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(2023)Marine debris is a problem that also affects sea birds. Several bird species are known to utilise marine debris among their nest materials in different parts of the world. Debris in nests can cause entanglement and increase the risk of debris ingestion, and hazardous substances leaching from plastics can have negative effects on birds. There are also anecdotal observations of debris in the great cormorant (Phalacrocorax carbo sinensis) nests in the Gulf of Finland, however, systematic studies are lacking. In this Master’s thesis I examined the prevalence of debris in cormorant nests in the Gulf of Finland, focusing mainly on plastic debris. The study was carried out in four nesting islets, which were located in Kotka, Porvoo, Espoo and Kirkkonummi. The sampling took place in autumn 2021. 50 nests were randomly sampled on each nesting islet, and plastic debris in the nest was counted and classified according to their type, colour and origin. Plastic debris was further categorized in the laboratory according to their polymer type using Fourier Transform Infrared spectroscopy (FTIR). Debris from the nesting islets was also counted and classified according to their type, colour and origin. In total, 58% of the nests contained debris, but the prevalence of debris in the nests varied between the colonies; In Kirkkonummi debris was found in 92% of the nests while in Porvoo only 34% of the nests included debris. Plastics constituted great majority of nest debris (95%). Most common source for plastic debris was consumers, most common plastic type threadlike and polymer type polyethylene (PE). The number of debris in the nests was linked to the width and location of the nests: core nests contained more debris than periphery nests and the number of debris in the nest was positively correlated with the width of the nest. The amount of threadlike plastics in the nests was higher than that in the surrounding environment, indicating active selection by cormorants for threadlike debris types as nest material. Based on the results of this thesis, nest surveys could be a useful tool in evaluating the effectiveness of certain reduction measures aiming to tackle marine plastic pollution.
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(2018)Nuorten kiinnostus luonnontieteiden opiskelua kohtaan on heikentynyt sekä Suomessa että kansainvälisesti ja nuoria hakeutuu luonnontieteellisille aloille yhä vähemmän. Samaan aikaan Eurooppaan tarvitaan yli 700 000 uutta tutkijaa. Eräänä syynä nuorten kiinnostuksen puutteeseen luonnontieteiden opiskelua kohtaan pidetään nuorten stereotyyppistä tutkijakuvaa. Tutkijakuvalla tarkoitetaan henkilön mielikuvia ja käsityksiä tutkijoista. Stereotyyppiseen tutkijakuvaan kuuluvat käsitykset laboratoriotakkiin ja silmälaseihin pukeutuneista miehistä, jotka työskentelevät laboratoriossa tehden kokeita ympärillään monenlaisia tutkimusvälineitä. Stereotyyppisen tutkijakuvan väitetään vaikuttavan negatiivisesti nuorten asenteisiin ja kiinnostukseen luonnontieteiden opiskelua kohtaan ja jopa heidän halukkuuteensa hakeutua opiskelemaan luonnontieteellisille aloille. Suomalaisten lasten ja nuorten tutkijakuvaa ei ole aiemmin kartoitettu. Tämän tutkimuksen tavoitteena oli selvittää suomalaisten lasten ja nuorten käsityksiä tutkijoista. Tutkimuskohteena olivat Helsingin yliopiston LumA-tiedekasvatuskeskuksen kesän 2017 tiedeleireille osallistuneet lapset ja nuoret (N=455). Tutkimuksessa selvitettiin sukupuolen, iän sekä tiedeleirin teeman yhteyttä leiriläisten tutkijakuvaan. Tutkimusmenetelmänä käytettiin kyselylomaketutkimusta, jossa vastaajat piirsivät omiin mielikuviinsa pohjautuvan kuvan tutkijasta. Piirroksia käsiteltiin määrällisenä aineistona. Jokainen piirustus analysoitiin tarkistuslistan avulla, johon listattiin kirjallisuudesta ja aineistosta nostettuja stereotyyppiseen tutkijakuvaan liittyviä piirteitä. Tulokset analysoitiin deskriptiivisellä analyysillä. Sukupuolten välisiä eroja tarkasteltiin khiin neliö -testien ja Mann-Whitneyn U-testin avulla. Iän yhteyttä tutkijakuvaan selvitettiin Kruskal-Wallis -testillä. Tutkimuksen luotettavuutta tarkasteltiin validiteetin ja reliabiliteetin avulla. Tutkimuksessa selvisi, että suomalaisilla lapsilla ja nuorilla on stereotyyppisinä pidettyjä käsityksiä tutkijoista, vaikkakin stereotyyppisiä piirteitä esiintyi piirroksissa vähemmän aiempiin tutkimuksiin verrattuna. Tyypillisimmät piirroksissa esiintyneet stereotyyppiset piirteet olivat työskentely sisällä, miestutkija sekä erilaiset tutkimuksen symbolit ja teknologiavälineet. Sukupuolella oli yhteys tutkijakuvaan tyttöjen piirtäessä merkitsevästi enemmän naistutkijoita ja hymyileviä tutkijoita kuin pojat. Vastaajan ikä ei ollut yhteydessä stereotyyppisten piirteiden määrään, toisin kuin aiemmissa tutkimuksissa. Leirin teema oli vahvasti yhteydessä niihin tarvikkeisiin, joita tutkijan ympärille piirrettiin. Tutkimuksessa havaittiin piirrosten tulkinnan olevan subjektiivista ja vaikuttavan tutkimuksen tuloksiin. Siten nuorten tutkijakuvaa tulisi jatkossa kartoittaa useiden metodien avulla. Tämä tutkimus antaa viitteitä tiedeleirien potentiaalista lasten ja nuorten tutkijakuvan muovaamisessa. Tutkimuksen tuloksia voidaan hyödyntää luonnontieteiden opetuksen kehittämisessä sekä formaalissa että nonformaalissa tiedekasvatuksessa: tiedostamalla nuoren oman tutkijakuvan muodostuminen voidaan opetuksessa tarjota oppijalle mahdollisuuksia muodostaa realistisempaa ja monipuolisempaa tutkijakuvaa esimerkiksi tutkijavierailujen ja toiminnallisten aktiviteettien kautta. Tämä voi lisätä nuorten kiinnostusta ja minäpystyvyyttä tutkijan uraa kohtaan.
