Browsing by Organization "Helsingfors universitet, bio- och miljövetenskapliga fakulteten, biovetenskapliga institutionen"

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  • Hyvönen, Hanna (Helsingin yliopisto, 2015)
    Northern aapa mires are important carbon sinks. Their CO2 exchange with the atmosphere is based on plant photosynthesis and respiration, and the decomposition of peat and other dead organic matter by microbial activity. The photosynthetic efficiency of plants depends on environmental factors and the amount and development of plant leaf area and biomass. There is not much research on the leaf area index and biomass of plants on aapa mires which makes them an interesting and important subject of research. This study investigated plant community composition, development and their effect on CO2 exchange at a northern aapa mire in Finland. The purpose of this study was to survey the biomass and leaf area index of plants within mire types and determine how they, together with water level and microbial activity, and explain the CO2 exchange between the mire and atmosphere. Another aim of this study was to construct regression models for predicting biomass and leaf area index using the plants height and coverage data. The study was conducted in summer 2014 at Halssiaapa, an aapa mire in Sodankylä. The mire was divided into oligotrophic, mesotrophic and eutrophic hummocks, lawns and hollows. The plant community species, their height and coverage were determined in early June, mid-July and mid-August. Moreover, the growth of plant groups was monitored weekly at 16 inventory squares between 6th June and 18th August. Biomass and leaf area samples were collected from different mire types in mid-July, and by the use of regression analysis, two equations were modelled for each plant group, one for predicting biomass and another for predicting leaf area index. The equations were used for predicting biomass and leaf area index for plant groups and mire types based on early June and mid-August data, and the weekly inventory squares. CO2 exchange, and factors controlling it, were measured via an eddy covariance method (measures exchange at ecosystem scale), and a closed chamber method (measures exchange from 1m2). Biomass, leaf area index, species composition, water level and soil factors (indicators of decomposer activity) were used to explain CO2 fluxes. The activity of decomposers in peat was measured via a decomposition test where litter bags containing tea or straw were placed at sampling sites on the mire. The regression models based on plant sample data explained well the biomass and leaf area indices of plant groups. The mire s overall and maximum biomass and leaf area indices were 147 g m-2and 0,73 m2 m-2 respectively for vascular plants, and 351 g m-2and 5,5 m2 m-2 respectively for mosses. Hollows displayed the lowest leaf area index and biomass values, whilst hummocks showed the highest values. Mesotrophic hummocks had the highest values for vascular plants and eutrophic lawns showed the highest values for mosses. Despite having a considerably higher level of biomass and leaf area index than vascular plants, Sphagnum mosses had a much lower gross photosynthetic capacity. Plant communities on lawns and hummocks with an abundancy of sedges (Cyperaceae) had a higher gross photosynthetic capacity and respiration level than plant communities in hollows. Factors leading to increased respiration were increasing vascular leaf area index, release of carbon from straw (indicating decomposer activity), decreasing water level (drier peat) and carbon content in surface peat. Factors leading to increased gross photosynthetic capacity were increasing vascular leaf area index, decreasing water level and decreased straw mass in surface peat (indicating decomposer activity). Temperature and PAR (Photosynthetically Active Radiation) explained 25 % of the variation in gross primary production and 39 % in respiration. The other environmental factors explained 55 % of the residual variation in gross primary production and 78 % in respiration. The mire s gross primary production showed highest increase rate in June and reached its maximum level in early August. Mean plant biomass and leaf area index had the same growth pattern as gross primary production, reaching peak levels at the end of July. The plants Menyanthes trifoliata , Potentilla palustris, Andromeda polifolia and the functional group containing sedges and Scheuchzeria palustris, had a similar growth pattern, but no change in biomass and leaf area index of Betula nana and Vaccinium oxycoccos was detected during the growing season. The models constructed in this study for predicting biomass and leaf area index can be used at Halssiaapa and other nearby aapa mires. Plant surveying and CO2 exchange measurements will be continued at the site in future. Longterm changes in plant community species and CO2 exchange can be researched by comparing results from year 2014 with in coming summers.
  • 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.
