavat lainsäädännön päivityksen ohjeistusta sekä tietopakettia siitä, mistä maista tuodessa tulee saada myös erillinen salmonellatodistus. Havaittiin, että jatkotutkimukselle olisi tarvetta ja varsinkin isomman vastaajajoukon saavuttaminen olisi merkityksellistä. Nyt tutkimukseen ei saatu osallistumaan niin paljon toimijoita, kuin olisi ollut tuloksien kannalta tärkeää. Vähäinen vastaajajoukko jätti tuloksiin tulkinnanvaraa.
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(2022)Merkittävä osa elintarvikeperäisistä mikrobiologisista ja kemiallisista vaaroista kasvaa, leviää tai syntyy kuluttajien kotona. Kuluttajat vaikuttavat ruoan turvallisuuteen käsittely- ja säilytystottumuksillaan, joiden arviointi on nykyisessä riskinarvioinnissa vaikeaa puutteellisen aineiston takia. Jotta riskinarviointi olisi paikkansapitävä, ja sen mukaan luodut ohjeistukset, säädökset ja lait mahdollisimman kohdennettuja, tulee kuluttajien vaaroille altistumisen arviointi olla aiempaa tarkempaa. Tutkimus suoritettiin Ruokaviraston toimeksiantona, ja sen tarkoitus oli luoda valmis kyselypohja riskinarvioinnin tueksi. Kyselylomakkeiden avulla pyrittiin selvittämään kuluttajien kalan ja lihan käsittely- ja säilytystottumuksia kotioloissa, millä on merkittävä vaikutus kemiallisille ja mikrobiologisille vaaroille altistumisessa. Tutkimus koostui kahden kyselylomakkeen luomisesta ja niiden validiuden arvioimisesta yksilöhaastatteluilla (n=30, 18–83 v.). Tutkimuksessa havaittiin, että lomakkeet eivät sellaisenaan olleet valmiita käyttöönottoon. Osa kysymyksistä ei soveltunut haluttuun tarkoitukseen, eikä niillä täten saatu kerättyä tarvittavaa aineistoa. Ennen lomakkeiden käyttöönottoa myös kyselyissä käytettyä 7-portaista ankkuroitua asteikkoa tulee muokata numeerisemmaksi, sillä sanalliset ankkurit olivat monitulkintaisia. Tässä tutkimuksessa ehdotettujen muokkausten jälkeen lomakkeiden validiteetti olisi tärkeää tutkia myös seurantatutkimuksen avulla, mutta myös sellaisenaan lomakkeet tuovat tarvittavaa aineistoa kuluttajien kotikäyttäytymisestä.
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(2020)Faba bean (Vicia faba L.) is a healthy and ecological pulse crop. Nevertheless, it contains antinutritive compounds, including lectins. Lectins are proteins or glycoproteins that bind to carbohydrates. Faba bean lectin is called favin and it binds specifically to mannose- and glucose-like carbohydrates. Agglutinatination assays have been traditionally used for the determination of lectins. These assays are, however, often inaccurate. The aim of this study was to adapt and optimize a method for the quantification of faba bean lectin and analyze lectin levels in untreated and treated faba beans. Enzyme-Linked Lectin Assay (ELLA), which is based on the ability of lectins to bind to specific carbohydrates, was adapted in the study. The hypothesis was that the method is suitable for the quantification of faba bean lectin. The commercial lectin standard did not react in the assay and thus the quantification of lectins was not possible. The faba bean samples, however, reacted and the absorbance values of varying samples were compared. The protein-rich faba bean fractions gave the highest absorbance values. Particle size affected the determination of lectins. Heating was efficient in lowering the absorbance values. Long-time roasting and boiling were the most efficient methods to reduce the binding capability of lectins.
