Bio- ja ympäristötieteellinen tiedekunta


Recent Submissions

  • Lappalainen, Juho (Helsingin yliopisto, 2016)
    The productivity and biodiversity of coastal areas, one of the most productive ecosystems on earth, are threatened by eutrophication and habitat loss which also drive deterioration of the macroalgal communities of shallow rocky bottoms and their perennial key species. The underwater light, being one of the most important factors determining the zonation and distribution of macroalgae, alternates in space and time. The water quality at the study area, Gulf of Finland, has deteriorated during the past hundred years which has lowered the amount of light at the bottom. Comprehensive studies on spatio-temporal changes at euphotic bottom and the their effects on macroalgae are yet to be done. This study investigates how the area of euphotic bottom at the Gulf of Finland has fluctuated during 2003 2011, and how the amount of light on the bottom determinates the zonation and distribution of macroalgae. Furthermore, the changes in the areas of euphotic bottom when the euphotic depth is altered and the effects on macroalgae are surveyed. One hypothesis is that in many areas macroalgae are not affected by too low light levels but the unsuitable bottom substrate that limits their distribution. The study material consists of euphotic depth GIS (Geographic Information System) layers derived from MERIS (MEdium Resolution Imaging Spectrometer) satellite images from May to September from 2003 2011, inventory data of the Finnish Inventory Programme for the Underwater Marine Environment (VELMU), water quality measurements and HIRLAM (High Resolution Limited Area Model) weather model. The distribution of euphotic bottom and its area were calculated for four parts of the Gulf of Finland. Changes in euphotic bottoms were evaluated in scenarios where euphotic depth changed -100 87,5 %. The effect of light on the zonation and distribution patterns of macroalgae were surveyed using distribution models. Boosted Regression Tree (BRT), Generalized Additive Model (GAM) and Climate Envelope Model (CEM) were utilized on bladderwrack (Fucus vesiculosus L.). In addition, scenarios of euphotic depth changing -50 50 % were modelled. The area of euphotic bottom varied seasonally and changed slightly between the study years. The area was larger in the inner archipelago compared to the outer arhcipelago and the difference was greater when the areas were normalized with local sea area. Always and occasionally euphotic bottoms were located near the shoreline and reefs. The altered euphotic depth affects euphotic bottoms the most in the outer archipelago. There were local differences in the performance of the distribution models. The change in euphotic depth affects the distribution of bladderwrack considerably: a deterioration of 25 % narrows off the distribution widely and a decline of 50 % suggests that the species is going to disappear from the Gulf of Finland. A decline in euphotic depth shifts the inner distribution limit towards the outer archipelago and narrows the macroalgae zone locally while even a small improvement expands the area significantly. However, the substrate of the newly exposed zone is only partially suitable for macroalgae and the portion of rocky substrate decreases as a function of euphotic depth. Changes in the optical properties of the sea affect the penetrance of light at the bottom and the area of euphotic bottom. Increasing turbidity of the sea is a remarkable threat to macroalgae. Vice versa, clarification of the water expands light-limited distribution and enlarges the macroalgal zones even though the growing amount of unsuitable soft substrate inhibits the distribution and zonation of macroalgae.
  • Niskanen, Julia (Helsingin yliopisto, 2016)
    Epidermolysis bullosa (EB) is a group of hereditary skin disorders caused by mutations in the genes that code for adhesion molecules in keratinocytes. The symptoms of the disease include blisters and erosions in the skin as well as abnormalities in the mucosal membranes, nails and tooth enamel. Depending on the causative mutation the severity of the disease ranges from mild to lethal. This master s thesis was carried out in professor Hannes Lohi s canine genetics research group. It is a case study aiming to identify the genetic cause of EB present in Central Asian shepherd dogs. Furthermore, the mode of inheritance, frequency of the mutation in the breed and the effect of the mutation on the tissue were also examined. Primary research material included blood and tissue samples from a family of Central Asian shepherd dogs. Additional samples were obtained from other Central Asian shepherd dogs as well as from dogs of closely related breeds. All dogs included in this study are owned by private persons, and participation in this study was voluntary. The research methods used in this study included both wet laboratory experiments and bioinformatic in silico procedures. The genome of one affected dog was sequenced in order to identify the gene causing EB, and data from the sequencing was filtered with multiple programs according to recessive model. The model was decided after analyzing the pedigree of the affected dogs. After finding the likely causative gene the mutation was validated in a larger cohort with Sanger sequencing. Protein expression in the tissue of affected dogs was also studied using immunofluorescence staining. As a result of this study, a new mutation causing recessive dystrophic EB was identified. The mutation is specific to Central Asian shepherd dogs. Affected dogs have a homozygous mutation in the COL7A1 gene, which codes for collagen VII α1 protein. The mutation causes a premature stop codon in the mRNA sequence, which results in abnormal protein production and separation of skin layers. The frequency of the mutation allele in the sample is approximately 18 % and more than a fourth of the dogs in the sample are carriers. Based on the pedigree analysis, the mutation is relatively new and it is only found in a small population. The disease can be prevented from becoming more common in the breed with the help of a gene test, and the test will be available in the commercial MyDogDNA gene test panel.