  • Jha, Sawan (Helsingin yliopisto, 2014)
    Lymphangiogenesis is the process that leads to the formation of lymphatic vessels from pre-existing vessels. Vascular endothelial growth factor C (VEGF-C), the ma- jor lymphangiogenic growth factor, is produced as an inactive precursor and needs to be proteolytically processed into a mature form in order to activate its receptors VEGFR-3 and VEGFR-2. A deficiency of VEGF-C during embryonic lymphangiogenesis results in embryonic lethality due to the lack of lymphatic vasculature. Hennekam lymphangiectasia-lymphedema syndrome (OMIM 235510) is in a subset of patients associated with mutations in the collagen- and calcium-binding EGF domains 1 (CCBE1 ) gene. CCBE1 and VEGF-C act at the same stage during embryonic lymphangiogenesis and their deficiency results in similar lymphatic defects. The mechanism behind the lymphatic phenotype caused by CCBE1 mutations is un- known. The aim of this study was to investigate the potential link between VEGF-C and CCBE1 that could contribute to the lymphatic phenotype. In this study, 293T cells were used to observe the effect of CCBE1 on VEGF-C pro- cessing. The co-transfection of constructs coding for CCBE1 and VEGF-C showed processing of the inactive pro-VEGF-C into the active, mature form. However, this processing was efficient only in 293T cells. When CCBE1 from 293T supernatant was purified, A disintegrin and metalloproteinase with thrombospondin type 1 motif 3 (ADAMTS3) co-purified with CCBE1. The levels of pro-VEGF-C and active VEGF-C were monitored by immunoblotting or immunoprecipitating metabolically labeled supernatant with specific antibodies or receptors followed by autoradiography. The activity of the processed VEGF-C was verified by proliferation of Ba/F3 cells stably expressing VEGFR-3/EpoR or VEGFR-2/EpoR chimeras. Furthermore, a VEGFR-3 phosphorylation assay was performed in PAE (Porcine Aortic Endotheial) cells to study details of the CCBE1-mediated regulation of VEGF-C. We found that CCBE1 increases the proteolytic processing of pro-VEGF-C, thereby resulting in increased activity of VEGF-C. CCBE1 itself has no effect on VEGF-C activity but regulates VEGF-C by modulating the activity of the ADAMTS3 protease. We also found that both pro- and mature- VEGF-C can bind to VEGFR-3 but only mature form is able to induce VEGFR-3-mediated signaling. In addition to cleaving VEGF-C, ADAMTS3 was found to directly or indirectly mediate CCBE1 cleavage. The N-terminal amino acid sequence of the ADAMTS3-processed VEGF-C confirmed that ADAMTS3 is the protease responsible for the activation of VEGF-C by 293 cells. Hence, we have identified a mechanism that regulates VEGF-C activity. This mechanism suggests the possible use of CCBE1 as a therapeutic means to treat diseases that involve the lymphatic system.
  • Kerminen, Sini (Helsingin yliopisto, 2015)
    Studies of population structure are motivated by the need to understand population history and to have well-characterised groups of individuals in studies of genetics of diseases and traits. A standard method to analyse genetic population structure is principal component analysis (PCA). A disadvantage of PCA is that it can reliably handle only independent genetic markers. This means that the genetic markers that are correlated with other genetic markers have to be excluded from the data. This leads to a loss of information. In 2012, Lawson et al. published a chromosome painting method that can utilise haplotype information, i.e. information from correlated markers, and thus it can detect more subtle differences in populations than the standard PCA. This thesis studies two questions. The first question is whether the chromosome painting method can provide more precise genetic clustering of geographically defined Finnish groups than the standard PCA method. The second question is whether the chromosome painting method can reveal new details of population structure in Finland. The data used in this study are from the FINRISK Study survey of 1997. This cohort includes the genotype data of about 4,000 individuals and the information about individuals and their parents birthplaces. 345 Individuals were randomly chosen from the cohort in such a way that both of their parents were originated from the same province. Ten provinces of Finland were used as study groups for the method comparison. First, the data were analysed with SmartPCA (a standard PCA method) and ChromoPainter (the chromosome painting method) and the results were compared both visually and quantitatively. Finally, the individuals were assigned to populations based on the ChromoPainter result using FineSTRUCTURE program and these genetic populations were compared to the geographic origin of the individuals. The results showed that the chromosome painting method clustered seven out of ten groups significantly tighter than the standard PCA. Nevertheless, SmartPCA was faster and easier to use than ChromoPainter. The main population genetic division was found between the eastern and western parts of Finland, which was consistent with earlier studies. All in all, 15 populations were detected and the results revealed that they were geographically clustered. The genetic populations correlated well with the borders of Finnish provinces and counties. As the first conclusion, the chromosome painting method was able to give more precise results than the standard PCA but the standard PCA is still more suitable for quick preliminary analyses of genetic data. As the second conclusion, the chromosome painting method was able to detect detailed subpopulation structure in Finland and these populations are geographically clustered. Results provide an excellent basis for the future studies of population structure and genetic diseases in Finland.