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(2020)The Baltic Sea is a unique and delicate brackish water ecosystem with high primary productivity driven by oceanic biogeochemical cycles of oxygen, iron, silicon, nitrogen and phosphorus. Elevated anthropogenic nutrient loading into the Baltic ecosystem has resulted in a large-scale increase in destructive cyanobacterial blooms in the open Baltic Sea over the past century. The toxic cyanobacterium Nodularia spumigena is a major component of surface blooms in the open Baltic Sea and continues to bloom even after the depletion of phosphate from the surrounding waters. This phenomenon has been attributed to an ability to scavenge phosphorus from recalcitrant sources. However, the exact phosphorus species that sustain N. spumigena growth in the Baltic Sea remain largely unknown. Here, I employ a comparative genomics approach to determine the evolutionary dynamics of phosphorus scavenging in eight strains of N. spumigena and predict the range of phosphorus sources that may support their growth. Then, I test these predictions by growing six strains of N. spumigena on a number of potentially bioavailable phosphorus sources. Among the phosphorus scavenging genes identified by the genomic analysis, putative pathways for the enzymatic degradation of phytic acid, phosphite, and phosphonates were present and highly conserved in the species. Subsequent growth experiments demonstrated that the organism may grow using phytic acid and phosphite, as well as the phosphonates methylphosphonic acid, ethylphosphonic acid, and nitrilotris(methylenephosphonic acid), as sole phosphorus sources. These results indicate that N. spumigena blooms may be supported by several phosphorus sources previously not known to contribute to eutrophication in the Baltic Sea. While additional growth experiments and further research on the environmental prevalence of these compounds are necessary, the findings presented in this study expand our knowledge of how N. spumigena dominates phytoplankton blooms in a phosphorus-scarce environment and may help to inform future eutrophication mitigation efforts in the Baltic Sea region.
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(2023)Cellular agriculture (CA) utilizes cells to produce alternatives for conventional animal or plant-based foods. Concepts for CA are available, but their feasibility for large scale production is not yet well documented. The aim of this work was to compare CA and conventional milk chain in terms of energy demand. Enzyme production was included to the analysis as a benchmark to precision fermentation. In the life cycle analysis (LCA), life cycle inventory was compiled from scientific literature for CA and enzyme production. Inventory data for milk powder production was taken from Valio Carbo Calculator. A functional unit of 1 kg protein was applied. Cumulative energy demand for each product was re-calculated applying a cradle-to-gate system boundary. Background data was compiled from Ecoinvent and Agri-footprint databases and analyzed with OpenLCA. Milk protein in general has lower requirement in non-renewable and renewable CED than CA alternatives. Main contributors to CED in CA were electricity, thermal energy, carbon source and in some scenarios cleaning-in-place (CIP). CED values were 185 MJ/FU, 179 MJ/FU – 1007 MJ/FU and 410 MJ/FU – 166 385 MJ/FU for milk protein production, CA, and enzyme production, respectively. Moreover, enzyme production revealed that CED of CA has potential to have much higher values than reported on CA production. In the future, studies with continuous fermentation utilizing different by-products and including more impact factors should be pursued.
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(2021)Enzyme treatments have been able to reduce the amount of oligosaccharides and phytates in legumes. Enzyme treatment has the potential to improve the sensory properties of the product and reduce the stomach symptoms they cause. The aim of the study was to find out how enzyme treatment affects to the sensory properties of spoonable yogurt-like faba bean and pea-based snack samples. In addition, an online survey was made to map stomach symptoms caused by legumes and to study their effect on the use of legumes and legume foods. The methods used in the study were generic descriptive analysis with a trained panel (11 panelists) and an online survey made with E-lomake (227 respondents). In addition, the benefit data from the second study of the project for pea snacks were used (27 evaluators). In the generic descriptive analysis, there were a total of 6 spoonable snack samples to be examined (3 faba bean samples and 3 pea samples). Both raw materials had a control sample (no enzyme treatment) and two differently enzyme treated samples. In the generic descriptive analysis, the panel evaluated 12 properties from the samples: color, fruity and legume-like odor, runniness, grainy, powderiness, thickness, sweet, bitter, legume-like, bitter aftertaste and total intensity of aftertaste. Enzyme treatment had an effect on texture and mouthfeel properties, but not on taste, color, or odor. As a result of the enzyme treatment, the structure thickened and became smoother. The raw material had an effect on all the properties to be evaluated, except for the legume-like flavor. Enzyme treatment had no effect on the pleasantness of spoonable pea snacks. According to the survey, the most common symptoms caused by legumes were flatulence and bloating. Of the legumes and legume foods, chickpeas and pea soup were the most common foods to cause symptoms. More than half (about 65 %) of the respondents stated that they would definitely or probably eat more legumes if they did not cause stomach symptoms. More than half (67 %) would also be absolutely or probably willing to try enzyme-treated legume foods. Based on the results, it is worth further investigating the effects of enzyme treatment on sensory properties, especially in terms of structure / mouthfeel. In addition, the effect of fermentation on the sensory properties of pea and faba bean spoonable snacks should also be studied, as fermentation has been found to improve the sensory properties and nutritional value of plant-based spoonable snacks. Based on the responses to the survey, there seems to be a demand for legume products that cause less stomach symptoms.