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(2023)It has been observed that children’s interest towards natural sciences decreases as they grow up and start middle school. The decrease of interest towards natural sciences and studying them has led to a situation, where science and technology students’ relative share of higher education students has been falling in some of the OECD countries. Formal education needs support to carry out fascinating science education for children and to maintain their interest towards natural sciences. One of the opportunities to fascinate children towards sciences are science centers and their activities either combined with formal education or organized in an informal form like science camps. The aim of this research is to survey the biological knowledge, the interest towards biology and the ability to apply the biological knowledge of science campers (mainly 5th and 6th graders) and to study the connections between them. At the same time, the effect of age and gender of the science campers is studied. To survey the biological knowledge of the campers, multiple-choice test was used and the fascination with biology was investigated with Likert scale variables. The ability to apply the biological knowledge was investigated with drawings that were produced during a biology-themed science camp program. The data was analyzed using quantitative methods. The results indicated that the science campers were relatively fascinated with biology and that they master biological knowledge quite well but the ability to apply the knowledge was varying. There were no differences between different ages nor genders but there are many factors such as the economic status of campers’ families that might have affected on the results. There was found a statistically significant connection between biological knowledge and fascination with biology, which is not surprising, but it speaks in favor of the importance of supporting fascination in terms of learning.
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(2021)During the Covid-19 pandemic in Finland, there was a debate about the usefulness of face masks in suppressing the epidemic. Lack of scientific knowledge was emphasised in the debate, and the participants sought to define the role of science in decision-making. In this thesis, the ways in which ignorance and uncertainty were discussed and used to define the boundaries of science in the Finnish face mask debate are studied. In the theoretical part of the thesis, the meanings of ignorance and uncertainty are clarified and the boundary-work of science as well as uncertainty as a boundary-ordering device are discussed. The politicisation of non-knowledge and the characteristics of policy-relevant science are also examined. In the empirical part, the knowledge/non-knowledge claims of the Finnish experts and decision-makers who participated in the face mask debate are analysed. The data consists of 99 quotations collected from news articles published from March 1 to October 31, 2020. Qualitative frame analysis is employed to examine the forms of knowledge and ignorance along with the boundary-ordering devices used in the debate. The results show that experts working at the science-policy boundary highlighted uncertainty and ignorance most often. They also used uncertainty as a boundary-ordering device the most, although overall, this came up very rarely in the debate. The main discrepancy was between the assessments of different expert bodies, as research scientists did not usually mention the underlying uncertainties of scientific findings. Different actors had different approaches towards knowledge and ignorance, reflecting differences in epistemic cultures. Regulatory science and academic science have different criteria for assessing the credibility of knowledge. Moreover, not all ignorance and uncertainty in decision-making can be reduced with scientific methods. Therefore, more resilient decision-making processes should be developed, in which ignorance and limitations of scientific knowledge are identified and embedded in the decisions.
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(2018)In this master’s thesis I examine transdisciplinarity in theory and practice. Transdisciplinarity is seen as an inevitable approach when we strive to understand and solve many of the complex problems of the modern world e.g. the environmental crisis. For this reason it has also quickly increased in popularity in the research funding. With this premise and despite the diverse theory on transdisciplinarity the implementation in practice is often relatively flimsy. This gap between theory and practice has acted as a motivation to the thesis, in which I am interested in how the transdisciplinary expectations based on the theoretical ideals and set on the cross-disciplinary environmental research intersect with the realistic transdisciplinary advancements in the research programs. In addition, I am interested to know why the practice doesn’t meet the expectations. The thesis is solidly theory-oriented. First I shed light on the background, characteristics and motivations of transdisciplinarity as well as disciplines, after which I present an array of the complex challenges of transdisciplinarity. In the results section I examine the manifestations of the challenges on a practical level that is based on three environmental research programs organized over the course of 2011–2014 by HENVI, the Helsinki University Centre for Environment (now HELSUS). In addition to the qualitative analysis based on the interview data, the results section also examines theory on a more practical level of implementing transdisciplinary research programs in general. This presentation thus enables a closer dialogue between the analysis data and practical theory. The primary results of this thesis are five problematics that are the manifestations of theory not meeting the practice properly. They are organized into the themes of funding, knowledge production, administration, socio-culture and education and help to organize and ultimately face the challenges of transdisciplinary research. From a comprehensive set of perspectives the problematics display strongly the highly disciplinary nature of the modern academia. This is the most significant single reason for the difficulties to accomplish transdisciplinarity. In addition, all the five problematics reflect the temporal restrictions that also undermine the potential of an effective transdisciplinary interaction. The essential measures to create solutions and hence also the ideal implementation of transdisciplinarity are mainly beyond the focus of the thesis. However, the problematics provide a problem-based framework that strives to contribute to the further studies focused more profoundly on the actual solutions
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(2020)In winter plants are exposed to harsh winter conditions with low temperatures being one of the major challenging factors. Traditionally winter has been considered a period unfavourable for plant growth and activity, but newer findings reveal higher levels of activity than previously assumed possible. Adaptations to different winter conditions are observed between species but also within species between populations which can be expressed in differing phenology between populations. Dormancy is a widespread phenomenon in the plant kingdom with major importance in plant evolution. Dormancy is considered to be present in seeds and buds of a wide spectre of plant groups, but asexual reproductive units like bulbils have been thought to lack the ability to undergo the phenomenon of dormancy. Findings suggest that a dormancy-like phenomenon can also be present in bulbils. Allium oleraceum is a bulb forming geophyte with a widespread distribution in Europe that grows on many differing habitats. The predominate form of reproduction in the species is the vegetative formation of bulbils. The wide distribution has led to adaptation to different environmental conditions, furthermore the species displays six levels of polyploidi partially differing in traits like ecology. The differences between cytotypes are regional and there are large intracytotytpic variations. In Finland tetra- and pentaploid populations have been reported, differing in their distribution patterns. The Finnish cytotypes exhibit differences in morphology but there is also evidence for ecological differences between the cytotypes. In addition, there is an atypical tetraploid population which differ significantly morphologically from other tetraploid populations. The objective of this master’s project was to examine the growth of bulbils from three different origins of Allium oleraceum. Another objective of the experiment was to give information on differences between the cytotypes in Finland, tetra- and pentaploids, but also the atypical