  • Pakarinen, Suvi (Helsingin yliopisto, 2011)
    The relationship between hosts and parasites is one of the most studied interactions between living organisms, and it is both universal and common in nature. Parasitoids are special type of parasites whose offspring develop attached to or within a single host organism that it ultimately consumes and kills. Hosts are arthropods and most parasitoids belong to the insect order Hymenoptera. For almost two decades metapopulation research on the Glanville fritillary butterfly (Melitaea cinxia) has been conducted in the Åland Islands, Finland. The studies have been concerned with the population dynamics, evolution, genetics, behavior, natural history and life history characteristics of M. cinxia, as well as with species interacting with the butterfly. The parasitoids of M. cinxia have been under long term studies and much has been learned about specific host-parasitoid interactions during the past decade. The research for this Master s thesis was done in the Åland Islands during summer 2010. I conducted a reciprocal transplant style experiment in order to compare the performance of host butterflies (M. cinxia) under attack by different parasitoid wasps (C. melitaearum). I used hosts and parasitoids from five origins around the Baltic Sea: Öland, Uppland, Åland, Saaremaa and Pikku-Tytärsaari. The host-parasitoid relationship was studied in terms of host susceptibility and parasitoid virulence, addressing specifically the possible effects of inbreeding and local adaptation of both parasitoids and their hosts. I compared various factors such as host defence ratio, parasitoid development rate, cocoon production rate etc. I also conducted a small scale C. melitaearum egg development experiment and C. melitaearum external morphology comparison between different parasitoid populations. The results show that host resistance and parasitoid virulence differ between both host and parasitoid populations. For example, Öland hosts were most susceptible to parasitoids and especially vulnerable to Pikku-Tytärsaari wasps. Pikku-Tytärsaari wasps were most successful in terms of parasitoids virulence and efficiency except in Saaremaa hosts, where the wasp did not succeed. Saaremaa hosts were resistant except towards Åland parasitoids. I did not find any simple pattern concerning host resistance and parasitoid virulence between inbred and outbred populations. Also, the effect of local adaptation was not detected, perhaps because metapopulation processes disturb local adaptation of the studied populations. Morphological comparisons showed differences between studied wasp populations and sexual dimorphism was obvious with females being bigger that males. There were also interesting differences among populations in male and female wing shapes. The results raise many further questions. Especially interesting were Pikku-Tytärsaari wasps that did well in terms of efficiency and virulence. Pikku-Tytärsaari is a small, isolated island in the Gulf of Finland and both the host and parasitoids are extremely inbred. For the host and parasitoid to persist in the island, the host has to have some mechanisms to escape the parasitoid. Further research will be done on the subject to discover the mechanisms of Pikku-Tytärsaari host s ability to escape parasitism. Also, genetic analyses will be conducted in the near future to determine the relatedness of used C. melitaearum populations.
