Browsing by department "Faculty of Biological and Environmental Sciences"

Lakes play a significant role in the carbon cycle, as they transport, modify, sequester and bury carbon. Climate has direct and indirect impacts on the carbon cycle of lakes. Small, shallow lakes in the northern boreal region are particularly sensitive to climate variability. By studying organic carbon accumulation and quality in lake sediments, and by comparing them to the Holocene climate reconstructions, we can deepen our understanding of the processes affecting carbon sedimentation, evaluate the current and future changes, and separate the on-going climate warming and other anthropogenic factors from natural ones. In this study, we examine carbon accumulation and quality during the Holocene in four lakes in one northern boreal catchment area. Sediment organic carbon content, accumulation rate, C/N-ratio, and d13C were measured and compared to each other as well as to the lake and drainage characteristics and temperature reconstructions. Temperature explained some of the variation in carbon accumulation and quality, in part the variability was attributed to the lake and drainage characteristics.

According to The Finnish Act on Water Resource Management, the ecological status of Finnish streams and lakes have to be monitored and assessed based on the severity of human impact on biota. The ecological assessment of freshwaters is based on comparing the impacted ecosystems with those freshwater ecosystems of a nearly intact state. The Finnish Act on Water Resource Management is based on the European Union Water Framework Directive, or WFD. Macrophytes (aquatic bryophytes, macroalgae, and vascular plants) are used as an element in freshwater assessment. In Finland, the used of macrophytes have been long established along with other organism groups in ecological assessment of lakes, but macrophytes have not yet been used extensively in ecological assessment of rivers. A rough method has been developed, but further study and improvement needs to be made before reliable ecological assessments using river macrophytes can be done. Currently, there is a great need for a uniform method for river assessment using macrophytes. In Finland, the ecological state of freshwaters is classified by using biological metrics based on the abundance and variety of different organism groups. The biological metrics are converted to a scale of 0-1 into a so-called Ecological Quality Ratio (EQR) in order to be able to compare their results. Suitable biological metrics have been studied in Finland, and so far, the Percent Model Affinity (PMA) and Observed-to-Expected-taxa index (O/E-taxa index) have proven to be promising. Both metrics have been observed to explain human impact in the catchment and changes in water quality. These metrics are hence used in this thesis. The variety and abundance of freshwater macrophytes was studied according to the rough method developed at the Finnish Environment Institute (SYKE) in 2008. In this thesis, the objective was to study how the results of the biological metrics varied between different river parts of Mätäjoki. The EQR and biological metrics results obtained earlier from diatoms and benthic invertebrates were also compared with the results obtained with macrophytes in the same river parts. A possible link to the results of the River Habitat Survey (RHS) and riverbank vegetation was also studied. The biological metrics used in this thesis are based on using reference sites (sites in natural condition) to assess the ecological condition of the studied sites. Data collected for the MaaMet-survey by the Finnish Environment Institute formed the reference conditions. The reference sites included were as pristine as possible. The field method consisted of gathering macrophyte data from two 50-metre-long adjacent river parts: a riffle and a pool. A total of 18 rivers and pools were included, forming 9 river-pool pairs. The riverbank vegetation was studied on the banks of the pools. In this thesis, we observed significant variation in both the biological metrics results and EQR results. The results of the biological metrics were surprisingly low, indicating a possibly bad ecological condition. The mean of EQR results using combined data, bryophyte data and vascular plant data were found to be very similar. The EQR results using macrophyte data were considerably lower than the EQR results of the diatom and benthic invertebrate data. Macrophytes thus indicated a possibly inferior ecological state than diatoms and benthic invertebrates. The species richness of Mätäjoki was found to be considerably lower than that of the reference sites. The surprising results may indicate shortcomings in the rough river macrophyte method. The small size of the reference condition data and issues in the national Finnish river classification system may also be responsible for some of the results. Low EQR results, indicating low ecological state, may be a result from the impaired ecological state of Mätäjoki due to human impact. Moreover, the ecological assessment of urban rivers based on biota has in some studies produced unreliable results on other organism groups. The results show that biological metric values show a large variation between river parts. This must be taken into consideration in the development of the river macrophyte method and in choosing the sampling sites of studied rivers.