  • Oikkonen, Jaana (Helsingin yliopisto, 2012)
    Genome wide linkage and association methods are used to map genes affecting traits with genetic predisposition. In this thesis, I compare the methods suitable for quantitative trait mapping in complex, extended pedigrees. As a case study, gene-mapping study of musical aptitude is performed with these methods. Linkage analysis methods are developed for family studies. However, only a few methods are suitable for extended families with a quantitative trait. Three linkage programs were successfully applied for such data in this study. These programs are the SOLAR, JPSGCS and KELVIN. All of these three programs are based on different methods and thus, the same calculations are not repeated. SOLAR is based on the variance components method, JPSGCS on a graphical method and KELVIN on the Bayesian method. Association analysis is also difficult to implement for large pedigrees, because it is best suited for case- control data. Fortunately, methods are extended also for family-based studies. Here, a genomic control method was used to correct for the familial relationships. The method evaluates the relatedness from the whole genome data and the association tests are corrected for the relatedness rates. This method was implemented from the GenAbel program. As a case study, these methods were applied to a musical aptitude study. The musical aptitude is here understood as an ability to perceive the melody, harmony and rhythm of music, and to recognize structures in set of sounds. These abilities were tested with Carl Seashore s tests for pitch and time and Kai Karma's test for auditory structuring. The data consists of 107 pedigrees and 93 sporadic subjects, comprising in total of 915 individuals. Each family includes 2 50 individuals. These individuals were genotyped with a SNP chip for over 700,00 SNPs. The linkage analyses revealed several promising loci for the musical aptitude. The best result was located in 4q12 and it was found with all of the three linkage programs. Most of the other results could also be identified with multiple programs, but some differences also occurred. However, none of the findings could be discovered with association analysis, probably due to a too small sample size.
  • Östman, Sanna (Helsingin yliopisto, 2015)
    This interdisciplinary study seeks to raise awareness of and generate interest in projects that combine science and art. A number of such projects are discussed and analyzed with the help of the concept Ecovention . The concept is operationalized to include works of art that ecologically restore, reclaim, and remediate damaged ecosystems by physical actions and inventions. They transform the ecosystem and often slowly disappear into the environment, contributing to the overall wellbeing of the ecosystem. These works of art are long-lasting and site-specific. They are built outdoors by using material that is already available in the ecosystem or by bringing in environmental-friendly material into the ecosystem. The central research question for the study is as follows: How significantly does environmental art affect the local ecosystem when the starting point is ecological restoration? This is a qualitative study. The data for the study consist of interviews with experts together with analyses of the historical, cultural, and ecological background material for two Finnish environmental artworks. The two artworks are Agnes Denes's Puuvuori (Tree Mountain - A Living Time Capsule, 1996) and Jackie Brookner's Veden taika (The Magic of Water, 2007- 2010). These works of art were chosen because of the availability of historical and natural scientific research data about how they were planned and how they were constructed. The availability of this kind of data related to environmental art is rare in Finland. The Magic of Water consists of three floating islands in Salo. They are situated in a lagoon that was formerly used as a clarification pool at the Salo Municipal Sewage Treatment Facility. The artwork has succeeded in supplying a peaceful nesting habitat for the birdlife in the area. It has been shown that a colony of black-headed gulls (Larus ridibundus) is a new species nesting in the islands. The Magic of Water did not provide a significant improvement of the water quality by phytoremediation since the islands are relatively small in relation to the area of the lagoon. Tree Mountain - A Living Time Capsule is to be found in Pinsiönkangas, at the most important groundwater area in Ylöjärvi. The artwork reclaims a former gravel pit. Tree Mountain is a 28 meter tall hill in an area of elliptical shape that spans nine hectares. 10,600 pine tree saplings (Pinus sylvestris) and about 40,000 cubic meters of soil from the area was used to build the artwork. Tree Mountain is nowadays owned by the town of Ylöjärvi and Pinsiönkangas is principally a conservation area. The Tree Mountain - A Living Time Capsule is argued to fit well in the regionally precious ridgescenary since the work of art has enough of biological values. Most likely the building of the artwork has had a preventive effect on possible ecological harm and it has made the community take responsibility for taking care of the reclaimed environment in the long term. In the face of high-quality ecological restoration plans it is important to approach the restoration of ecosystems from a holistic perspective. The artist s vision of how an ecosystem can be restored adds a surplus value to ecological restoration work since also the aesthetic and ideological dimensions are reconstructed. The probable positive view of the community towards the restored ecosystem can promote not only the attendance by the community to that particular area in the future, but it can also promote the attendance of a community to other areas as well.
