Browsing by study line "ingen studieinriktning"

Cyanobacteria of the order Nostocales, including Baltic Sea bloom-forming species Nodularia spumigena, Aphanizomenon flosaquae, Dolichospermum spp., produce resting stages, known as akinetes, under unfavorable conditions. These akinetes can persist in the sediment and germinate if favorable conditions return, simultaneously representing past blooms and possibly contributing to future bloom formation. The present study characterized cyanobacterial akinete survival, germination, and potential toxin production in 40-to-175- year-old brackish water sediment archives in order to understand historical bloom expansion, akinete persistence, and cyanobacteria life cycles in the northern Baltic Sea. Results showed that cyanobacterial akinetes can persist in and germinate from northern Baltic Sea sediment up to 424 and 174 years old, at coastal and open-sea locations respectively. Akinete abundance and viability decreased with age and depth of vertical sediment layers. Increases in sediment organic matter content and akinete abundance largely corresponded with the historical expansion of anthropogenic eutrophication-fueled blooms of cyanobacteria in the northern Baltic Sea, beginning in the mid-twentieth century. The detection of potential hepatotoxin production from akinetes and revived cultures was minimal and restricted to the coastal sediment core. Phylogenetic analysis of culturable cyanobacteria from the coastal sediment core indicated that the majority of strains likely belonged to benthic genera Anabaena. Findings also supported the notion that, in comparison with Nodularia and Aphanizomenon spp. akinetes, Anabaena/Dolichospermum spp. akinetes play a more significant role in their life cycle and bloom initiation strategies. Further research is recommended to accurately quantify akinetes and create a higher rate of toxin gene detection from brackish water sediment samples in order to further describe species-specific benthic archives of cyanobacteria. Overall, measuring cyanobacterial akinete abundance, germination experiments, and genetic methods can be effectively used to determine akinete persistence, viability, and potential toxin production in brackish water sediment samples. This study highlights the prolonged survival of cyanobacterial akinetes in northern Baltic Sea sediment samples, up to 174 years old.

This study examines international doctoral candidates’ decision to apply to the University of Helsinki. It aims to shed light on the factors that result in choosing a doctoral programme at the Doctoral School in Humanities and Social Sciences as well as illustrating what that decision making process constitutes of. Finally, it seeks to understand how newly started doctoral candidates evaluate the decision that they made. For this case study 10 international doctoral candidates in humanities or social sciences were interviewed individually about their journey from a prospective student to an enrolled doctoral candidate. The interviews reveal different motivations and aspirations as well as the influence on the service evaluation. The decision making process constitutes of need recognition, search of information, evaluating information, making the choice and post-purchase evaluation. A dominant factor waking the need for a doctorate is a wish for career improvement either by advancing in one’s career or by making it possible to enter a research career. Personal and interpersonal reasons can also influence the desire for a PhD in a specific institution, for example, because of plans of migrating to that country or finding a supervisor there. The doctoral candidates evaluated their decision cautiously but in a positive manner. Some described challenges at the onset of their journey but none of those challenges were implied to be so serious that they would consider dropping out. The challenges were mostly related to academic and social integration, funding or figuring out how to organise one’s doctoral studies, however, the informants were mostly optimistic about overcoming these challenges. * Tässä tutkimuksessa tarkastellaan kansainvälisten tohtorikoulutettavien päätöstä hakea Helsingin yliopiston Humanistis-yhteiskuntatieteellisen tutkijakouluun. Tutkimuksen tarkoituksena on valaista valintaan vaikuttavia tekijöitä sekä havainnollistaa, mistä päätöksentekoprosessi koostuu. Lisäksi se pyrkii ymmärtämään, miten hiljattain aloittaneet tohtorikoulutettavat arvioivat tekemäänsä päätöstä. Tätä tapaustutkimusta varten haastateltiin 10 kansainvälistä tohtorikoulutettavaa, jotka opiskelevat jossakin Helsingin yliopiston Humanistis-yhteiskuntatieteellisen tutkijakoulun tohtoriohjelmassa. Haastatteluissa kartoitettiin heidän reittinsä tohtoriopintoja harkitsevasta opiskelijasta tohtoriohjelmaan hyväksytyiksi tohtorikoulutettaviksi. Haastattelut paljastivat syynsä hakeutua tohtorikoulutukseen sekä päätöksentekoprosessin eri vaiheissa vaikuttavat tekijät. Hakuprosessin ja opintojen alkuvaiheen palvelukokemukset heijastuivat palvelun arviointiin. Päätöksentekoprosessi koostuu tarpeen tunnistamisesta, tiedonhausta, tiedon arvioinnista, valinnasta ja päätöksen jälkeisestä arvioinnista. Merkittävä tohtorikoulutukseen hakeutumiseen kannustava tekijä on toive urakehityksestä joko etenemällä urallaan tai mahdollistamalla tutkijanuralle pääsy. Henkilökohtaiset syyt sekä ihmissuhteet voivat vaikuttaa tohtoriohjelman valintaan tietyssä yliopistossa, esimerkiksi jos suunnitelmissa on muuttaa kyseiseen maahan tai tohtorikoulutettava löytää sieltä ohjaajan. Tohtorikoulutettavat arvioivat päätöstään varauksella, mutta positiivisesti. Jotkut kuvailivat haasteita matkansa alussa, mutta mikään näistä haasteista ei ollut niin vakava, että he harkitsisivat lopettamista. Haasteet liittyivät enimmäkseen akateemiseen ja yhteisöön integroitumiseen, rahoitukseen tai tohtoriopintojen organisointiin, mutta informantit suhtautuivat enimmäkseen optimistisesti haasteista selviytymiseen.