tetraploid cytotype. Furthermore, I investigated whether the bulbils exhibit a dormancy-like phenomenon, with a special focal point on dormancy according to Vegis’ theory (1964). Earlier findings have shown considerable capability of growth during winter in Allium oleraceum, which is also examined in this project. The experiment included collected bulbils from two localities. Tetra- and pentaploid bulbils were collected from a mixed population of both cytotypes in Tvärminne, Hangö, and tetraploid bulbils were also collected from the atypical tetraploid population on Sveaborg, Helsingfors. Growth experiments were done outside and in growth chambers with controlled temperature and light conditions. The bulbils were planted outside in early autumn. Of each origin one group was kept outside during the entire winter, one group was put in growth chambers in December and one group was put in growth chambers in February to examine the effect of differing winter length on growth. During the experiment, the timing of growth onset in bulbs and leaf growth was followed up. The origins included in this project exhibited considerable differences. The pentaploid cytotype from Tvärminne had bulbils of greater size than the tetraploid cytotypes, between which there was only an indication of a difference. For the bulbils from the atypical tetraploid population growth onset took place early in the autumn and the vast majority of the bulbils started growing in a short period of time. For the two origins from Tvärminne the growth onset took place later and a considerable number of bulbils started growing in the spring. The tetraploid cytotype from Tvärminne exhibited earlier growth onset and a higher share of bulbils started growing in the autumn than the pentaploid cytotype from Tvärminne. In the growth chambers the differences between the three origins were not as obvious but the two cytotypes from Tvärminne were affected by the timing of the experiment more than the atypical tetraploid cytotype from Sveaborg. The observed differences between the origins in the experiment are thought reflect the different distribution patterns of the cytotypes and could hence be adaptations to different conditions. The atypical tetraploid population could be of Central European origin which would mean that it could have adaptations to mild winters which would explain the big difference between this origin and the two other origins. Between the two experiments in the growth chambers significant differences were observed. The growth was considerably greater in February than in December for all origins, especially in the midmost temperatures. The observed differences between the two experiments signifies that bulbils of Allium oleraceum exhibits a dormancy-like phenomenon and according to Vegis’ theory. In contrary to earlier findings, only little growth was observed during winter. The lack of considerable growth could be explained by the thick snow cover which made the amount of light that reached the plants very low which then led to little growth. The results from this project suggest that there are differences between the three different origins of bulbils included. Further studies are needed to find out if the observer differences are adaptations to local conditions or if there are differences on a higher level between the Finnish cytotypes.
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(2021)Energy consumption of apartment buildings account for a significant part of European Union’s total greenhouse gas emissions and improving the energy efficiency of buildings is a major part of reaching Union’s climate goals. To reach these goals the EU has revised some of its legislation and one of the latest reforms is the complete revision of Energy Efficiency of Buildings directive in 2018. Directives article 14 decreed that member states need to implement energy efficiency measures on large apartment buildings and to meet these measures member states were given three options on how to implement article 14. Finland implemented the article with so called voluntary advice method. The goal of this study is to understand the conclusion of the national implementation of article 14 and explain it with implementation theory. The study tries to understand what factors led to the implementation of voluntary advice method and whether this selection can be explained with implementation theory. Study design is one case explanatory case study. Seven semi-structured interviews were conducted for this research and the material was analysed with qualitative methods. All the interviewees were either officials in charge of the implementation or experts and researchers who took part in the implementation process. The study shows that the factors leading up to the selected implementation method were earlier experiences from other implementations, the straightforward nature of implementing advice method and the cost estimates between the given implementation options. It also became clear that the method was favoured by the officials, experts and target group and this volition might have affected the result. Study helps to understand the process of implementing EU legislation in a member state, what challenges officials face during the implementation and what kind of expectations steer the process. The study found out that previous implementation methods may have a significant impact on the implementation of revised directives. Study also verified the factors affecting implementation defined by implementation theories.
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(2022)Tiivistelmä – Referat – Abstract The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase is a master regulator of cell growth. In the presence of environmental cues, such as nutrients and growth factor, mTORC1 is transported to the lysosome where it is activated by a small GTPase Rheb. Dysregulation of mTORC1 has been linked to several diseases such as cancer and neurodegeneration. Despite our growing understanding of the nutrient-driven activation mechanism of mTORC1, we still do not fully understand how nutrients are transported out of the lysosome or how nutrient sensing is connected to nutrient transport. Recently, SLC38A9, a small lysosomal transmembrane protein, was identified as a mediator of the efflux of essential amino acids from the lysosome to the cytosol. It also acts as an amino acid sensor for mTORC1, playing a role in its activation. Due to poorly vascularized tumor cores, cancers such as pancreatic ductal adenocarcinoma, have access to very scarce amounts of free nutrients. Consequently, they rely on scavenging of protein macromolecules from the extracellular environment, followed by digestion inside lysosomes. The digested nutrients are released to the cytosol via transporters such as SLC38A9 and activate the mTORC1 pathway which carries out the growth processes. In fact, recent studies in mouse xenograft models have shown a severely slowed down growth of PDAC tumors with SLC38A9 knocked out. Blocking of SLC38A9 activity with pharmacologics or biologics would prevent the release of digested amino acids from the lysosomes, starving cancer cells of nutrients, while sparing normal cells that do not feed on extracellular proteins. However, SLC38A9 is still poorly understood, and development of selective inhibitors first requires mechanistic understanding of the protein and knowing what its binding pockets look like. In order to obtain this information, we aimed to determine the three-dimensional structure of SLC38A9 through cryogenic electron microscopy (cryo-EM). However, two significant challenges hindered our ability to obtain high-resolution images of this membrane protein: (i) its small size, and (ii) its constant conformational changes. To address this, I proceeded to develop a set of nanobodies that would bind SLC38A9 with high affinity and specificity. Nanobodies allow for locking of target proteins in specific conformational states, and they can also serve as chaperones for visualizing proteins in cryo-EM. To obtain these nanobodies, I used a library of 100 million unique nanobodies, displayed on the surface of yeast cells. Specific SLC38A9 binder nanobodies were obtained through multiple rounds of selection and sorting, using decreasing concentrations of fluorescently- labeled SLC38A9. After the final selection round, single colonies were picked and the strength of binding to SLC38A9 was evaluated. High-throughput screening results showed that we were able to obtain specific SLC38A9 binders and that there was variation in binding strength among the selected nanobodies. These nanobodies will enable the determination of the cryo-EM structure of SLC38A9 and also serve as tools to further dissect the function and mechanisms of SLC38A9 in amino-acid efflux from lysosomes to cytosol, providing further insights for the development of novel cancer therapeutics.