  • Mutanen, Justus (Helsingin yliopisto, 2015)
    The International Biology Olympiad is a yearly science competition; hundreds of high school students from over 60 countries take part in it. In Finland, the students are chosen by the national biology competition and the national Olympiad training camp. The research subject of this study is Finnish training for International Biology Olympiad (IBO). About ten high school students who are interested in biology take part at each training camp. Science competitions, such as IBO and training camps, are classified as non-formal or out-of-school science education. Since there is very little scientific knowledge about non-formal biology education, especially about science competitions, the theoretical framework of this study consists of non-formal science education, the relevance of science education and the development of interest. In this study, design research methodology with three research cycles was applied to develop the course. In the study, both theoretical and empirical problem analyses were used. There were two main research questions: 1) What are the needs for the development of the training camp? 2) What kind of training is relevant for the participants? The first research question was elaborated by examining a) what kind of topics of interest the participants have, b) how the participants expect the training to be relevant for them, c) what kind of relevance the previous participants experienced, and d) what kind of effects the previous training camps had on the participants interest in biology and career choice. The features of relevant biology Olympiad training were searched in the second research question. The data was collected from pre-camp and post-camp questionnaires, post-camp interviews and a questionnaire sent for the previous camp participants. The qualitative data was analyzed by content analysis and quantitative data from the questionnaires was analyzed by statistical methods. The main results were following: 1) The biggest needs for development were diversifying the contents and balancing the workload of the camp. The participants of the training camps were interested mostly about medicine and human biology -related topics and cell and molecular biology. In addition, it was found out that the previous participants considered biology education to be individually, vocationally and societally relevant for them. According to them, the training camps were especially individually relevant and had some effects on the career choice. 2) The new training camp for biology Olympiad is especially individually relevant for the participants but it has also some vocational relevance. In the science Olympiad training, special attention should be directed towards developing vocational and societal relevance. A new model for Biology Olympiad training camps was developed based on the collected research data. The individual dimension can be improved by i) diversifying the contents of the camps, ii) including inquiry-based learning modules and by iii) taking a student-centered approach to the development process. The vocational and societal dimensions of relevance can be targeted by iv) allowing the teachers of the participants to take part at camps. The vocational dimension of relevance can be enhanced v) by organizing visits to research laboratories and companies and vi) by enabling the participants to meet university students. The results of this study can be applied to not only to Science Olympiad training but also to non-formal biology education. This research provides models for developing out-of-school biology education and its relevance. This is the first design research study about Biology Olympiad training and it opens up discussion about the relevance of science competitions and Science Olympiad training.