Yeasts are a major spoilage threat in carbonated and fermented beverages, causing considerable economic losses for the manufacturers. Dekkera bruxellensis and Zygosaccharomyces bailii are the two most common spoilage yeast in beverages due to their high tolerance towards beverage-related stress factors. For industry, early and reliable detection of contamination is necessary to minimize spoilage potential and maintain product quality. Cultivation on selective/differential media remains the main method for detection of these organisms, with incubation times from 3 to 15 days. Beverage-related stresses may generate sub-population of injured yeast cells and further delay or even prevent the detection in regular media. PCR, flow cytometry and other alternative detection methods also rely on enrichment cultivation to achieve the required sensitivity for the industry. Therefore, reduced incubation time of sample enrichment and improved detection of injured cells is crucial for a more rapid and reliable detection method. Modification of specific compounds in the culture medium composition has been reported to improve recovery of bacteria after stress. As analogue studies have not been performed on spoilage yeast, modification of the culture medium composition offers a possibility to improve the growth of injured and healthy yeast cells. The aim of this study is to reduce cultivation time required for detection of healthy and injured Dekkera bruxellensis and Zygosaccharomyces bailii cells. Initially, conditions for inducing organic acid and heat injury in D. bruxellensis, D. anomala and Z. bailii cells were studied in an artificial beverage containing basic components of soft drinks. Selective and non-selective plate cultivation and fluorescent viability stains were used to assess the level of injury. The organic acid treatments resulted in inconsistent injury of spoilage yeasts, and thus, recovery from organic acid injury could not be screened. The heat treatments resulted in consistent 1-3 log reduction of viable cell counts. Altogether, 46 potential injury-relieving or growth-enhancing supplements were screened for their effects on the growth rate and lag time of heat-treated and untreated cells in non-selective YM broth using high-throughput automated turbidometry. During individual screening, the growth of Z. bailii strains was significantly improved (p<0.05) only by supplementation with three ion sources: calcium chloride, potassium chloride, and magnesium sulphate. Synergistic effects of the three ion sources was optimized for D. bruxellensis and Z. bailii individually using surface response analysis. Optimized D. bruxellensis YM medium showed no consistent impact on healthy or heat-treated D. bruxellensis strains. On the other hand, two out of the three Z. bailii strains showed significant lag time reduction of 63-66% in untreated cells and 34% in heat-treated cells when incubated in optimized Z. bailii YM medium. The lack of differentiation between improvement of growth of untreated and heat-treated cells point to a generalized ionic deficiency in YM medium. In conclusion, the optimized Z. bailii YM medium is a promising candidate for reducing the detection time of the common spoilage yeast, but it would still require validation with additional Z. bailii strains and quality control samples. It would be also interesting to study the benefits of the medium for cultivation of other spoilage yeasts and in the presence of Z. bailii selective compounds. The information about the importance of various salts for growth of Z. bailii may also prove useful in biotechnological applications of this yeast.

In the past 20 years, three known disease emergence events of highly pathogenic coronaviruses have highlighted the importance of monitoring wildlife for the presence of these viruses. Their peculiar characteristics, like high mutation and recombination rate, have increased their potential for species adaptation and interspecies transmission. Understanding the diversity of these viruses in wildlife and increased surveillance might be key to predicting and preventing future spillovers and pandemics. Studies on wildlife coronaviruses commonly focus on the order Chiroptera, mainly in temperate and tropical regions of the Asian continent. Even though animals belonging to this order are considered the main reservoir, the importance of other small terrestrial mammals should not be overlooked. Rodents, for instance, are animals of great interest for many zoonoses, as they often host parasites, bacteria and other groups of viruses that cause diseases in humans. A recent description of several lineages of coronaviruses recovered from rodents from China highlighted and suggested the presence of these viruses in small terrestrial rodents. In this project, we aimed to investigate the presence of coronaviruses in small mammals from France. Samples were collected during spring 2021 in twelve different locations, within two regions of eastern France, Auvergne Rhône-Alpes and Franche Comté. A total of 448 rodents, 13 shrews and 416 bat samples were collected. The samples were screened and coronaviruses sequences were recovered in 20 different samples. Nine Betacoronavirus genus sequences were recovered from rodent colon samples, and one Alpha- and ten Betacoronavirus sequences from bat guano. These results confirmed previous evidence of these viruses’ presence in small mammals from France and provide the first evidence of betacoronaviruses circulating in wild French bats. The study covers two eastern regions that have not been surveilled in previously released studies therefore this highlights the need to increase the efforts in monitoring these viruses and their wildlife host