Tutkimus on perinteisesti keskittynyt taloudellisesti merkittävien, jalostettujen tuotantokasvien tauteihin. Luonnonkasvien tauteja on tutkittu huomattavasti vähemmän, vaikka niillä on suuri merkitys kasviyhteisön monimuotoisuuden säätelijöinä. Etenkin virusten vaikutuksista on hyvin vähän tietoa, koska tartuntoja on hankala havaita. Virukset ovat ehdottomia solunsisäisiä loisia ja tarvitsevat vektoreita levittäytyäkseen kasvien välillä. Virusten esiintymisten ja vaikutusten on havaittu vaihtelevan runsaasti ajallisesti sekä lajien ja populaatioiden välillä. Tässä työssä selvitettiin Plantago lanceolatan latenttiviruksen (PlLV) ja Plantagon latentin caulimoviruksen (caulimovirus), esiintymistä kolmessa eri puolilla Ahvenanmaata sijaitsevassa heinäratamon (Plantago lanceolata) populaatiossa. Kustakin populaatiosta valittiin 20 satunnaista kasvia tutkimukseen. Lehdistä kerättiin näytteitä kerran viikossa kolmen viikon ajan touko-kesäkuussa 2017. Kasvien kukkien ja lehtien lukumäärä sekä pisimmän lehden pituus kirjattiin ylös. Lisäksi mahdolliset viroottiset oireet ja herbivorien aikaansaamat syömäjäljet kirjattiin ylös. Virusten havaitsemista varten kehitettiin qPCR-menetelmä aiempien virussekventointien pohjalta. Alukkeet suunniteltiin mahdollisimman konservoituneille alueille virusten perimässä. qPCR-menetelmän kynnysarvon asettamisen apuna oli lisäksi 218 kasvihuonekasvinäytettä, jotka oli testattu valmiiksi jo olemassa olevalla PCR-menetelmän alukkeilla. Luonnonkasvinäytteet tutkittiin sekä qPCR- että PCR-menetelmillä, joiden tulokset yhdistettiin. Sekä PlLV:ä että caulimovirusta esiintyi kaikilla populaatioilla, mutta esiintymisessä ei ollut merkitseviä populaatioiden välisiä eroja. PlLV-havainnot vähenivät merkitsevästi tutkimusaikana, mutta caulimoviruksen esiintyminen ei vaihdellut. Caulimovirushavainnot korreloivat positiivisesti lehtien lukumäärän sekä erään syömäjälkiluokan kanssa. Muut kasvin ominaisuudet tai herbivorien jättämät syömäjäljet eivät selittäneet virustartuntoja. Viroottiseksi tulkittuja oireita oli sekä virustartuntaisilla että terveiksi todetuilla kasveilla. Vanhat PCR-menetelmät tunnistavat jossain määrin qPCR-menetelmiä paremmin virustartunnat, mutta menetelmät tunnistavat osittain eri tartunnat. Tulokset vahvistavat aiempia havaintoja siitä, että virusten esiintyminen luonnonkasveilla on vaihtelevaa, eivätkä ne aina välttämättä aiheuta näkyviä oireita, mikä tekee niiden vaikutusten arvioinnista haastavaa. Virukset ovat täysin vektoreista riippuvaisia, ja tulos antaa mahdollisia viitteitä caulimoviruksen vektorilajista. Suurikokoiset kasvit vaikuttavat olevan alttiimpia caulimovirustartunnalle. qPCR-menetelmä täydentää PCR-menetelmää, mutta vaatii lisäoptimointia tehokkuuden parantamiseksi. Jatkotutkimukset suuremmalla otannalla ja pidempiaikaisella seurannalla valottaisivat, millaisia vaikutuksia virustartunnoilla on kasveihin missäkin olosuhteissa.