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(2021)Glucuronoxylans (GX) from birch and galactoglucomannans (GGM) from spruce are capable of forming and stabilising oil-in-water emulsions. Phenolic compounds co-extracted with wood hemicelluloses enhance the stability of an emulsion. The stabilising mechanisms of emulsions prepared from GGM have been studied in detail, while emulsions stabilised by GX require further investigation due to the complexity of their chemical compositions. On the contrary to GGM-based emulsions, pectin was found at the interface of GX-based emulsions. We hypothesise that pectin plays a role in emulsification and affects the bimodal droplet size distribution of an emulsion. Therefore, this study aimed to assess the functionality of pectin in GX-based emulsifiers with pectinase. First, pectinase treatment conditions were optimised, namely reaction medium, time, temperature and pectinase dosage. The enzymatic hydrolysis of pectin was confirmed quantitatively by gas chromatography (GC). To investigate the role of pectin in emulsion stabilisation, rapeseed oil-in-water emulsions were prepared from pressurised-hot-water-extracted (PHWE) spray-dried GX (sGX), sGX treated with pectinase (p-sGX), sGX treated with pectinase and centrifugation (c-sGX), ethanol-precipitated GX (eGX), eGX treated with pectinase (p-eGX), and eGX treated with pectinase and centrifugation (c-eGX). The stability of the 6 emulsions was measured in a 2-week accelerated storage stability test. Phenolic compounds originating from lignin were characterised by pyrolysis gas chromatography-mass spectrometry (pyrolysis GC-MS) to monitor the changes of lignin contents before and after pectinase treatment. It is concluded that the optimum conditions of pectinase treatment were: reaction medium: 0.1 M sodium acetate buffer (pH 4.5), reaction temperature: 50 °C, reaction time: 2 hours, pectinase dosage: 304 U per gram of birch hemicellulose. Results from GC analysis of free monosaccharides confirmed that only pectin was hydrolysed under the abovementioned pectinase treatment conditions and that the hemicellulose backbone structure remained intact. Emulsions prepared from sGX remained stable for over 2 weeks, while creaming was observed in emulsions stabilised by p-sGX and c-sGX during the second week of storage. Emulsions prepared from eGX, p-eGX, and c-eGX remained stable for over 2 weeks. Results from pyrolysis GC-MS indicated that pectinase treatment removed some of the phenolic compounds in GX. Therefore, it was concluded that associations existed among GX, lignin, and pectin. Pectin took part in the formation and stabilisation of emulsions prepared from sGX and eGX by connecting lignin to GX.
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(2019)Fungal wood-decayers play an important role in the recycling of biomass and circulation of nutrients in nature. Fungi are capable to convert cellulose, hemicellulose, pectin and lignin, by the action of carbohydrate-acting enzymes (CAZymes) secreted and also by non-enzymatic reactions, depending on the ecology and decay strategy of the fungus. In the present study, four Basidiomycota fungi with different decay strategies were studied to compare their enzyme activity profiles. The white rot fungus Phlebia radiata, brown rot fungus Fomitopsis pinicola and “grey rot” fungus Schizophyllum commune were cultivated on birch (Betula pendula) wood pieces for twelve weeks, whereas the litter-decomposing fungus Coprinopsis cinerea was cultivated on cut barley (Hordeum vulgare) straw for six weeks. All fungi were also cultivated on liquid medium (malt extract 2%) for four weeks. Laccase, manganese peroxidase (MnP), β-glucosidase, xylanase and endoglucanase activities were followed weekly by measuring the absorbances on 96-well plates. The pH and the production of organic acids at each time point were also followed. The results showed that P. radiata produced high laccase and MnP activities. Additionally, high amounts of succinic acid in the aqueous phase of the solid-state cultivations were detected. F. pinicola had a notable production of xylanase activity on birch, in contrast to the moderate β-glucosidase and endoglucanase activities observed on the same substrate. S. commune was a strong producer of β-glucosidase, but especially xylanase activity on solid substrate. Lastly, the litter-decomposer C. cinerea seemed to have a poor performance in enzymatically decomposing the lignin portion from barley straw, whereas a preference on hemicellulose decomposition was observed. Overall, the results indicated the ability of the studied fungi in decomposing the components of the plant cell wall to different extents according to their decay strategy, which is key in the understanding of the ecophysiology of wood-decay and litter-decomposing fungi, and the potential of fungal enzymes for biotechnological applications.