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(2021)Trace element analysis is a useful tool for the study of migration and migratory connectivity in birds. Trace elements are present in the environment and, through the food chain, can be incorporated into tissues such as growing feathers. Since the concentrations of elements remain stable after the feather has stopped growing, and trace element abundances can vary at very small geographical scales, the concentration of trace elements in feathers can provide information on the location where a feather was moulted. Trace element analysis is still rarely used and there are important gaps in our understanding of how trace elements can vary at different organizational levels such as within a feather, between individuals or even between species. It is also not clear if large-scale geographical patterns can be detected by the method, as trace element concentrations can vary a lot even at small scales, which could make it impossible to see larger-scale patterns. To address that, my objectives were (1) analysing the variability of trace element concentrations within feathers, between individuals and between species and (2) determining whether trace element levels differed in feathers grown in Africa compared to feathers grown in Europe. This would shed insight on the suitability of trace element analysis for the study of migration and migratory connectivity. I analysed the concentration of 18 trace elements in the rachis of feathers from willow warblers (Phylloscopus trochilus) and barn swallows (Hirundo rustica) collected in Finland. I plucked three belly feathers from willow warblers collected in spring, whose feathers had grown in Africa. These feathers were used to analyse variability of trace element concentrations within feathers and between individuals. They were also compared to feathers plucked from barn swallows collected in spring (two feathers per bird) to analyse variability between the feathers of two species that winter in the same region. Finally, African-grown feathers of willow warblers were compared to European-grown feathers of willow warblers collected in autumn (two feathers per bird) to look for differences in trace element concentrations in feathers grown on two different continents. Trace element concentrations were analysed using Laser-Ablation Inductively-Coupled-Plasma Mass-Spectrometry (LA-ICP-MS), which allowed to measure concentration at hundreds to thousands of points along the feather rachis. The concentration of each of the 18 elements was used as the response variable in linear mixed models (LMM). To model variation in concentration within the feather I used location along the feather rachis as the explanatory variable and explored how well it predicted concentration of each element. To compare variation between feathers and individuals I fit models including and excluding the feather and individual that each measurement belonged to as random effects and compared them using AIC. To compare between willow warbler and barn swallow feathers grown in Africa I included species identity as the explanatory variable and looked at how the concentration of the 18 elements differed between them. Finally, I followed the same approach to compare willow warbler feathers moulted in Africa and in Europe. For most elements there was little variation along the feather rachis, with concentration remaining stable from feather base to tip. Zn and S showed an increase in concentration starting at the feather base until the central part of the feather and then remained constant toward the tip. Feathers belonging to the same individual showed mostly similar trace element concentrations, although there were exceptions and differences between feathers of different willow warbler individuals were also little. 10 out of 18 elements showed significant differences in feathers of willow warblers and barn swallows grown in Africa. Eight of those elements were more abundant in willow warbler feathers, while only two were more abundant in barn swallow feathers.12 out of 18 elements showed significant differences between their level in African-grown feathers and European-grown feathers. Of those, 10 elements showed higher levels in African-grown feathers, while only two were higher in European-grown feathers. My results suggest that trace elements can show variation at different organizational levels. Variability within feathers was important in at least two elements, which could be caused by physiological processes. This means that when designing sample collection for trace element analysis, unless we know that an element does not vary along a feather, it is important to consider which part of feathers we are sampling. Variability between feathers and individuals was lower than within feather variability, but still significant. Future studies should account for possible within and between individual differences in their design. Differences between barn swallows and willow warblers were large, which was expected based on the literature. It is still unknown what drives these differences between species: some explanations suggested have been physiological and dietary differences or differences in their habitats. I also found clear differences between feathers of willow warblers grown in Europe and Africa. While the exact cause is still not known, this means that at least in willow warbler feathers it is possible to study large scale geographical patterns by trace element analysis. LA-ICP-MS has potential to be a powerful tool to study migration and migratory connectivity in birds. It allows to detect variation in trace elements at continental scales while also allowing to control for different levels of variability in the study design. I encourage researchers to adopt its use in their research.
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(2017)Baltic Sea has undergone major changes in the last few decades and its ecological condition has changed. Paleolimnology provides methods to detect changes in the past, mostly from the times when no surveillance was conducted. This Master's thesis is about the response of a common Cladocera, Eubosmina maritima to the past environmental change in Sandöfjärden, Gulf of Finland. I studied past isotopes, δ13C and δ15N to detect past changes in the eutrophic changes from sedimented subfossil remains to detect how the E. maritima population abundance and morphology have changed due to eutrophication and increased predation pressure. I analyzed a 30 cm sediment core of which I counted E. maritima remains. I also measured the lengths of carapaces, mucros and antennules in order to detect changes in their morphology. I used carbon nitrogen ratio, total carbon, total nitrogen, and their stable status of the sea area. To indicate predation pressure on E. maritima, I used the resting egg data of a predatory cladocera Cercopagis pengoi, that was introduced to the area at the beginning of the 1990's. The sediment core is stratigraphic, meaning that the layers are connected to each other and therefore cannot be treated as independent samples. The data was first viewed graphically to reveal correlations. I applied redundancy analysis (RDA) to find out if changes in the Eubosmina-populations are explained by the environmental changes. Associated is Monte Carlo permutation test to check which explanatory variables are the most important. Finally I performed variance partitioning to separate the effects of the environment caused by time in the sediment time series. My results show that E. maritima population has increased in number since the 1950's and a positive correlation with δ15N suggests that this has a connection to increased nutrient levels. It also seems that big E. maritima individuals became more common in eutrophic conditions. Increased predation pressure affected E. maritima populations the strongest right after C. pengoi was introduced to the area when also the longest mucros were found. There also was a slight decrease in the E. maritima abundance at that time. The changes of the lengths of the appendages seem to be more connected to predation pressure, whereas the abundance and the overall body size seem to have a connection with eutrophication. Along with the eutrophication increased the number of E. maritima in the Gulf of Finland. The effect of predation pressure was the clearest right after the introduction and then later smoothened.