  • Autio, Mirka (Helsingin yliopisto, 2015)
    Phosphorus is traditionally considered to be the primary nutrient limiting primary production in lakes. More recent studies show that sometimes nitrogen can be the limiting nutrient for phytoplankton production in temperate lakes. This study investigated whether the nitrogen has a major role along with phosphorus in the primary production of lakes. In addition, it was studied if the limiting nutrient changes during the growing season and does the residence time of the lake affect the level of nutrient limitation. The subject lakes were Ormajärvi, Suolijärvi, Lehee, Pyhäjärvi and Iso-Roine, which are the headwater lakes of the Kokemäenjoki in Kanta-Häme. The lakes were sampled for bioassays once a month from June to September in 2004 and in May 2005, a total of five times. There were four treatments: control, lake water + P, lake water + N, lake water + P + N. For each treatment there were five replicates. There was one concentration level for each nutrient treatment. The nutrient concentration of treatments depended on the nutrient content of the lakes. To determine the combined effect of nutrients both of them were added at the same time. Nitrogen treatment solution was prepared from potassium nitrate and phosphorus treatment solution from potassium dihydrogen phosphate. Bioassays were conducted as a pure culture of Pseudokirchneriella subcapitata Prinz- algae. Zooplankton was removed from the lake water samples, which were then sampled for nutrient analysis. The water samples were autoclaved and filtered prior to the bioassays. Bioassays were carried out in Erlenmeyer flasks containing 60 ml of lake water, the nutrient solutions and 0.5 ml pure culture of P. subcapitata. Algae were grown in continuous illumination until the exponential growth stopped. Algal growth was monitored by taking samples of a few ml from the flasks roughly every other day. Algae in samples were counted by a microscope in Lund chambers. The actual variables were the maximum number of cells or yield and the growth rate. The limiting nutrient was found out by comparing the yield and the growth rate of different nutrient treatments to the control. The results of the bioassays were tested statistically with non-parametric Kruskal-Wallis H-test. Algal bioassays expressed only phosphorus limitation. Phosphorus limited the yield in the bioassays of Suolijärvi in August 2004 and May 2005. In Lehee and Pyhäjärvi phosphorus limited growth rate in May 2005. There was neither nitrogen limitation nor co-limitation in any of the bioassays. So the limiting nutrient didn t change during the growing season. Phosphorus treatments inhibited the growth of algae from time to time in 2004 in Ormajärvi, Suolijärvi, Pyhäjärvi and Lehee. In May 2005 there was no inhibition. Nutrient limitation was stronger in lakes with a long retention time. These bioassays indicate that reducing phosphorus loading would control eutrophication of this chain of lakes. The phosphorus treatments couldn t cause the inhibition. The cause of inhibition originated most likely from the drainage area due to heavy rains in summer 2004. It could be, for example, zinc or arsenic.
  • Raulo, Aura (Helsingin yliopisto, 2015)
    Abstract Microbiota, the microbial communities living in the gut, skin and glands of vertebrates, is the functional link between a physiological individual and it s surrounding ecosystem. Mutualistic microbes play a role in social systems as well, since they are transmitted through social behaviors and claimed to affect host sociality and behavior. Furthermore, individual stress physiology can affect both behavior and microbiota. I took first steps to reveal the role of gut microbiota in the social dynamics of a group-living cooperative primate, the red-bellied lemur (Eulemur rubriventer). Gut microbiota was affected by seasonal change, stress hormonal profile and pregnancy, and individuals were found to have a strongly group-specific gut microbial composition, highlighting the role of social environment in determining gut microbial composition. Unlike expected, individual sociality was negatively associated with gut microbial diversity. Gut microbiota seems to be largely determined by social factors in this species, indicating that social transmission of beneficial microbiota might have played a role in the evolution of sociality.
  • Pankkonen, Pietu (Helsingin yliopisto, 2015)
    Heterotrophic bacteria are essential for carbon cycling in water ecosystems as they bind dissolved organic carbon (DOC) to the biomass and return it to the classical food chain through microbial loop. The treated wastewater from Viikinmäki wastewater treatment plant is discharged to the Gulf of Finland where it increases the quantity of dissolved organic matter (DOM) in the water and furthermore can be an extra energy source for heterotrophic bacteria. There are not yet further studies how the heterotrophic bacteria exploit DOM in the treated wastewater or a monitoring programme for DOC concentrations in the wastewater treatment plants. DOC is the limiting factor for heterotrophic bacteria growth in the Gulf of Finland in the summer. As the bacteria exploit DOC, they consume oxygen and release carbon dioxide. DOM compounds may also diminish light penetration in water which can inhibit the growth and photosynthesis of phytoplankton and macrophytes. The aim of this thesis was to find out 1) the DOC concentrations in the treated wastewater and DOC load in the treated wastewater discharged to the the Gulf of Finland from Viikinmäki wastewater treatment plant, 2) the biodegradability of DOC and DOP in the treated wastewater and 3) how the disc filter about to be used in Viikinmäki wastewater treatment plant affects the quantity and quality of DOC and DOP in the treated wastewater. The DOC load entering the Gulf of Finland with the treated wastewater was quantified by measuring the DOC concentrations in the treated wastewater during the spring and summer 2014. The DOC concentrations correlated positively with chemical oxygen demand (COD) which is regurarly measured in wastewater treatment plants. By dividing the COD with 3,66, the DOC concentrations were successfully estimated for a longer period. In order to evaluate the biological degradability of DOC and DOP in the wastewater effluent, treated wastewater was incubated (+15 °C) for two months with surface water heterotrophic bacteria from the Gulf of Finland and changes in DOC concentrations, the biological oxygen demand and nitrogen and phosphorus concentrations were measured. Furthermore the heterotrophic bacteria were incubated for one month in disc filtered wastewater effluent and also in regularly treated wastewater to find out the effect of the new filter on DOM quantity and quality. The yearly DOC load from Viikinmäki wastewater treatment plant to the Gulf of Finland was estimated to be about 1460 tons which is approximately one fifth of the annual DOC load from River Vantaanjoki. The ratio between DOC and COD concentrations calculated here can only be used to quantify the amount of DOC load from Viikinmäki wastewater treatment plant and similar ratio must be calculated individually for every point source. The biodegradability of DOC in the treated wastewater was equally low to the biodegradability of DOC in River Vantaanjoki. The quantity of DOC bound to the bacterial biomass was rather low and the amount of DOC lost via respiration was relatively high. Accordingly the DOC in Viikinmäki wastewater effluent does not become efficiently available to higher trophic levels. The disc filter has the potential to remove DOC and DOP from treated wastewater which would decrease the DOC and DOP load significantly in the Gulf of Finland. The disc filter decreased DOC concentrations 14 % in comparison to regularly treated wastewater. The disc filter didn t affect the quality of DOC, i.e. there was no difference in the biological degradability of DOC between the two wastewater treatment processes. However the disc filter was possibly able to remove the biologically available part of DOP from treated wastewater but the issue still needs further investigation.