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(2020)Securing an adequate protein intake raises questions for the future, and various plant protein products have grown in popularity in recent years. Tofu is one of the most popular vegetable protein products due to its versatility. Also, its different structural types are appealing to consumers. One way to increase the value of other grain legumes closer to soybeans would be to develop a tofu analogue from them. Faba beans are potential for this purpose, as they can be cultivated under the northernmost conditions, they are as rich in protein like soybeans and the proteins within soybean and faba bean are similar in structure. This study complements research related to the gelation of faba bean proteins. The aim was to study how different coagulants, their contents and different faba bean protein contents in the emulsion affect the resulting gel structure. The gels produced by each coagulant were examined separately so that the variables, i.e., coagulant and protein contents, were given three different values. The protein content of the emulsion was either 6, 7 or 8% (w/v), and the contents of coagulants were as follows: transglutaminase (TG) 5, 25 or 50 U/g of protein, gluconodeltalactone (GDL) 0.3, 0.65 or 1%, citric acid 0.14, 0.16 or 0.18% and calcium sulphate (CaSO4 · 2 H2O) 0.5, 1 or 1.5% (w/w). The structures of the gels were compared based on the results of Texture Profile Analysis (TPA) and sensory observations, and in addition, the samples were examined for the interactions formed between the proteins. This was done by dissolving the gels in various solvents. Of the gels studied, the most different structure was produced by transglutaminase, which provided a solid-like gel structure at the highest content combined with the highest protein content in the emulsion. Its TPA value for hardness was the highest. The interactions between proteins also differed most when comparing the results of other gels to transglutaminase gels. A probable explanation for these results was the strong isopeptide bonds formed by TG. GDL, citric acid or calcium sulfate did not produce such a solid gel structure, but the structures of the samples were much softer, part almost liquid. The protein content had a statistically significant effect on the hardness of gels coagulated with TG and calcium sulfate, among others. The coagulant content also affected the results of the TPA measurements, but they had less effect than the protein content.
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(2021)Cryptosporidium, a parasitic eukaryote, is the causative agent of cryptosporidiosis, a diarrheal disease with the potential to be life threatening in immunocompromised people. The number of cases has been rising as diagnostics have improved, suggesting the disease is more common than previously thought. Currently in Finland, samples are only typed to the genus level. The objective of the study was to establish a Cryptosporidium typing protocol for outbreak investigation nationally at the Finnish Institute of Health and Welfare with the long-term goal of preventing outbreaks. Reliable typing methods could also help find new reasons behind the increase in cases, monitor the emergence of new subtypes, and reveal new transmission routes. Typing was set up with samples from the Helsinki and Uusimaa Hospital District laboratory as well as the Finnish Food Authority. DNA was extracted from stool samples, species were identified with real-time PCR of the 18S rRNA gene, and gp60 subtypes were determined with nested PCR as well as Sanger sequencing. The Zymo QuickDNA Fecal/Soil Microbe Miniprep Kit was suitable for extracting troublesome parasite DNA. Out of the successfully subtyped samples, the majority was identified as Cryptosporidium parvum, out of which 60 % belonged to the IIaA15G2R1 subtype. The typing method described in this study was successful in typing 19 of 22 samples and will be utilised by the Finnish Institute of Health and Welfare for outbreak investigation on the national level.