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(2020)Psychrotrophic lactic acid bacteria (LAB) play a versatile role in research, food, farming and medicinal applications, but also play a role as a source of food spoilage. The effects of temperature changes has yet to be studied in depth. In this study, to analyze in a transcriptome level, cold and heat shock stress to spoilage lactic acid bacteria, a time-dependent RNA-seq for Lactococcus piscium with a temperature of 0 °C and 28 °C was conducted. The data of protein regulation during the experiment shows that Lactococcus piscium has the essential machinery to survive against different types of environmental stress. I observed known heat shock related genes and stress related genes to be present in the regulated response of both temperature extremes. Cold shock upregulation is observed after 35 minutes, which could indicate that the metabolic response at cold temperatures is related to growth rate. With a clear downregulation of pathways of energy consumption and an adaptation in terms of RNA being more prominent that at 28 ºC. Certain surface, cell wall and transport proteins are noticeable more upregulated at 0 ºC in addition to a downregulation of energy related proteins, which in correlation with its growth curve, we can assume it is part of a mechanism of protection against cold environments, in comparison with the regulation of proteins at 28 ºC. This gives an insight of a well controlled preservation mechanism that Lactococcus piscium exhibits that can be linked to its environment. The findings of this research offer new understandings into the survival skills of Lactococcus piscium to a cold and heat shock. Future studies should focus on analyzing the regulation and function of possible new genes for the response to heat stress, as well as the specific function of proteins related to temperature stress in the events where change of temperature plays a constant role in the environment.
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(2023)Biallelic germline mutations in ERCC6L2 cause bone marrow failure (BMF) and predisposition to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The patients often develop varying cytopenias, and underlying hypoplasia in the bone marrow is usually evident. The aim of this thesis was to characterize the transcriptome of patient -derived fibroblasts with biallelic germline ERCC6L2 mutation. Moreover, the aim was to study changes on the gene expression at the RNA level in fibroblasts in different media conditions, ROS levels in ERCC6L2 -mutated fibroblasts, and whether addition of glutamine impacts the ROS levels. Fibroblasts from 16 skin biopsies were cultured; eight samples were from healthy controls and eight samples from patients with known mutations in ERCC6L2. Fibroblasts were cultured in different media conditions, followed by RNA extraction and RNA sequencing. We observed downregulation in base excision repair, nucleotide excision repair, mismatch repair, DNA replication, homologous recombination, and cell cycle in ERCC6L2 -mutated cells. MAPK signaling pathway, p53 signaling pathway, apoptosis, AMPK signaling pathway, and TGF-beta signaling pathway were in turn upregulated in ERCC6L2 -mutated cells. The medium did not affect the gene expression significantly across samples. We suspect that the effect of medium was not detected at the RNA level, but it might affect post-translational modifications. We also detected increased ROS levels in ERCC6L2 samples compared to control and observed decreased ROS levels in ERCC6L2 and control samples with excess glutamine. This study shows that biallelic mutations in ERCC6L2 do not only affect the bone marrow but can also affect tissues outside of the hematopoietic system. The transcriptomic analysis identified important biological processes, which could be studied with more detail in the future to further explore the pathology of the ERCC6L2 disease.
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(2021)Transfer RNA (tRNA) is one of the most extensively modified RNA molecules. The role of tRNA modifications become apparent during physiological condition such as oxidative stress, where it serves as an adaptive response to the changing environment. These modifications are upregulated mainly at the wobble position of the tRNA to enhance the translational efficiency of the stress response genes through enhanced decoding rate and tRNA–mRNA interaction. Hence, tRNA modification has a crucial role in regulating translational fidelity, and such modifications can be utilized to fine-tune the translation for improved production of heterologous protein. Therefore, this study aimed to analyze the tRNA modification changes in two laboratory-significant E. coli strains (BL21 (DE3) and K12) during oxidative stress and utilize these modifications to enhance the production of heterologous protein using a defined cell-free protein synthesis system. Ultra-performance liquid chromatography-mass spectrometry was used to detect and quantify the tRNA modification changes in the hydrogen peroxide-treated E. coli cells. The results showed unique tRNA modification patterns and intensities between the two bacterial strains in response to oxidative stress. Modifications such as ac4c and m2,2G were upregulated in E. coli BL21 (DE3) following hydrogen peroxide treatment, whereas k2C and chm5U were increased in E. coli K12. Further analysis of the dataset revealed that most of the upregulated ribonucleoside modifications were predominant at the anticodon loop of the tRNAs, indicating the potentiality of these tRNA pools to impact on translation. Likewise, I optimized an E. coli-based cell-free protein synthesis system to investigate the effect of modified tRNA pools on translation. Hence, this study serves as a stepping stone to understand the tRNA modification landscape of E. coli and provides a platform to depict the function of post-transcriptional tRNA modifications in translation with the CFPS system.