  • Mäkelä, Mirka (Helsingin yliopisto, 2015)
    Archaea are known to thrive in different kinds of extreme habitats. Halophilic archaea are found in environments where the salt concentration is high, like in salt lakes and solar salterns. The habitats of halophilic archaea have salt concentration varying from higher than sea water to the saturation of salt. In high salinity habitats, the biodiversity is typically low and archaea are dominant microorganisms. The cell density of haloarchaea can be up to 107 cell/ml.When there are no predators for archaea and other halophilic microbes, viruses are thought to be the driving agents for their evolution. To this date, 130 archaeal viruses are described and 90 of them are known infect halophilic archaea. Most of the isolated haloarchaeal viruses are head-tailed. These head-tailed viruses can be divided into three different groups by the properties of the tail structure. Those three types of head-tailed viruses are myo-, sipho- and podoviruses. The infection cycles, receptors or lysis mechanisms used by archaeal viruses are still poorly known. Few studied archaeal viruses use seemingly similar strategies to attach to the surface of the host cell, to penetrate the cell surface and to release new virions, as bacteriophages and viruses of eukaryotic cells do. Since archaeas differ so much from eukaryotic or bacterial cells, their viruses must have developed different strategies to carry out their infection cycle. Several filamentous viruses of archaea are known to attach to the pilus structures of their host cells and some of the enveloped archaeal viruses attach straight to the cell membrane of the host. These strategies are seemingly similar to those used by bacteriophages and viruses of eukaryotic cells. Strikingly different mechanism to release virions has been seen on SIRV-2, virus of a hyperthermophilic archaeon. The SIRV-2 infection induces pyramid shaped extrusions on the surface of the host cells. In the end of the infection cycle these pyramids open and release new virions from the cell. This is the first lysis mechanism described for an archaeal virus. In this work, the infection cycle of a head-tailed virus infecting extremely halophilic Haloarcula vallismortis was studied. The Haloarcula vallismortis tailed virus 1 (HVTV-1) is head-tailed siphovirus with a double stranded DNA genome. In previous studies the infection cycle of HVTV-1 is described to be lytic. The genome sequence, 3D-structure of the capsid and the major capsid protein of HVTV-1 is known. HVTV-1 infection has been seen to induce large, roundish structures on the surface of the infected cell. These structures may have a role in the course of the infection cycle. Several animal viruses are known to cause massive rearrangements in the host cell so that replication proteins, viral genome and the replication agents needed from the host are concentrated in specific locations. These rearrangements facilitates and enhances the viral replication. The roundish structures induced by HVTV-1 might play the same role as the virus factories of animal viruses do or these structures may be involved in the release of new virions in somewhat similar manner as those virus induced pyramid structures. In this study two main goals were set: 1.) To explore the adsorption of HVTV-1 in more details and see if the host cell receptor could be solved. 2.) To solve the possible role of the virus induced structure seen in the host cell and to find out, in which point of the infection cycle those structures appear. Based on this study, it can be said that the adsorption of HVTV-1 is efficient and very fast. The virus attaches to the archaella structures of the host cell and the attachment is mediated by the tail of the virus. One archaella may serve as a receptor for several viruses and they are not saturated. The intracellular phase of the infection cycle of HVTV-1 is long and the virus production starts 8 hours after infection. Virions are released when the host cells is lysed 12 hours after the infection. Two hours before the lysis, two virus induced structural changes of the cell are seen. The roundish structures at the surface of the cell and wide areas in the cytoplasm filled by a structure looking similar as lipid membranes. At the same time when the virus production begins, at least two virus induced or coded proteins are produced in the cell. The other one of these proteins was identified and it is predicted to be the virus encoded ribonucleotide reductase. Ribonucleotide reductase is an enzyme known to catalyse the synthesis of deoxyribonucleic acids from ribonucleic acids. If the ribonucleotide reductase is a part of seen structures, the timing of their appearance and the known function of the enzyme, could suggest those structures to play a role in the maturation or release of the virions. Many questions still remains and there would be lot more details to study in the HVTV-1 infection. Especially interesting would be the identification of the other virus induced protein, purifying those roundish structures and analysing them in more details.