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(2024)Antimicrobial resistance (AMR) is a crucial problem in the clinical field worldwide. The need for novel antimicrobials to tackle AMR is imminent. Image-derived data can be used to understand the mechanism of action (MoA) of newly discovered compounds and classify them within known classes of antibiotics. This study aimed to develop a simple image-based measurement method for screening new antimicrobials and simultaneously defining the MoA. In the process, Escherichia coli ATCC 25292 was selected as a model strain from the Gram-negative bacterial group. This strain was treated with antibiotics belonging to different classes. Treated bacteria were imaged with Cytation 5 Cell Imaging Reader and analyzed using ImageJ2 software. The developed workflow was validated by testing the pipeline to be applied for some ESKAPE strains categorized as antibiotic-resistant bacteria. The results revealed that this pipeline enables us to observe the bacterial single-cell phenotypic changes in response to antimicrobials, such as the elongation caused by ampicillin and ciprofloxacin treatments, which are cell wall synthesis and DNA replication inhibitors, respectively. The treated bacterial cells were significantly longer than untreated cells from the sample without antibiotic. Thus, the image-based-high throughput assay can support the drug discovery by identifying the preliminary MoA of new antimicrobials against AMR bacteria. Promising data obtained on E. coli and some pathogenic bacteria allow for pursuing similar approach with other AMR Gram-negative bacterial species.
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(2023)Carbapenemase-producing Enterobacteriaceae (CPE) resist carbapenem class of antibiotics in addition to the other type of antibiotic resistances they usually carry. The blaKPC-3 gene is one of the genes causing the carbapenemase production in bacteria. The aim of this study was to establish the Oxford Nanopore Technologies MinION sequencing method and integrate it with Illumina sequencing into a hybrid assembly for investigating the location of the blaKPC-3 gene in the bacterial genome. We used 14 isolates suspected of plasmid-mediated gene transfer and prepared three libraries using different DNA extraction methods. The contigs from the hybrid assembly sequences were used to annotate the target genes, which were then included in a phylogenetic tree and distance matrix analysis. DNA extraction method had an impact on the amount of data and the length of reads produced in MinION and the Smart DNA prep extraction kit with InnuPure C16 touch extraction device produced the best results. The blaKPC-3 gene was located on plasmids in each isolate, and the similarity of the plasmid sequences indicated that horizontal plasmid-mediated gene transfer has likely occurred between different species. However, the clonal spread cannot be excluded, and further research is needed to confirm these findings.
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(2023)Plant-based milks can be unstable during storage due to the colloidal structure of these drinks. In general, e-coded additives are used to increase the viscosity of the drinks and hence, improve stability. Oat beta-glucan, microbially or enzymatically produced exopolysaccharides, such as dextran, and flaxseed mucilage are natural hydrocolloids that are known to have the ability to increase viscosity. These hydrocolloids could potentially be used to replace e-coded additives. The aim of this thesis was to study the stabilizing potential of oat beta-glucan, exopolysaccharides, and flaxseed mucilage in oat drinks. Oat drinks with added hydrocolloids were compared to control samples that were oat drink without added hydrocolloids and oat drinks with pectin at concentrations of 0.2% and 0.4%. Oat beta-glucan, exopolysaccharides, and flaxseed mucilage were added to the prepared drinks by replacing 10% of water with the extracts. Additionally, stabilizing properties of isolated and freeze-dried microbially produced dextran was studied by adding it to the drinks at concentrations of 1.5%, 1.0% and 0.5%. Stability of the oat drinks was assessed during a 14−day storage period by measuring the viscosity, pH, and phase separation. Results of this study demonstrated the stabilizing potential of the natural hydrocolloids. The addition of hydrocolloids increased the viscosity in all samples. The inclusion of natural hydrocolloids led to a similar stability, and in some cases also significantly lower viscosity, compared to pectin added drinks. Oat beta-glucan had a remarkable positive impact on the stability of oat drinks. This was most likely due to the network formation of oat beta-glucan molecules, which decreased the sedimentation of colloidal particles. Enzymatically produced dextran also improved the stability of oat drinks, which might be attributed to the viscosity-increasing -capacity of dextran. However, the stabilizing role of microbially produced exopolysaccharides was not shown. For future study, the molecular interactions of natural hydrocolloids in the colloidal solution should be investigated.
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