Tutkin tässä pro gradu -tutkielmassani eräiden suomalaisten ruohovartisten kasvilajien ja biohiilen vaikutuksia huleveden määrään ja laatuun. Tutkimuksessa järjestettiin koekasteluita, joiden avulla oli tarkoitus selvittää kasvilajien kykyä vähentää huleveden määrää ja poistaa siitä ravinteita sekä biohiilen vaikutusta huleveden määrään ja laatuun. Kasvillisuuden ja biohiilen vaikutusta on tutkittu aikaisemminkin, mutta erityisesti tiettyihin kasvilajeihin liittyviä tutkimuksia ei ole tehty Suomessa. Tutkimus on osa Luonnonvarakeskuksen Hulevesialueiden kasvit ja kasvualustat (HuleKas) -projektia. Kaupungistuminen lisää talojen, parkkipaikkojen ja teiden rakentamista. Tämä kasvattaa läpäisemättömien pintojen määrää, ja se puolestaan estää veden imeytymisen maan läpi. Kaupungeissa ongelma on ratkaistu rakentamalla hulevesiviemäriverkostoja, mutta erityisesti muuttuva ilmasto lisää sateiden ja sitä kautta huleveden määrää. Rankkasateilla kaupunkien hulevesiviemärit osoittautuvat usein riittämättömiksi. Lisäksi hulevesi huuhtoo epäpuhtaudet kaduilta, ja hulevesi onkin todettu yhdeksi tärkeimmistä hajakuormituksen aiheuttajista. Nyttemmin on kehitetty perinteisten sadevettä pois johtavien viemäriverkostojen rinnalle ekologisempia ja kestävämpiä ratkaisuja. Hulevesi pyritään käsittelemään sen syntysijoilla, ja tähän voidaan päästä rakentamalla erilaisia hulevesirakenteita, kuten hulevesipainanteet tai sadepuutarhat. Hulevesirakenteiden tärkeimmät osat ovat kasvualusta ja kasvillisuus. Hyvällä kasvualustavalinnalla voidaan pidättää mm. fosforin yhdisteitä ja kuparia, kun taas nitraatin pidättyminen vaatii rakennetta peittävää kasvillisuutta ja hapettomia olosuhteita. Kasvillisuuden avulla voidaan myös hidastaa huippuvirtaamia, pidättää kiintoainesta ja poistaa metalleja ja ravinteita hulevedestä. Myös kasvualustan mikrobeilla on tärkeä merkitys ravinteiden sitojina. Tutkimusasetelmani oli astiakoe. Astioihin oli istutettu seitsemää suomalaista luonnon kasvilajia, nurmea ja kontrollina toimivat kasvittomat astiat. Osaan astioista oli lisätty biohiiltä. Tutkimusjakson aikana järjestettiin kolme koekastelua, joissa liuoslannoitteilla lisättyä tekohulevettä kaadettiin jokaiseen astiaan sama määrä. Tämän jälkeen kirjattiin ylös tietyin aikavälein, paljonko vettä astiasta on valunut ulos. Tutkielman aineisto koostuu kahdesta osasta. Ensimmäinen osa muodostuu koekasteluiden valuntatiedoista ja kolmas osa koekasteluiden vesinäytteiden laboratorioanalyyseistä. Parhaita kokonaistypenpidättäjiä olivat viiltosara, jänönsara, korpikaisla, luhtakastikka ja rantatyräkki. Kokonaisfosforin pidätyksessä puolestaan erottuivat viiltosara, korpikaisla, ja rantatyräkki. Kaikki kasvikäsittelyt alensivat tekohuleveden kokonaisfosforin konsentraatiota. Biohiili paransi kaikkien edellä mainittujen kasvilajien ravinteenpidätyskykyä. Myös mikrobitoiminnan merkitys ravinteiden sidonnassa on tärkeä. Eniten vettä koekastelussa käyttivät viiltosara, luhtakastikka sekä jänönsara. Jänönsaran suorituskyky on kiistanalainen johtuen epätasaisesta kastelusta kolmannen jakson aikana. Jaksojen aikaisessa veden käytössä tehokkaina veden käyttäjinä nousevat esiin viiltosara, jänönsara, korpikaisla, luhtakastikka ja rantatyräkki. Kaikki kasvikäsittelyt tuottivat vähemmän valuntaa, kuin kontrolli. Biohiilen avulla voidaan hidastaa valunnan alkamista ja kertymistä.

Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) is a plant pathogen which causes bacterial speck in the host plants, especially tomato. The genome sequence of Pst DC3000 was resolved in 2003 by Buell et al. and since then it has served as an important model organism in plant pathology. Pst DC3000 secretes proteins through so-called type III pathway (T3SS). The secreted proteins, called Hrp (Hypersensitive response and pathogenicity) or Hop (Hrp outer protein), are considered as main virulence determinants of the bacterium. Aim of the study was to find out the suitability of the phage Mu DNA transposition complex to generate a transposon insertion mutant library for Gram-negative phytopathogen. Then further screen the mutant library for Hop effector protein knock-out mutants and evaluate their virulence in Lycopersicon esculentum cv. Moneymaker tomato plants. The thesis was part of a research project that characterized virulence determinants of Gram-negative phytopathogenic bacteria, including their gene regulation and effects on the plant-bacterium interaction. Pst DC3000 transposon insertion mutant library was generated by electroporation of phage Mu DNA transposition complex and a nested PCR method was used for screening the library. Three hop transposon insertion mutants were found, and those strains were extracted from the library. The three mutant strains where then used to infect tomato plants. Virulence was evaluated through phenotypic lesions and bacterial endophytic growth. Some of the results were different from the previous studies. The ability of HopM1 mutant to form lesions was weakened and it´s endophytic growth was slowed down. In previous studies the ability to form lesions was also weakened, but the endophytic growth was not affected until avrE gene was also deleted. HopM1 deletion alone did not have an effect to bacterial growth. In HopAO1 mutant the virulence was not affected. In other studies, HopAO1 deletion weakened bacterial growth in Arabidopsis and tobacco plants, but in tomato it has not been tested. HopD1 mutant was avirulent in this study. In previous studies HopD1 was essential for Pst DC3000 bacteria in defeating plants effector-triggered immunity (ETI), but hopD1 deletion alone did not make the bacteria avirulent. Pst DC3000 has 28 different effector proteins so usually one effector protein mutation does not affect its virulence. Hence the next step of the study was to make double mutants for Hop proteins, and this included deletion of the antibiotic marker by Cre-lox mechanism, which was started in this study.

In my thesis I analyzed the ongoing discussion about the relationship between economic growth and the environment by the means of content analysis and discourse analysis. As the continuously growing use of natural resources has a connection to many environmental problems, the functioning of the economy is essential when discussing the alternative solutions to environmental problems. I wanted to investigate what the discussion about the relationship between economic growth and the environment includes, and what kind of phenomenon is economic growth represented as. Theoretical frameworks I used were the environmental discourse analyses of Hajer (1995) and Dryzek (2005). I also paid attention to the organizations behind the discourses by classifying the writers due to the organization they represented. The material I used were texts published in the Internet, with no limitations concerning the form of the publication or the publisher. The only limiting factors I used, were the search terms. The material was taken from a database called “Economy and the Environment” (translation from Finnish), and it was not originally collected for this thesis, but for any scientific or educational purposes. I analyzed three discourses in the discussion concerning the relationship of economic growth and the environment: “Belief in growth”, “Green growth” and “Growth critique”. In Belief in growth, economic growth was an intrinsic goal. Pursuit for higher material standard of living was unquestionably a good thing. Belief in growth seemed to be the discourse especially for business interest groups. There were quite many academic writers too, but the academics were not mainly writing in belief in growth discourse, but were also presented in great numbers among the writers of all three discourses. In Green growth discourse economic growth was not an intrinsic goal, but was considered necessary for financing the welfare state. There were hopes that technological development, ecoefficiency and a transformation towards service and information economy would lessen the adverse environmental effects of economic growth. Technology had a major role in Green growth, and it was even seen as a major force itself, solving environmental problems without any role from the users. Amongst the writers of Green growth, Officials and members of the political Green party of Finland were presented in large numbers. In Growth critique discourse endless economic growth was seen impossible on a finite planet, and the ongoing strive for economic growth was seen to cause environmental and social problems. The discourse wanted to change our economic system, so that the pursuit for growth could be abandoned. Abandoning the pursuit for growth was seen also as a question of global equality: the rich countries were hoped to abandon the pursuit for growth, so that the developing countries would have resources left for growth. Compared to other discourses, amongst the writers of Growth critique, NGO’s, social movements, and civilians were presented in large numbers. The discussion about the relationship of economic growth and the environment constituted as a whole in such a way that in the discourses there were expressed opinions about other discourses and their writers. On the other hand, the discussion included many disconnecting elements. This was for example due to the