  • Pousi, Suvi Päivikki (Helsingin yliopisto, 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.
  • Viljanen, Samu (Helsingin yliopisto, 2015)
    Autophagy is a eukaryotic cellular process where intracellular material is recycled by transporting it in newly formed vesicles to lysosomes for degradation. In normal conditions autophagy supports cellular homeostasis. Different stress conditions can induce autophagy and then it helps the cell to avoid an unnecessary or uncontrolled cell death. RAB proteins are small GTPases that regulate vesicle traffic and fusion events in endocytic and exocytic pathways. RAB24 has recently been shown to participate in autophagy, but there is very little information about how it works at the molecular level. GOSR1 is a Golgi SNARE protein that regulates membrane fusion events, and it has been observed to interact indirectly with RAB24. The participation of GOSR1 in autophagy has not been studied yet. The aim of the study was to find out if RAB24 and GOSR1 colocalize into the same vesicle structures and if they interact within each other. HeLa cells were used as a model organism, and to induce autophagy amino acid starvation was used. For GOSR1 detection a DNA construct was created where GOSR1 was tagged with green fluorescent protein GFP-sequence. Localization was studied with immunofluorescence staining where in addition to RAB24 and GOSR1 also the autophagosomal marker protein LC3 was labeled. The labeled cells were photographed with a confocal microscope. The pictures were analyzed with ImagePro software. Interaction between the proteins was studied using immunoprecipitation. GOSR1 and RAB24 were not observed to colocalize into same structures in significant amount. Instead it was found that GOSR1 colocalized into LC3-positive autophagic vesicles. In immunoprecipitation studies no interaction between RAB24 and GOSR1 could be shown. In order to ensure the results more immunofluorescence stainings should be done using several time points and GFP-tagged GOSR1. Also GOSR1 silencing with siRNA should be used in order to find out if GOSR1 is necessary for autophagy. The immunoprecipitation protocol should be optimized, and the possible interaction could be studied by using other methods, for example yeast-two hybride technology.
  • Kervinen, Anttoni (Helsingin yliopisto, 2015)
    Viime vuosikymmeninä tiedonalakohtaista oppimista on tutkittu paljon käsitteellisen muutoksen näkökulmasta. Käsitteellinen muutos tarkoittaa oppijan tietorakenteiden muuttumista tai jäsentymistä virheellisistä kohti tieteellistä mallia. Käsitteellisen muutoksen teorioiden mukaan oppijoiden aikaisempien virhekäsitysten tunteminen ja huomioiminen on keskeistä oppimisen ja opetuksen onnistumisen kannalta. Tässä tutkimuksessa selvitettiin biologian yliopisto-opiskelijoiden fotosynteesiin liittyviä virhekäsityksiä, niiden muuttumista opetustekstin lukemisen seurauksena sekä biologian pääaineopiskelijoiden ja sivuaineopiskelijoiden virhekäsitysten eroja. Suomalaisten opiskelijoiden virhekäsityksiä on aiemmin tutkittu niukasti. Tämän tutkimuksen tavoitteena oli selvittää virhekäsityksiä suomalaisten opetussuunnitelmien mukaan opiskelleilta opiskelijoilta sekä selvittää virhekäsitysten yksityiskohtaista muuttumista käsitteellisen muutoksen näkökulmasta. Tutkimuksen aineistona oli yliopiston biologian peruskurssin opiskelijoiden (n=171) vastaukset fotosynteesiä ja sen ekologista merkitystä koskeviin avoimiin kysymyksiin. Opiskelijat vastasivat kysymyksiin ennen opetustekstin lukemista, heti opetustekstin lukemisen jälkeen sekä kaksi viikkoa lukemisen jälkeen. Aineisto analysoitiin laadullisin menetelmin kuvaamalla, tyypittelemällä ja tulkitsemalla havaittuja virhekäsityksiä. Virhekäsitysten tulkinnassa hyödynnettiin tiedon ja ajattelutaitojen tasojen luokittelua. Opiskelijoilla havaittiin yhteensä 58 fotosynteesiä koskevaa selkeästi virheellistä käsitystä ja 14 puutteellista tai epämääräistä käsitystä. Virhekäsitykset liittyivät fotosynteesireaktioon, kasvien rakenteisiin, kasvin energiatalouteen ja fotosynteesin ekologiseen merkitykseen. Lähes kaikki virhekäsitykset ja puutteelliset käsitykset olivat yleisempiä biologian sivuaineopiskelijoilla kuin pääaineopiskelijoilla. Virhekäsitykset vähenivät opetustekstin lukemisen seurauksena, ja monimutkaisempia tiedon ja ajattelutaitojen tasoja ilmentävät virhekäsitykset vähenivät vähintään yhtä paljon kuin muutkin. Lukuisia virhekäsityksiä kuitenkin säilyi oikeat vastaukset antaneesta opetustekstistä huolimatta. Kaksi viikkoa opetustekstin lukemisen jälkeen osa jo virhekäsityksensä korjanneista opiskelijoista vastasi jälleen virheellisesti. Tutkimus osoittaa, että suomalaisen peruskoulun ja lukion fotosynteesin oppimista koskevat tavoitteet eivät täyty edes monen biologian