Gas chromatography (GC) is one of the most widely used method for analysis of lipids and it is commonly combined to a flame ionization detection (FID), since GC-FID is an excellent combination for quantitative analysis of wide range of lipids. Before GC analysis can be performed, lipids must be extracted from the sample and derivatized. Some common extraction methods include Soxhlet and Soxtec extraction, Folch extraction and extraction with the help of acid hydrolysis. To be able to analyse the extracted fatty acids by GC, they must be in a volatile form. This can be achieved by forming fatty acid derivatives by, for example, methylation. The commissioner wishes to have a way to analyse the fatty acid composition of pork by GC in their laboratory. The aim of the study was to take in use an easy, safe-to-use and simple method for determination of fatty acid composition of pork by gas chromatography, using the instruments and equipment already found from the laboratory. The research had three different parts. First, heptane-isopropanol extraction, Bligh & Dyer extraction and Caviezel extraction were compared. Then the chosen extraction method was validated. Finally, two different pork samples were compared to test the method’s ability to differentiate them. Caviezel extraction was chosen as the best extraction method, and it was validated by parameters repeatability and robustness. The method was able to differentiate samples that had similar, but slightly different fatty acid compositions. However, method still requires some fine tuning since the GC column seemed to be highly sensitive to any disturbances.

Aflatoxin B1 (AFB1) is a naturally occurring toxic compound produced by various types of fungi. The presence of AFB1 in food and feed can lead to severe illness, which makes it a serious threat to humans and animals. Due to global climate change, the cases of AFB1 contamination in food will increase since high temperature and humidity favour fungal growth and the production of AFB1. The bioavailability of AFB1 can be decreased by adsorption or biotransformation. Adsorption happens by the utilization of different AFB1 binding agents, which can be either mineral and organic or biological adsorbents. Mineral and organic adsorbents are only used in feed since they may also bind to nutrients. Biological adsorbents are being studied more actively since they maintain the nutritional value of the food. Studies show that Lactic acid bacteria (LAB) can be used to bind AFB1 from contaminated foods. The aim of this research was to study the capacity of different LAB (viable and nonviable) to adsorb (bind) AFB1 under different pH conditions. The research first evaluated the binding ability of AFB1 by 13 viable and nonviable LAB strains at pH 7. The best binding strains were selected for further study at pH 3 to mimic gastric pH. The AFB1 binding with cells was performed at 25℃ for 90 min. To determine the binding capacity, the solutions were centrifuged and free AFB1 in the supernatant was extracted with acetonitrile, and quick, easy, cheap, effective, rugged, and safe (QuEChERS) method was used to clean up the samples. AFB1 concentration was determined by ultra-performance liquid chromatography and fluorescence detection (UPLC-FLD). The LAB strains used in this research were shown to have the ability to bind AFB1. Binding efficacy of AFB1 depended on the bacterial strain. Viability and pH also affected the binding ability. All nonviable cells showed better binding ability (44.9–71.3%) compared to the viable cells (29.0–49.4%). The strains also had better binding capacity at lower pH regardless of the cell viability. The highest binding efficacy (71.3%) was achieved by the nonviable cell of Lactobacillus helveticus FAM 22155 at pH 3. The results of this thesis showed that some LAB strains bind AFB1 and that the binding is stable under stomach conditions. Studies to investigate the stability of the binding under simulated upper and lower gastrointestinal (GI) tract conditions (in vitro digestion) and in vivo studies are needed in order to provide further evidence of the applicability of LAB in lowering the bioavailability of AFB1.