underlying perceptions of environmental problems, and the nature itself, which differed clearly among the three discourses. This finding is convergent with the discourse analyses of Hajer and Dryzek. In Belief in growth environmental problems were local, and mostly described as pollution, which can be removed with the means of cleaning technology. Nature, in this discourse, was a collection of elements which can be used and organized by humans how ever needed. Also in Green growth environmental problems were mostly described as pollution, but the existence of other kinds of environmental problems were recognized as well. In this discourse the global scale existed, as there was a lot of discussion about climate change. In Growth critique environmental problems were seen as one big global crisis, caused by the excessive use of natural resources by humanity. In both, Green growth and Growth critique, nature was seen as a system of which humans are strongly dependent on. The weakest points in the discussion were related to the use of concepts of economics and environmental sciences, and weakly justifiable arguments. In Growth critique, some complicated concepts of economics and environmental sciences were used, which seemed to be poorly understood by the writers of other discourses. Green growth seemed to be suffering of a lack of historical perspective, especially considering the discussion about ecoefficiency, where strong presumptions about the significance of ecoefficiency in reducing the adverse effects of economic growth were made without any historical perspective. In Belief in growth there was incoherence with the concept of economic growth, and means and ends got mixed in the discussion about economic growth and wellbeing. In both Green growth and Belief in growth there were very weakly justified arguments about hopes for information technology and services creating immaterial economy. Interesting topics for future research in Finnish environmental discourse would be the discourse of Green politics, discussion about immaterial economy and the weaknesses in the arguments related to ecoefficiency.

Social insects such as ants live in societies and have a strict division of labor between reproductive and worker castes. A colony can consist of even millions of individuals and the number of queens can vary a lot. Populations where each colony comprises just one or few queens are often called kin structured because the relatedness between nestmates is high. Colonies that have lots of queens and the society lives in many connected nests (polydomy) in are referred to as supercolonies. In these colonies relatedness between individuals is low and the workers represent many genetic lineages. Depending on species and the environment where the colony lives societies can behave aggressively towards individuals from other nests to protect their own nest. Ants must be able to recognize members of their own colony from the intruders to be able to protect the nest. Nestmate recognition is a key element in the interaction between nests and species and makes it possible for the workers in the colony to favour their own nestmates in form of care, defence or food acquisition to gain inclusive fitness benefits. To recognise nestmates ants must be able to sense chemical cues. Ants detect these chemical signals through the proteins expressed mainly in their antennas. In this thesis I studied gene expression of genes related to chemosensation in seven Formica species using the RT qPCR method. My study species were kin structured Formica exsecta, F. pratensis and F. fusca and supercolonial F. truncorum, F. pressilabris, F. cinerea and F. aquilonia. My study genes belong to gene families that code for odorant binding proteins (OBP), chemosensory proteins (CSP) and gustatory reseptors (GRT). I want to find out whether the expression of these genes differs between castes, and whether the caste difference varies between kin structured and supercolonial species. Workers have many tasks in the ant colony and to take care of them, they need to have a sophisticated sensory system. For that reason, I expect to find out that the study genes are expressed more in the worker than the queen caste. In addition, I expect the caste difference in gene expression to be higher in the kin structured species than in the supercolonial species. That is because kin structured species behave more aggressively towards intruders and possibly confront intruders more often than the individuals living in supercolonies. Furthermore, in the supercolonies low relatedness between individuals sometimes lead to conflicts inside the nest. For that reason, I suppose queens of the supercolonies express chemosensory genes more than the queens from the kin structured colonies. Overall expression level was the highest for the OBP and the lowest for GRT. The expression level of CSP was in between these extremes. In accordance with my hypothesis gene expression of OBP and CSP was higher in workers in all the study species. GRT expression was worker biased in six of the seven species. Caste difference in expression of chemosensory genes was similar in kin structured and supercolonial species. The expression level varied between species but did not show a pattern depending on the degree of the polygyny. The study revealed that the expression of OBP and CSP is correlated. My results revealed expected worker biased pattern in the expression. The result might be a consequence of better olfactory or taste abilities in the worker caste compared to queens or it may even be consequence of more sophisticated nestmate recognition skills of the workers. This study reveals valuable information about the gene expression of chemosensory genes related to the recognition system in the ants and awakes many new study questions. Chemical sensory system has been studied a lot in the ants, but in the field of expression studies there is still lot to reveal.