yliopisto-opiskelijan kohdalla. Suomalaisilla opiskelijoilla on pitkälti samoja virhekäsityksiä kuin kansainvälisesti tehdyssä tutkimuksessa on havaittu. Fotosynteesin oppimisen kannalta keskeisin tutkimuksessa havaittu ymmärryksen puute on vaikeus ymmärtää fotosynteesin merkitys Auringon valoenergian ja ravintoketjujen energian välisenä linkkinä. Opiskelijoiden vaikeudet korjata virhekäsityksiään selittyvät käsitteellisen muutoksen prosessin haastavuudella ja hitaudella. Fotosynteesiä koskevan oppimisen edistämiseksi opetuksessa tulisi aiempaa paremmin huomioida käsitteellisen muutoksen haasteet kognitiivisesta, sosiaalisesta ja motivaatioon liittyvistä näkökulmista. Tämä tutkimus tarjoaa tietoa niistä fotosynteesin oppimista koskevista erityispiirteistä, joita ilmiön tehokkaaseen oppimiseen pyrkivän opetuksen tulee huomioida.
  • Silvennoinen, Emmi (Helsingin yliopisto, 2015)
    Infiltration rates in urban areas are low due to a high proportion of impervious structures. Impermeability results in increased rates of urban runoff, which often leads to degradation in receiving waters. Stormwater retention in urban areas can be increased, for instance, with green, vegetated roofs. While impervious, normal roofs produce the runoff immediately, studies with green roofs have shown that they cause delays in peak runoff and reduce the runoff rate and volume by water retention and attenuation. The water retaining capacity of green roofs vary due to local weather conditions and roof characteristics. Several studies and experiments considering stormwater management and other ecosystem services that green roofs provide have been performed worldwide, mainly in temperate regions, while more studies are needed in cold climates especially to quantify the performance of green roofs in winter. The purpose of this thesis was to evaluate the effects of various types of precipitation events on runoff rates, timing and water retention in locally built new green roofs from late summer to early winter in southern Finland. Data on precipitation and green roof runoff as well as soil temperature and humidity were monitored automatically. Green roofs included a) precultivated readymade vegetation mats and b) built on site novel substrate mixture with plug plants and seedlings. My principal aim was to study the capability of green roofs in retaining and attenuating water in relation to the intensity and duration of precipitation, the length of the antecedent dry weather period as well as to temperature and moisture of the green roof substrate. I hypothesised that green roofs retain low intensity events better than high intensity events and more effectively in dry and warm than in wet and cold weather, being negligible at temperatures below 0 ºC. Furthermore, I studied whether retention capacity can be improved by the amendment of biochar. Finally, readymade green roofs with dense vegetation was hypothesised to have better retention capacity than the newly created roofs with very sparse vegetation but only in summer due to evaporation. Based on cumulative runoff, green roofs retained 52 % of rainfall, which is close to the retention capability found in previous studies. Retention was generally higher at warm temperatures and for biochar-amended roofs,in agreement with my hypothesis. Against expectations, roofs with readymade vegetation mats had lower retention than those built on site. In summer and autumn, before freezing temperatures occurred, results were generally according to the hypotheses and previous research: retention rates decreased as rain depth or rain peak intensity increased. When the amount of rain preceding the measurement event was low, and the substrate moisture content was low, retention was better. During wintertime, results were contrary to my hypotheses: Total retention rates increased with the amount of rain and rain intensity, or when substrate moisture content increased. However, a long antecedent dry weather period resulted in better retention, especially during winter. Mean peak flow attenuation for rain events in this study was 64 % and results are in accordance with my hypothesis and previous research. Furthermore, delay times from when the rain event started to when runoff started and from rain peak to runoff peak were detected in this study, mean values of more than 1 h being comparable to what has been reported in the literature. Results from my thesis can be used to improve hydrological models for local stormwater management purposes. Furthermore, results can be compared with those of other ecological stormwater treatment methods. Possible future research topics include the functioning of green roofs during different seasons and especially during freezing and melting periods with assumedly complex hydrological interactions.