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(2015)Neurotrophic factors are essential for the development of the central nervous system. By signalling through Trk receptors, they have multiple effects on for example the survival of neurons, growth of axons and dendrites and stability of synapses. BDNF, which signals through TrkB receptor, is a neurotrophic factor with an important role in the formation and stabilization of glutamatergic synapses. It is also known to be released in an activity dependent manner. The mechanisms by which BDNF and TrkB signalling regulate synaptic transmission depend on the type and developmental stage of the synapse, and they are not well known. The electrical activity of immature networks consists of intrinsic activity with intermittent bursts of synchronous activity, which is believed to fine tune the synaptic connectivity through Hebbian plasticity mechanisms, which are stabilized by homeostatic mechanisms. Homeostatic regulation can be especially important during the development of the neural network while the glutamatergic transmisson is very labile. Little is known of the signalling routes that participate in the homeostatic plasticity during the development of the neural network. The aim of the thesis was to investigate how the long-term inhibition of TrkB signalling affects the glutamatergic transmission and the homeostatic regulation in area CA3 of neonatal hippocampus by using gene manipulated TrkBF616A mouse strain. The TrkB receptors in the TrkBF616A strain are modified so that they can be blocked with a kinase inhibitor (1NMPP1). In part of the work C57BL/6 -mice were used as control. In addition to the acute measurements the hippocampal slices were incubated in control conditions and with inhibitory drugs (TTX and 1NMPP1) for 15 to 20 hours, after which miniature excitatory postsynaptic currents (mEPSCs) were recorded with whole-cell patch clamp from area CA3 pyramidal cells. The research shows that continuous TrkB signalling is essential for the maintenance of AMPA receptor mediated synaptic transmission in CA3 area of neonatal hippocampus in TrkBF616A mice. Long-term inhibition of TrkB signalling decreases the amplitude of mEPSCs. TrkB-signalling seems to be needed also for the homeostatic response caused by network activity deprivation. The results also indicate that the inhibition of TrkB signalling increases the frequency of mEPSCs, possibly by a homeostatic mechanism. However, the results also show that the TrkBF616A mice strain might differ from wild type mice and the kinase inhibitor 1NMPP1 might have non-specific effects that are not currently known, so more extensive research on the matter is still needed to confirm the results.
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(2022)Aims and methods: Global plastic production is increasing annually and microplastics (MPs, particles of <5 mm in size) have been reported in the environment worldwide. In aquatic systems plastic pollution is present especially in coastal habitats, and MPs can concentrate within littoral zone vegetation. Numerous marine animals are known to be able to ingest MPs, and plastics can also have adverse effects on the health and behaviour of the exposed animals. This Master’s thesis examined trophic transfer of MPs in a Baltic Sea littoral food chain. Laboratory experiments with 10 µm fluorescence microspheres were conducted to study trophic transfer between food chains of different lengths. The longest food chain had three trophic levels: zooplankton, chameleon shrimp (Praunus flexuosus) and rockpool prawn (Palaemon elegans). Also, the gut passage time of rockpool prawn was experimentally studied. The digestive tracts of the studied animals were analysed for MPs under an epifluorescence microscope. Results: The results show that trophic transfer may be an important pathway of microplastic exposure for animals at higher trophic levels. The number of ingested microspheres in both chameleon shrimp and rockpool prawn was higher when the animals were exposed through pre-exposed prey in comparison to direct exposure from the water. In addition, the prawns ingested more MPs in the experiment with three trophic levels than in the two-level experiment. The results support earlier findings, that the feeding mode affects the microplastic exposure of animals. There were no clear results from the gut passage time experiment.
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(2018)Riisi (Oryza sativa) on yksi maailman viljellyimmistä ravintokasveista. Siltä tunnetaan maailmanlaajuisesti 20 merkittävää tuhohyönteistä, joista monet ovat yöllä lentäviä perhosia ja jotka runsaina esiintyessään voivat aiheuttaa huomattavia satotappioita riisinviljelijöille. Tässä tutkielmassa selvitettiin, mitkä riisin tuholaisperhoslajit ovat runsaimpia Kaakkois-Madagaskarin runsastuottoisilla märillä ja pengerretyillä riisipelloilla ja mitkä ympäristömuuttujat vaikuttavat näiden runsaimpien lajien esiintymiseen. Aiemmissa maaseutuelinympäristöjen tutkimuksissa on havaittu, että maanviljelyn tehostuminen ja sen aiheuttama luontaisten elinympäristöjen häviäminen saattaa johtaa tuholaisten runsastumiseen. Kaakkois-Madagaskarin sademetsävyöhykkeellä metsien väheneminen lisääntyneen maanviljelyn takia on viime vuosikymmeninä ollut huomattavaa voimakkaan väestönkasvun seurauksena. Tutkimus suoritettiin kenttäkokeina Kaakkois-Madagaskarilla Ranomafanan kansallispuiston läheisyydessä vuoden 2015 marras- joulukuussa. Perhosia kerättiin vetisiltä riisipelloilta kolmella valopyydyksellä kolmen yön ajan kahdeksassa, maisemarakenteeltaan erilaisessa kylässä. Pyyntijaksojen aikana mitattiin ja kerättiin tietoa pyyntiöiden sääolosuhteista. Tutkimusalueelta aiemmin tehdyn maanpeiteluokituksen avulla tarkasteltiin maisemamuuttujien vaihtelua pyyntipaikkojen läheisyydessä. Pyydyksillä kerätyt hyönteiset säilöttiin ja tuotiin Suomeen lajintunnistusta varten. Suomessa peltojen runsaslukuisimpien perhosten lajit ja sukupuolet määritettiin ulkoisten tuntomerkkien, lisääntymiselinten ja DNA-viivakoodauksen avulla. Tulosten perusteella Parapoynx-suvun (Crambidae) lajit, tunnettu riisituholainen Parapoynx stagnalis ja P. fluctuosalis, jonka tuholaisstatus vaihtelee kirjallisuuslähteistä riippuen, olivat selvästi tutkimusalueen riisipeltojen runsaimpia perhosia. Kaikkein runsain oli P. fluctuosalis -lajin tumma värimuoto. Aiempien tutkimusten mukaisesti tarkasteltavien yöperhosten runsauteen vaikuttivat ympäristömuuttujista eniten säätekijät ja maisematekijöiden vaikutus oli lähinnä suuntaa antavaa. Säätekijöistä lämmin ja kuiva sää lisäsivät perhosten määriä, kun taas pyyntiyöllä loistanut täysikuu vähensi pyyntisaalista