  • Ketola, Katri (Helsingin yliopisto, 2015)
    Darwinian selection can be measured and investigated from gene sequences. A certain gene form favored by positive selection will become more common in the population. Detecting strong positive selection is rare, but it has been found to affect genes involved in immune defense and perception of odorants. Genes under positive selection have a possible role in speciation or adaptation. This is why chemical communication, being based on the sense of smell, is an interesting topic for measuring natural selection and positive selection in particular. Social insects, such as ants, are model organisms for chemical communication. They use chemical communication not only for finding nutrition and detecting intruders, but also in coordinating the activities of several thousands of colony members. Insects perceive odorant signal molecules with their antennae. Odorant binding proteins (OBP) and chemosensory proteins (CSP) bind and transport odorant molecules through the sensillar lymph. OBPs and CSPs are also suspected to have a role in selecting odorants. This work focuses on two OBP genes and two CSP genes to study natural selection. All of these genes are conserved among all ant species. Three of these genes, OBP1, CSP1 and CSP7, are strongly expressed in the antennae suggesting that they function in chemical communication. CSP7 also has a known function in nest mate recognition in ants and OBP1 is known to bind a queen pheromone in the honeybee. The data includes gene sequences from 7 Formica ant species (270 sequences in total). The main goals of the research were to find out 1) the extent of variation between and within closely related ant species, 2) which evolutionary forces, natural selection or random drift, are behind the variation and 3) are there systematic differences between the two social forms of ants suggesting that these genes would affect the social structure of an ant colony. The variation in the sequence data was visualized by phylogenetic, principal coordinate and fixed differences analyses. Differences between populations were studied by FST values. The evolutionary forces shaping chemical communication genes within the species and populations, were studied by McDonald-Kreitman test, Tajima s D, Fu and Li test and MFDM test. The data shows that two of the species, F. cinerea and F. exsecta, significantly differ from the other five ant species, the F. rufa group species, and that the F. rufa group species don t significantly differ from each other based on these genes and this data. This could be due to their recent speciation or crossing between the species leading to hybrids in the data. The results of the evolutionary analyses are inconsistent. However, CSP7 has the strongest indication of selection based on all of the tests. Possible selection and sequence variation was detected at a predicted transcription factor binding site in F. cinerea. This indicates that selection might affect the regulation of CSP7. In the future it would be interesting to check the true transcription factor binding sites experimentally.
  • Nordling, Emilia (Helsingin yliopisto, 2010)
    During the last century increased emissions of greenhouse gases have caused global climate warming. While the temperatures are still rising, the largest increases have been observed in spring-time temperatures. This may affect the phenology of multiple species. If the increase in temperature affects different species differently, then the lifecycles of various species may become unsynchronized. For interacting species, a disturbance like this may be catastrophic: for example, if the phenology of host plants is drastically altered, then many herbivores may be left without food. Previous research on the effects of climate change on interspecific interactions has focused on bitrophic interactions. My research expands this past emphasis to a tritrophic level: to interactions between plants (penduculate oak, Quercus robur), herbivorous insects (moths: Tischeria ekebladella, Phyllonorycter quercifoliella and P. harrisella) and parasitoids (wasps in the family Eulophidae). Since bud burst in oaks varies significantly among individuals, I also investigated how host genotype may affect the synchrony between species. My hypotheses were that higher spring-time temperatures will disrupt the synchrony between species, and that this disturbance will affect the growth and reproduction of species at higher trophic levels. I also posited that the effects will vary with the genotype of the host. I tested these hypotheses in a field experiment running from April to September 2009. To manipulate temperatures I used a greenhouse, transplanting multiple oak-specific moth and parasitoid species to oaks of different genotypes growing inside and outside of the greenhouse. During the field experiment, the temperature differed by 3.19°C between the interior and the outside of the greenhouse. As a result, the phenology of all species was advanced in the greenhouse interior as compared to ambient conditions. Interpsecific synchrony was affected differently in different species pairs: Inside of the greenhouse, the synchrony between oaks and Phyllonorycter moths and between oaks and parasitoids was decreased. The synchrony between oaks and the moth T. ekebladella remained unaffected. Likewise, the synchrony between moths and parasitoids was left intact. The larvae of T. ekebladella grew bigger inside of the greenhouse than outside of it. In addition, a second generation of T. ekebladella occurred inside of the greenhouse, but not under ambient temperatures. Host plant phenology had a significant effect on associated insects: moth larvae of T. ekebladella grew bigger on oaks sprouting leaves early in the season. This increase in performance suggests that moth larvae prefer old leaves. In summary, my study shows that climate change may affect different species and different interspecific interactions in highly different ways. My study also upsets the previous view that mature oak foliage would offer food of inferior quality to moth larvae. In addition, it depicts host plant genotype as a less prominent determinant of insect performance than has been previously assumed.