  • Tolvanen, Oula (Helsingin yliopisto, 2015)
    Tutkielman tavoitteena oli laatia todennäköisyyspohjainen kanta-arviomalli merivaelteisen taimenen (Salmo trutta L.) juveniili vaiheen populaatiodynamiikan kuvaamiseksi. Mallin tarkoituksena on kuvata taimenen jokipoikasvaihe kuoriutumisesta merivaellukselle lähtöön tai sukukypsyyteen saakka, tiivistämällä saatavilla oleva tieto taimenen ekologiasta populaatioparametreiksi. Näitä parametreja olivat ikäryhmäkohtainen selviytymisen todennäköisyys ja ikäryhmäkohtainen syönnösvaellukselle lähdön todennäköisyys. Epävarmuuden huomioimiseksi mallin parametrien kuvaamiseen käytettiin todennäköisyysjakaumia. Ikäryhmäkohtainen syönnösvaellukselle lähdön todennäköisyys kuvattiin käyttämällä käyräfunktiota, jonka parametrit liitettiin aikaisemmin julkaistuihin aineistoihin taimenen keskimääräisen vaellusiän vaihtelusta leveyspiirin mukaan. Mallin muiden parametrien odotusarvojen asettaminen ja mallin rakenteen laatiminen perustui asiantuntija-arvioihin ja aikaisemmin julkaistuun taimenta tai sen sukulaislajeja koskevaan tutkimustietoon. Mallissa käytettyjen parametrien posteriorijakaumat ratkaistiin käyttämällä Markov chain Monte Carlo (MCMC) simulointia. MCMC simuloinnin toimivuus tarkastettiin käyttämällä keinotekoisesti tuotettua havaintoaineistoa. Mallin yhteensopivuutta todellisiin havaintoaineistoihin tutkittiin sovittamalla malli kahdesta Suomenlahteen laskevasta joesta kerättyyn sähkökoekalastus ja vaelluspoikaspyyntiaineistoon. Viron puoleisen Pirita joen aineisto koostui vuosien 2005 2013 sähkökoekalastusaineistosta ja vuosien 2006 2014 vaelluspoikaspyyntiaineistosta. Suomen puoleisen Ingarskilan joen aineisto koostui vuosien 2009 2013 sähkökoekalastusaineistosta ja vuosien 2012 ja 2013 vaelluspoikaspyyntiaineistosta. Molempien jokien aineistojen, sekä kirjallisuudesta kerätyn 41 muun joen vaelluspoikasten keskimääräisistä i'istä koostuva aineiston analysointi toteutettiin samanaikaisesti hierarkkisena meta-analyysina. Mallin sovituksen yhteydessä havaittiin, että malli systemaattisesti yliarvioi keväisin tutkimusjoista alasvaeltavien taimenen poikasten määrän. Mallin havaittiin kuitenkin ennustavan onnistuneesti analyysistä poisjätetyn Piritajoen vuoden 2014 vaelluspoikaspyyntiaineiston ikäjakauman. Kirjallisuudesta kerätyn aineiston pohjalta taimenten syönnösvaellukselle lähtemisen todennäköisyyttä kuvaavan käyrän μ parametrin havaittiin korreloivan positiivisesti leveyspiirin kanssa. Kirjallisuuskatsauksen perusteella tämä työ on ensimmäinen yritys laatia todennäköisyyspohjainen populaatiodynamiikkaan perustuva kanta-arviomalli, joka pystyy huomioimaan myös taimen populaatioiden vaelluskäyttäytymisen. Mallin laajamittainen käyttö kalastuksen säätelyn tukemisessa vaatii vielä parannuksia mallin rakenteisiin.