huomattavasti. Maisematekijöistä ainoastaan riisipeltojen suuri määrä pyydyspaikan läheisyydessä lisäsi merkitsevästi vain P. fluctuosalis -lajin raidallisen värimuodon runsauksia. Lajimääritysten yhteydessä tarkasteltu tutkimuslajien sukupuolijakauma oli poikkeuksellinen: naarasperhoset olivat merkitsevästi runsaampia kuin koiraat. Tulos oli vastoin aiempia tutkimuksia, joiden mukaan valopyynti houkuttelee yleensä enemmän koiras- kuin naaraperhosia. Naaraiden runsautta suosi todennäköisesti lyhyt yökohtainen pyyntiaika, joka oli vain neljä tuntia auringonlaskusta eteenpäin. Parapoynx fluctuosalis -lajin eri värimuotojen morfologinen ja geneettinen tarkastelu varmistivat todennäköisesti ensimmäistä kertaa, että värimuodot edustavatkin kahta eri lajia, eivätkä saman lajin eri värimuotoja. Tutkielman tulokset kyseenalaistavat nykykäsityksen Parapoynx-lajien taksonomiasta. Tutkielman tulokset osoittavat ensimmäistä kertaa, että Ranomafanan kansallispuiston alueella, Kaakkois-Madagaskarilla esiintyy tunnettuja riisin tuholaisperhosia. Tulokset eivät kerro tuholaisten aiheuttamista mahdollisista satovaikutuksista, mutta vaikutukset ovat oletettavia siellä missä lajeja esiintyy. Tuholaisten tunnistamisen ja niiden alueellisen kartoittamisen sanotaan kuitenkin olevan ensimmäinen askel, jotta niiden mahdollisesti aiheuttamia haittoja pystytään myös torjumaan ja ennustamaan. Riisin tuholaisperhosten kartoittaminen tutkimusalueella on myös tärkeää, jotta paikalliset riisinviljelijät ymmärtäisivät luontaisten elinympäristöjen tärkeyden niiden torjunnassa. Tutkimukset ovat nimittäin useaan otteeseen osoittaneet, että viljapeltojen ympäristöjen eliöt ovat tärkeässä roolissa tuholaisten biologisen torjunnan suhteen. Aihetta jatkotutkimalla olisi ehkä mahdollista löytää yhteys alueen metsien häviämisen ja tuhohyönteisten määrien suhteen, mikä auttaisi paikallisia maanviljelijöitä ymmärtämään luonnontilaisten elinympäristöjen tärkeyttä myös heidän elantonsa osalta. Tutkimuksen tuottama massiivinen, Luonnontieteellisen keskusmuseon Luomuksen kokoelmiin tallennettava hyönteisaineisto antaa joka tapauksessa mahdollisuuksia moniin lisäselvityksiin. Aineisto sisältää valtavan määrän hyönteisiä, joiden biologiasta, taksonomiasta ja esiintyvyydestä ei tiedetä välttämättä mitään.
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(2020)Within the field of cancer immunotherapy, immune checkpoint inhibitors have been a revolution since they provoke re-activation of T-cell immune responses towards cancer. Despite their success, they only work in 13% of the patients because of a poorly immunogenic tumor, mostly due to weak T-cell infiltration. Oncolytic viruses have shown the ability to work in synergy with checkpoint inhibitors because of their tumour-specific tropism, innate immunogenicity and ability to secrete immunostimulatory agents into the tumor microenvironment. Regardless of the great potential, we lack suitable pre-clinical models to test this effect. In this study we developed renal cell carcinoma-derived organoids as in vitro platforms due to their high pre-clinical predictability compared to that of murine and in vitro 2-dimensional cell culture models. To test the ability of oncolytic viruses to stimulate the immune system, we generated three cytokine-expressing (CXCL9, CXCL10 and IL-15) oncolytic adenoviruses using a novel cloning method that we developed. We have shown that these viruses successfully produce high amount of the cytokine and attract peripheral blood mononuclear cells freshly isolated from Buffy coats. Genetically modified oncolytic adenoviruses were also shown to infect and kill human renal cell carcinoma organoids. Together, our results demonstrate the potential of organoids as test platforms for oncolytic virus -based therapy and the importance of adequate cytokine expression in T-cell recruitment. The tumor organoid platform we developed will be useful for advancing patient-specific treatment strategies and serve as a base for innovative immunotherapy models.
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(2022)Domesticated horses have been used for various tasks over their thousands of years of shared history with humans. To be able to perform these tasks every horse needs to learn the needed skills, and this requires systematic training. Training of adult horses has been studied for a long time and comparisons between the efficacy of different training methods have been done. There have also been some studies comparing how much and when young foals need to be handled for them to grow into easily trainable adults. From adult horses it is known that emotional state affects cognitive processes and with that also their learning efficiency and speed. The early stages of training young horses have not been studied very well. There is no clear picture about how young horses feel during training and how that affects their learning. In my thesis I studied young horses’ emotional states while learning new tasks and how that affects their learning. I followed the early training of 19 young horses (11 one-year-olds and 8 two- and three-year-olds) by videotaping five training sessions and collecting saliva samples before and after three of those sessions to analyse cortisol and oxytocin. From the videos I analysed how fast horses responded to trainer’s asks and how unfocused they were. From the hormone samples I measure the change in cortisol and oxytocin levels during training. Salivary cortisol has been widely used to measure acute stress. Oxytocin on the other hand is a newer indicator for positive emotions. To the best of my knowledge salivary oxytocin has never been used in horses. My data showed that the horses learned the required tasks: they became quicker at their responses and focused better during the course of training. Because my data was quite small and individual variation in the hormone levels was high, the results might have been affected by these factors. Linear mixed effect models showed that higher oxytocin levels before training session predicted quicker responses during training and lower levels after training predicted lower focusedness. Bigger increase in cortisol levels during training compared to the before level explained quicker responses and better focusedness, but higher levels before training resulted to lower focusedness and slower responses. This is in line with previous studies of adult horses, that showed that horses in a better emotional state and with less stress learn faster and are more interested in working with humans. This shows that it is important to not only focus on physical wellbeing but also mental wellbeing from early on in horses’ life.