  • Tentke, Annika (Helsingin yliopisto, 2014)
    This project was about the molecular mechanisms involved in the generation of eicosanoids in human mast cells with particular emphasis on lipid bodies as a source and/or site of lipid mediator biogenesis. The cells to be used are isolated from human peripheral blood provided by Finnish Red Cross Blood Transfusion Service and collected from healthy donors. Human mast cells are found in connective tissue. They contain granules filled with histamine, heparine and proteases. Human mast cells are potent effector cells in host-defense mechanisms of innate immunity, including inflammatory diseases such as atherosclerosis. Activation of mast cells by different stimuli triggers the release of a huge range of mediators, including de-novo synthesized eicosanoids, which are highly biologically active lipid mediators. The major eicosanoid released by activated mast cells is prostanoid prostaglandin D2 (PGD2). The aim of this project was to find out whether mast cell lipid bodies are the cellular compartments of PGD2 synthesis, what are the enzymes involved in AA liberation from TGs, and whether TG-derived AA is a source for PGD2 production. The enzymes of special interest were hormone sensitive lipase (HSL) and adipose triglyceride lipase (ATGL). We were also interested about hematopoietic prostaglandin D synthase (HPGDS), the key enzyme in the production of D and J series of prostanoids. Methods used in this pro gradu work include siRNA transfections, RNA isolation, cDNA synthesis, qPCR, immunoblotting, ELISA and conventional fluorescence microscopy. Immediate increase in the amount of PGD2 released from mast cells sensitized with human IgE (1µg/ml) and activated by polyclonal rabbit anti-human IgE (1µg/ml) was observed. The increase was most prominent after one hour of activation, and slowly decreased to basal levels at 48 h post-activation. siRNA transfection affected the amount of enzyme DNA in mast cells and the amount of PGD2 released. HSL, ATGL and HSL+ATGL double knockdowns all reduced the amount of PGD2 released in acute (5 to 30 minutes) term activation compared to control cells. However, no significant changes were observed in the mRNA expression levels of ATGL, HSL, CGI-58, HPGDS or COX-1 under mast cell activation. The only significant changes in mRNA expression levels were observed with COX-2. However, the relative expression of HPGDS increased in IgE treated mast cells compared to control treated cells and the expression was even greater in mast cells treated with αIgE also. Both ATGL and HPGDS were recognized throughout the cytosolic area in the non-activated Ctrl cells. Although HPGDS located also in the circumference of mast cells, no clear localization of HPGDS was observed in the circumference of mast cell lipid droplets. The experiments carried out at the Wihuri Research Institute, including those presented here, have established that, in addition to phospholipids, the triglycerides present in mast cell lipid droplet core are also an important source of eicosanoids, and that also ATGL and HSL, not just cPLA, can release arachidonic acid for eicosanoid production. The ramifications of this study include the possibility that arachidonic acid release from triglycerides for the formation of eicosanoids could take an indirect or a direct route to supply precursors for cellular eicosanoid biosynthesis. The key is the pathway of AA release. In the direct pathway, AA is released from LD TGs by ATGL or HSL and this free AA is used for the generation of PGs by either COX-1 or COX-2, depending on the status of the cell. In the indirect pathway, AA is liberated from LD TGs by ATGL or HSL and then further re-esterified into phospholipids from where AA is then finally released by cPLA2 for the generation of eicosanoids.
  • Lönnberg, Kerstin (Helsingin yliopisto, 2015)
    The purpose of this thesis was to explore the relationships between phytoplankton biomass in lake Pääjärvi and environmental factors. These factors were divided into two categories: external phosphorus loading (total phosphorus, PO4 and organic phosphorus) and thermal conditions (Schmidt stability, heat volume and parent thermocline depth). The data sets at my disposal spanned the years 1994-2010 and contained phytoplankton observations, measurements of lake water temperature and measurements of phosphorus loading from the main rivers and streams flowing into lake Pääjärvi. Heat volume and stability were calculated based on the provided temperature data using a macro for Microsoft Office. The same data were used to calculate parent thermocline depth using LakeAnalyzer. The main statistical analysis performed on these data sets was Redundancy Analysis (RDA) in Canoco for Windows. The data were divided into three different periods: June, July-August and September-October. Each period was examined separately. In addition to total phytoplankton biomass, phytoplankton main groups and selected diatom and flagellate taxa were also examined in relation to the environmental factors. Heat volume proved statistically significant in June in the analysis of total biomass and the main groups and in September-October in the analysis of selected diatom taxa. A statistically significant relationship between PO4 loading and phytoplankton biomass was only detected for Peridinium sp, Rhodomonas lacustris and Mallomonas caudata for July-August. The lack of significance for phosphorus loading in the other contexts may in part be attributed to the distances between the phytoplankton sampling location and the loading measurement sites. The loading would have to drift some time in the lake to traverse these distances before it would come into contact with the measured phytoplankton. During that time, the loading would be susceptible to variations in weather or hydrological conditions as well as susceptible to uptake by other organisms. This may be the reason, or a contributing reason, why phosphorus loading was not significant for most of the contexts explored. However, since phosphorus loading was significant in at least one context, it clearly exerts some influence on the phytoplankton in Pääjärvi. The greater significance for heat volume could be attributed to the cumulative nature of the variable as well as the lack of spatial distance between the temperature sampling distance and phytoplankton sampling location.