Antibiotic resistance is an increasing, terrible threat to human health, leading to a growing need for alternative therapies. Phage therapy, using bacterial viruses to fight infections, is a promising alternative to antibiotic therapy. However, several obstacles need to be overcome. Regrettably, phage therapy remains inaccessible to many laboratories worldwide due to the need for expensive machinery to establish sensitivity of bacteria to phage. Moreover, shipping phages between laboratories remains challenging. In the current study a device-free bacteriophage typing PhagoGramAssay was developed. In the assay bacteria suspended in soft agar were poured onto a 60-well Terasaki plate containing phages suspended in fibrillated nanocellulose separated from the bacteria by a seal. Phages were released into the bacterial agar layer by puncturing the seal to test for sensitivity observable with the naked eye. Contrast between lysis zone and bacterial lawn was enhanced using 2,3,5-triphenyltetrazolium chloride. Optimized parameters included the amount of bacteria and phage added, volume of phage suspension, agar percentage and thickness and puncturing tool size. In addition, a prototype of such a puncturing tool was developed. The optimized PhagoGramAssay was tested using several bacteria-phage combinations. Moreover, infectivity and stability of phages stored on Terasaki plates was followed over the course of 4 weeks. The optimal bacterial amount added was found to be a 1:300 dilution in soft agar taken from a OD600 = 1 culture. Phage suspensions used in the assay were found to need to have a titer of at least 108 PFU/ml in the original lysate, with 8 µl of 1:10 dilution in fibrillated nanocellulose present in the wells. Optimal agar conditions were found to be 0.4% – 0.5% (w/v) with a thickness of 2 mm – 3 mm. The optimal puncturing tool shape was found to be a slit with a thickness of 0.5 mm. When using these conditions sensitivity could be established for a vast number of bacteria-phage combinations. All phages remained stable and infective over the course of 4 weeks . The newly developed PhagoGramAssay can be further developed into a kit-like phage typing assay that would enable laboratories to test for sensitivity on site whenever a multi-drug resistant bacterial strain is isolated from a patient sample, effectively making phage therapy accessible to laboratories that cannot afford expensive machinery. Additionally, the use of fibrillated nanocellulose should enable laboratories to exchange phages. The final form of such a kit, however, is dependent on manufacturers and investors and may need to be adjusted accordingly.

Non-communicable diseases such as cardiovascular diseases (CVDs) and erosive, unsustainable industrial fat-production methods pose two of the biggest threats to human health in great part of our planet. CVDs and obesity have been linked to diets high in fat and low in dietary fibre, pushing food manufacturers to adapt to more sustainable ingredients. For this reason, this research developed and researched about a new and sustainable plant-based oleogel intended to act as a substitute for saturated and hydrogenated fats. Its characterization was conducted through several techniques, including optical and field emission electron scanning microscopy, differential scanning calorimetry, Fourier transmission infrared spectroscopy, and synchrotron X-ray powder diffraction. The results showed that the build-up of the formation of the new oleogel was possible, while ensuring that both processing requirements and ingredients are readily available at food manufacturing plants, globally. These findings pose a great opportunity for plant-based fat-replacement formulations, through a sustainable approach. Considering previous studies, this novel system could potentially help in reducing the burden of obesity and CVDs, turning it into a functional food component. Further research on food applications and digestibility models could give more insight on the future applications of this fat-replacement system.

The porcine gut microbiome is a complex mixture of diverse microbes. During some diseases, the microbial balance of the gut can be disturbed, and harmful bacteria might multiply to concentrations that are harmful to health. To restore balance, the increase of beneficial bacteria that have probiotic potential plays a big role in avoiding the use of antibiotics. In order to develop a probiotic product containing these beneficial bacteria, it is necessary to concretely isolate them from a fecal sample. In this pilot study, the aim was to find an optimal selective growth medium that would allow to grow bacterial species with probiotic properties serving as a potential product in pigs and which would reduce the growth of redundant bacteria. A total of 12 different media were tested with four different sole carbon sources in M9 minimal salts, of which four being supplemented with volatile fatty acids were further tested. The results suggest that cellobiose or xylose could be the best alternatives of the investigated carbon sources for the species of interest. In addition, it was found that certain volatile fatty acids can inhibit the growth of Escherichia coli and several species of the genus Bacteroides.

African crops are sustainable and healthy alternative ingredients for potential use in various gluten-free products among traditional African foods. In this thesis maise-based, gluten-free crackers with 50% cereal (amaranth, sorghum and teff) and 50% and 75% legume (Bambara groundnut and cowpea) replacements were produced, and their baking performance and technological properties were examined. The effect of sorghum and cowpea flour's bioprocessing and mechanical raw material modifications on cracker technological and sensory properties was studied. The thesis aimed to solve whether maise and African crop flours could be used in gluten-free crackers and how would they affect nutritional values, baking performance and technological and sensory properties in gluten-free crackers. The nutritional calculations indicated that African crop replacement increased fibre content at least by 2.4% and protein by 1.9 E% compared to 100% maise cracker. Crop replacements improved the dough elasticity and bakability and darkened the cracker surface. African crops and higher protein content increased cracker hardness and improved the rising ability. The highest hardness rate was measured with protein fractionated cowpea (31.55 ± 3.17 N, maise 4.02 ± 1.79%) and puffiness with Bambara groundnut 75% (43.57 ± 3.29%, maise 21.93 ± 0.002%). Raw material modifications changed the sensory profile of sorghum and cowpea crackers significantly by decreasing graininess in sorghum and beaniness in cowpea.