Animals and humans communicate in various ways, using for instance motion, gestures and sounds. Through domestication humans now share the same habitat with a number of species. A centuries-old common history with cats has affected both cats’ behavior and vocalization and possibly human behavior as well. Human speech contains acoustic information beyond the linguistic content. An example of the acoustic structures are fast-repeated, pulsed vocalizations, shown to activate for instance dogs. These structures are thought to be universal in communication with domestic species, possibly for all mammals and birds. Still, not all sounds work the same way for all species. Besides universal structures there are probably species-specific features in calls initiated by humans. We call all domestic animals differently and in a species-specific way, but the common goal is to engage the individual’s attention, and have it approach the caller. People call cats in various ways in different countries, but nevertheless the calls share some common acoustical features. Here, the goal of the study was to find out if people from various language and cultural backgrounds use short, fast-repeated sounds to call cats and to find out similarities in the usage of call sounds higher in frequency than speech. For this, I asked people from various language and cultural background to fill in a questionnaire and give audio samples of a call, instructing them to have an unknown cat approach them. The short, fast-repeated sounds from the calls were extracted and features analyzed using various computer programs. The data were statistically analyzed to find out 1) if the repeated sound frequency spectra differ from the spectra of calls including only speech, 2) the effect of cat ownership and language background to call repetition, 3) the effect of cat ownership and language background to call frequency, and 4) the effect of call origin (inheritance) and experience (cat ownership) to call properties. Altogether 56 adults participated in the study. The subjects were from 19 different countries and represented 16 different native languages. 86% of the calls included fast-repeated, short, pulsed segments. The duration and frequency of the calls differed depending on the repeated sound. The fastest repetition rate was with various clicking sounds. The highest frequency content was with calls including “s” sound, such as “pss” and “kss”, and various lip-smacking sounds. While there were differences in the repeated segments depending on the language background of the caller, the common pattern was that the spectral center of gravity in sound frequency was higher for the fast-repeated, short segments than for calls including only speech. In summary, human-to-cat calls have a high frequency content and include short, fast-repeated sound segments regardless of the language background of the caller, in order to get cat’s attention and have it approach the caller. For the follow-up study I suggest expanding the subject population to different language backgrounds. In addition, the call sounds should be compared to predator sounds. Further, the effectiveness of the call sounds could be tested with cats or kittens.