  • 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.
  • Kettunen, Henna (Helsingin yliopisto, 2010)
    Elinympäristön vaikutusta eliölajien esiintymiseen voidaan tutkia habitaattimallinnuksen keinoin. Havainnot lajin esiintymisestä ja puuttumisesta eri kohdissa maisemaa suhteutetaan tilastollisen mallin avulla ympäristötekijöihin, jolloin saadaan kuva lajin elinympäristövaatimuksista. Tällöin oletetaan, että laji esiintyy kaikkialla siellä, missä sen elinympäristövaatimukset täyttyvät. Metapopulaatioteorian valossa näin ei kuitenkaan aina ole: maisemassa voi olla runsaasti lajille soveltuvia mutta asuttamattomia kasvupaikkoja, koska uusien yksilöiden leviäminen ja vanhojen häviäminen eivät välttämättä ole yksittäisten kasvupaikkojen tasolla tasapainossa. Siten myös lajin leviämiskyky vaikuttaa siihen, millaiseksi sen levinneisyyskuvio maisematasolla muodostuu. Tässä työssä keskityn tammen (Quercus robur) alueellisen levinneisyyden mallintamiseen. Tammen suhteellinen harvinaisuus Suomessa sekä sen rooli luonnon monimuotoisuuden merkittävänä tukipilarina tekevät siitä mielenkiintoisen kohdelajin ekologiselle tutkimukselle. Tutkimuskohteekseni valitsin Wattkastin saaren, n. 5 km2:n alueen Länsi-Turunmaalta. Wattkastissa on tutkittu kahdeksan vuoden ajan tammella elävien hyönteisyhteisöjen rakennetta ja kannanvaihteluita, ja saaressa kasvaa yli 1800 luonnonvaraista tammea, joiden tarkat sijainnit tiedetään. Tässä ympäristössä tutkin, rajoittaako tammen alueellista levinneisyyttä ensisijaisesti sopivien elinympäristöjen tilajakauma vai pikemminkin sen leviämiskyky. Yhdistin tammen esiintymiskuviota kuvaavaan habitaattimalliin kokeellisen aineiston, jonka avulla arvioin tammen paikallisen esiintymiskuvion ja tammelle soveltuvien elinympäristöjen tilajakauman vastaavuutta. Kokeellisen aineiston muodostivat 104 Wattkastiin vuonna 2004 istutettua pikkutammea, joiden selviytymisen ja kasvupaikkaolot kartoitin syksyllä 2009. Tutkin yleistetyillä lineaarisilla malleilla puiden menestymiseen siis selviytymiseen ja kuntoon vaikuttavia tekijöitä. Etsin potentiaalisia selittäjiä tammen menestymiselle kasvupaikan ympäristötekijöistä sekä istutetun puun sijainnista suhteessa luontaisiin tammikasvustoihin. Lisäksi tutkin habitaattimallin avulla, selittävätkö ympäristötekijät tammen nykyisen esiintymiskuvion Wattkastissa. Havaitsin, että istutetut puut olivat selviytyneet keskimäärin hyvin ja ettei niiden menestyminen riippunut sijainnista suhteessa luontaisiin tammikasvustoihin. Habitaattimallin selitysaste oli vain 19 %, eli kasvupaikkatekijät selittivät heikosti tammen nykyisen esiintymiskuvion Wattkastissa. Tulosten perusteella tammen paikallinen esiintymiskuvio ei vastaa sille soveltuvien elinympäristöjen jakaumaa maisemassa, joten tammen levinneisyyttä Wattkastissa rajoittaa ilmeisesti sen leviämiskyky. Tulokseni viittaavat siihen, ettei tammen elinympäristön laadussa ole suuria vaihteluita Wattkastin sisällä, koska sopivia kasvupaikkoja on tarjolla tammen nykyesiintymiseen nähden runsaasti. Tämä on tammihyönteistutkimusten kannalta kiinnostava tulos, koska se tarkoittaa, että aiemmat havainnot isäntäpuun sijainnin ja hyönteisten kannanvaihteluiden välisestä yhteydestä edustavat todellisia, tilaan sidottuja populaatioprosesseja eivätkä isäntäpuun välittämiä eroja elinympäristön laadussa. Lisäksi tutkimukseni osoittaa, että yhdistämällä habitaattimallinnukseen kokeellinen lähestymistapa saadaan realistisempi kuva lajin levinneisyyttä rajoittavista tekijöistä kuin tutkimalla pelkästään ympäristötekijöiden vaikutusta lajin esiintymiseen. Jos lajin rajoittunut leviämiskyky on vaikuttanut sen esiintymiskuvion syntyyn, pelkästään ympäristötekijöihin perustuva levinneisyysmalli liioittelee levinneisyyttä. Kokeellisen tutkimuksen avulla on tällaisessa tapauksessa mahdollista paljastaa myös leviämiskyvyn rooli esiintymiskuvion taustalla.