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(2015)Suoturpeen energiankäyttö kattaa n. 7 prosenttia Suomen energiantuotannosta. Tätä käytetään erityisesti talojen lämmitykseen kaupungeissa. Turpeenpoltto tuottaa kuitenkin runsaasti hiilidioksidia, kattaen n. 20 % koko energiasektorin hiilipäästöistä. Tämä taas kiihdyttää ilmastonmuutosta, joka tekee turpeenpoltosta kansainvälisen asian. Suomi on osana YK:n ilmastosopimusta sitoutunut vähentämään kasvihuonekaasupäästöjään. Vain noin 1 % Suomen suoalasta on turvetuotannossa, mutta silti sen vaikutukset paikallisesti suoekosysteemiin ja vesistöihin voivat olla huomattavat. Suomella on lisäksi kansainvälinen vastuu soiden säilyttämiseksi, sillä alun perin kolmannes pinta-alastamme on ollut suota. Soiden moniulotteisuuden vuoksi maa- ja metsätalousministeriö valmisteli vuonna 2011 soiden ja turvemaiden kestävän käytön strategian. Tässä pro gradu -tutkielmassa tarkastellaan turpeen energiakäytön ympärille muodostunutta konfliktia, jota kutsutaan aineistossani turvekiistaksi. Siihen ovat vaikuttaneet soiden käytön ristiriitainen luonne ja strategian julkaisu, joka on herättänyt keskustelua intressiryhmien, erityisesti turvetuotantosektorin ja luonnonsuojelijoiden, välille. Molempien osapuolten intressit ovat törmänneet toisiinsa monella tapaa, ja seurauksena keskustelu on jämähtänyt paikalleen. Tilanteen ratkaiseminen parantaa kestävää soiden käyttöä ja auttaa kestävän energiapolitiikan suunnittelussa. Jotta turvekeskustelussa päästään kehittävässä mielessä eteenpäin, on tärkeää selvittää Suomen turvekeskustelun kenttä. Siihen pohjaavat tutkimuskysymykseni: 1. Mistä turvekiista koostuu ja 2. millaisia ratkaisuja kiistalle on löydettävissä? Aineisto koostuu 2008 2014 aikana kerätystä kirjallisessa muodossa olevasta medianäytteestä aina sanomalehdistä adresseihin ja kommenttiketjuihin. Menetelmänä käytän laadullista sisällönanalyysiä, jonka avulla turvekiistan osapuolten intressikenttä ja kiistelyn takana olevat tulkintakehykset voidaan hahmottaa. Tulkintakehykset ovat yhtenäisiä tapoja ymmärtää ilmiö mielekkäänä kokonaisuutena, minkä kautta turvetuotannon kokonaisvaikutukset nähdään joko uhkana tai mahdollisuutena, mikä jakaa kiistan osapuolet turvetuotannon puoltajiin ja vastustajiin. Analyysin mukaan turvekiistan intressikentässä on teollisuutta edustava puoli, vesistön virkistyskäyttäjät sekä luonnonsuojeluorientoitunut puoli. Kiistan keskeiset vastakkainasettelut on jaettu ekologiseen ja teknis-taloudelliseen kestävyyteen sekä hallinnon heikkouksiin. Niissä kiistellään muun muassa turvetuotannon vesistövaikutuksista, suon luontoarvoista, turpeen uusiutuvuudesta, sen energiakäytön huoltovarmuudesta, ympäristöluvasta ja sen valituksista sekä poliittisen ohjauksen nykytilasta. Vesistön virkistyskäyttäjien hahmottuminen osana kiistaa oli tärkeä havainto, koska keskustelua tulkitaan helposti pelkästään luonnonsuojelijoiden ja teollisuuden väliseksi vastakkainasetteluksi. Kiistan osapuolia hahmottavat tulkintakehykset nimesin kotimaisen tuotannon ja luonnon kestävän käytön kehyksiksi, jotka omilla tulkinnoillaan osallistuvat edellä mainittuihin vastakkainasetteluihin. Turvekiistassa esiintynyttä retoriikkaa on havaittavissa muissakin ympäristökonflikteissa. Mahdolliset ratkaisut kiistan selvittämiseen ovat jaettavissa tiedolliseen, arvo- ja intressikiistaan. Ratkaisuja ovat esimerkiksi paikallisen tason huomiointi ympäristöluvassa, turvetuotannolle ominaisiin vesistövaikutuksiin keskittyvän tutkimuksen lisääminen ja osapuolia yhdistävän kehyksen tietoinen rakentaminen, joka toimisi ns. sillanrakentajana. Kiistassa on lopulta kyse siitä, kumpi osapuoli pystyy yhdistämään oman tulkintansa paremmin sosiokulttuuriseen kestävyyteen.
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(2012)Core-fucosylation of N-glycoproteins is associated with different cancers and other pathologies. Identification of glycoproteins and determination of their glycan structure manually by mass spectrometry (MS) is time-consuming and laborious. In this Pro gradu thesis, the use of the mass spectrum-analyzing software Glycopeptide ID for identification of core-fucosylation from a known standard, immunoglobulin G, was studied. Also, a plasma sample with unknown glycoproteins was analyzed. For the MS analysis, the proteins were digested with trypsin, and the resulting glycopeptides were enriched using lectin affinity chromatography. From IgG and plasma, also samples treated with α-Lfucosidase were prepared in order to cleave the core fucose. The presence of glycopeptides was determined by high-performanve liquid chromatographymass spectrometry (HPLC-MS) analysis, and they were fragmented using collision-induced dissociation (CID) in a tandem-MS (MS/MS) analysis. The MS/MS spectra were analyzed with the Glycopeptide ID software. The software was found to identify core-fucosylation reliably from high-quality spectra, but identification of proteins were often incomplete from spectra with poor quality. From the plasma sample with unknown proteins, a probable corefucosylation was found from IgG2, fetuin A, serotransferrin, hemopexin and ceruloplasmin. As a conclusion, the software Glycopeptide ID can be considered as an appropriate tool for identification of core-fucosylation in N-glycopeptides.
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