New Zealand is an isolated landmass laying in the Southwest Pacific waters, far away from any major islands or continents. It was the last major landmass to be colonized by people, discovered by the first Polynesian explorers around a thousand years ago. Historically, New Zealand lacked all native mammals (apart from three species of bats) and so has developed a plethora of bird species and other endemic wildlife. The absence of mammalian predators, combined with the continuous isolation for millions of years, has led the evolution of some very unique and charismatic species. One of these species is the iconic symbol of New Zealand – the kiwi (Apteryx spp). The biggest challenge to the New Zealand wildlife has been the introduction of mammalian species to the New Zealand ecosystem. There are 25 species of introduced mammals in New Zealand today that are regarded as pests. The devastation caused by these species is the main cause for the dramatic decline of the endemic New Zealand wildlife, including the iconic kiwi. Nationally, kiwi continue to decline by more than 2% annually and there are estimates of the species going extinct from the wild within 50 years. Since the first more permanent human settlement, more than 50% of the New Zealand breeding birds have gone extinct. In this thesis, the relation between kiwi and introduced mammalian species around the township of Whakatāne, New Zealand, was studied. During summer 2018-2019, three out of eight monitored kiwi chicks were predated by a suspected mustelid/mustelids and DNA swabs were obtained from the bite sites. Volunteer pest trappers were then asked to bring in all their catches in an attempt to catch the individual/individuals responsible for the predations. Molecular tools including microsatellites were used to create ID profiles in an attempt to match the profiles to those obtained from the kiwi chicks. In the second part of the study, the stoats’ stomachs were analysed as part of a diet study. A new, kiwi specific DNA probe was trialled and the remaining stomach contents were sequenced for other native wildlife species. Out of the three predated kiwi chicks, all of them were confirmed to be stoat predations. Unfortunately, none of the stoat ID profiles obtained matched the profile of the kiwi chick Ranui who was the only chick a good micro-satellite profile was obtained for. This confirmed that the stoat/stoats responsible for the predation of Ranui was not caught as part of this study. In the diet part of this thesis, we trialled the kiwi specific probe but could not identify any kiwi DNA in the stoat stomach contents. The DNA sequencing however revealed five other species: tomtit (lat. Petroica macrocephala, 100%), common chaffinch (lat. Frigilla coelebs, 100%), tui (lat. Prosthemadera novaseelandiae, 96%), European hare (lat. Lepus europaeus,100%) and copper skink (lat. Cyclodina aenea, 100%). These findings shed new light on the extent introduced mammalian species contribute to the species loss taking place in the New Zealand forests today. The use of molecular techniques and tools in conservation offers an often faster, cost-efficient and more reliable alternative to traditional monitoring methods of introduced species. The rapid development of these tools has seen New Zealand taking critical steps towards one day becoming predator free. The ambitious goal to rid New Zealand of target introduced species (mustelids, possums and rats) by year 2050 (Predator Free 2050), has been compared as the New Zealand equivalent of putting the man on the moon.

Charcot-Marie-Tooth disease is a clinically and genetically heterogeneous group of disorders of the peripheral nervous system. It affects both peripheral motor and sensory nerves that lead to progressive degeneration of muscles in the lower limbs. Prevalence of CMT is 1:2500. It can be divided into two groups: CMT1 is the demyelinating type and CMT2 is the axonal type. There are 20 known genes associated with CMT2 but not all of them have been found yet. Hereditary spastic paraplegia (HSP) is a group of inherited neurological disorders and it is also genetically and clinically heterogeneous. HSP is caused by degeneration of the upper motor neurons in the brain and spinal cord. HSP can be divided into pure and complex forms. In pure forms the main symptoms are progressive spasticity and weakness in the lower limbs. In complex forms there are additional symptoms such as epilepsy and mental retardation. The prevalence of HSP is 2-10:100 000. There are over 70 loci associated with HSP and 55 genes identified so far but there is probably more to be found. With both of these diseases it has been difficult to diagnose patients at the genetic level because of the great amount of disease genes. The aim of this study was to identify potential disease causing mutations by using targeted next-generation sequencing (NGS) and also to do functional testing with the discovered mutations. There were 48 patients, 28 diagnosed with CMT and 20 with HSP. For the targeted sequencing there was a gene panel with 167 genes, including genes associated with neuropathy, paraplegia, ALS and mitochondrial functions. Analyzing of the gene variants was largely based on their frequencies in the population and several exome databases were used. All possibly pathogenic mutations were confirmed with Sanger-sequencing and also sequenced from the patients’ relatives, if DNA samples were available. Possible genetic diagnosis was found for five CMT patients and six HSP patients. Only one of the mutations was previously known. One of the probably pathogenic mutations was a deletion, others were missense mutations. Large portion of the patients were left without a genetic diagnosis probably because there are many more genes associated with these diseases to be found. De novo heterozygous missense mutations in the KIF1A gene were found to cause a novel phenotype. Symptoms of these patients include classical HSP symptoms and additionally intellectual disability and other symptoms, such as cerebellar atrophy, in some patients. In this study we found a deletion in the gene HSPB1 that causes premature STOP codon that leads to disappearance of nearly the entire C-terminus. In this study I built a HSPB1-Western blot assay that was used in further research. It was found out that the truncated protein was stabile, it forms dimers with the normal protein and impairs the cells response against stress caused by misfolded proteins.