  • Ahvenainen, Terhi (Helsingin yliopisto, 2015)
    Huntington's disease (HD) is a progressive neurodegenerative disorder that causes involuntary muscle movements, deteriorates muscle coordination and cognitive decline. Typical onset age of the disease is in mid age, although a juvenile form of HD is also known. The disease is inherited in an autosomal dominant manner via a mutation in the huntingtin gene (HTT). The characteristic mutation in HTT is an expansion of the glutamine stretch at the 5 end of the gene. Excessive amounts of glutamine residues alters the conformation and chemical features of the huntingtin protein (HTT) leading to accumulation of cellular aggregates. Although to date there are several known alterations in the cell that contribute to the disease, the pathogenesis of HD is not fully understood. Ubiquitin proteasome system (UPS) dismantles proteolytically unneeded or damaged proteins, which are targeted to proteolysis when ubiquitin tags are added to them. Deubiquitinating enzymes (DUB) recycle ubiquitin molecules by releasing them from proteasome substrates. Recycling of ubiquitin is critical to a cell as it maintains the free pool of the targeting molecule. Ubiquitin-specific protease 14 (USP14) is one of the DUB family enzymes and its distinctive function is to remove ubiquitin molecules from the tip of the ubiquitin chain and thus antagonize protein degradation. Although the specific function of the protein is unclear, it seems that USP14 operates as a fine regulator of protein turnover rate and in ER stress both in catalytic and non catalytic manner. The role of USP14 is especially emphasized in the nervous system, as it regulates synaptic transmission and neuronal development. Although it is suggested that dysfunction of UPS is involved in the pathogenesis of HD, the role of USP14 in the disease remains to be unknown. IU1 is a novel inhibitor of the catalytic domain of USP14. Studies with IU1 indicate that inhibition of USP14 enhances the clearance of aggregate prone proteins. The approach of this thesis was aimed to elucidate the routes of HD pathogenesis from diverse approaches. The general aim of the thesis was to investigate the role of USP14 in the wild-type PC6.3 cell model, and in the pathogenesis of HD by expressing HTT proteins with different lengths of glutamine stretches in PC6.3 cells. The specific aim of the study was to examine by western blot and microscopy analysis the pathogenic routes of HD that involve ER stress, oxidative stress, autophagy and mutant HTT aggregate dynamics. The function of USP14 was studied with overexpression of USP14, or by inhibiting its catalytic activity by IU1. The findings of this thesis show that overexpression of USP14 enhances the clearance of mutant HTT aggregates, and this effect is obtained in catalytic activity dependent manner. I show that upregulated USP14 is connected to improved clearance of mutant HTT and inhibition of autophagy, suggesting that the degradation is mediated via UPS. The catalytic activity of USP14 might also be important in ER stress regulation, as the results indicate that IU1 activates phosphorylation of both JNK and eIF2α. I was also able to establish a connection between USP14 and GADD34, as I show that GADD34 upregulates USP14. Finally, I show that catalytic inhibition of USP14 decreases the expression of antioxidant SOD2. The data in this thesis is lacking statistical significance, and it can be considered solely as a guideline. However, together these results indicate that the deubiquitinating activity of USP14 increases survival in PC6.3 cells in both a healthy and a HD model.