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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.

Keeping dogs (Canis familiaris) affects the environment. One significant effect of dogs in the environment is the production and deposition of urine. Unlike other waste, dog urine cannot be easily collected by owners, leading to unfiltered introduction into the soil. Dog urine is high in urea, which hydrolyzes to ammonium and nitrate. These soil nitrogen forms have the potential to change other soil properties that may cause harm in plant or microbial health, and contributing to eutrophication. In this thesis I investigate the impacts of dogs on soil nitrogen properties and their connection with human population density and closeness to walking paths in urban remnant forests. To evaluate the level of impact of dogs and to gain knowledge on the current nitrogen content and δ15N in urban remnant forests, five urban remnant forests were examined. Within each forest, soil nitrogen forms, δ15N in the soil and foliage samples, as well as total carbon and nitrogen content of the soil were compared, besides basic soil properties between dog-affected and control areas. The study revealed elevated levels of soil electrical conductivity, ammonium, and nitrate, as well as soil and foliage δ15N in dog-affected areas. Unexpectedly, soil acidity was lower in samples taken next to paths where dogs can potentially urinate. Organic matter content and total nitrogen and carbon content of the soils were higher where dogs are not frequent visitors, meanwhile the carbon-to-nitrogen ratio was also higher. These findings show that the impacts of dog urine on the soil should be considered in urban planning and further research is needed to understand the significance of it.

Chitinolytic enzymes belong to a group of pathogenesis-related proteins, which are induced in plants by a pathogenic attack. They have also been shown to function in abiotic stresses and related to signalling. Chitinases catalyze the degradation of β-1,4-N-acetyl glucosamine units of chitin. Chitin is not found in plants, but for example the shells of invertebrates, cell walls of certain fungi, algae and bacteria contain it abundantly. Lately chitinases have gathered attention because of their potential utilization possibilities in medicine, agriculture, food industry and biofuels. Strong chitinase gene expression and also chitinolytic activity has been found in a spruce (Picea abies L. Karst.) cell culture, which produces apoplastic lignin into the medium. Plant chitinases are known to be induced also in developmental processes. Chitinase-like genes have been shown to be essential in cellulose synthesis and in development of cell walls and tracheary elements and also affected the localisation of lignin in tissues. Therefore, the secretion of chitinases into the culture medium has not necessarily been caused by stress and chitinases might use also some endogenic substrate in addition to chitin. Because chitin is a structural component of plant pathogens but not present in plants and the growing circumstances of the studied aceptic spruce cell culture were stable, the research hypothesis was, that the secreted chitinases in the culture medium were not a stress reaction but related to development and besides chitin of the pathogens they utilize some own polysaccharide substrate of spruce. Additional hypothesis was connection of the strong expression of chitinases and chitinase-like genes in the culture medium and the production of apoplastic lignin by the spruce cell line. The aim of the study was to characterize the chitinases and chitinase-like enzymes of the spruce cell suspension culture medium and developing xylem by isolating, purifying and cloning them and by producing them heterologously. The aim was also to identify the putative endogenous substrates for the chitinases and chitinase-like proteins to reach better understanding about the meaning of the chitinases in the development of the spruce tissues. Two chitinases of the spruce cell suspension culture were isolated and purified by chromatographic methods. One chitinase gene in spruce cell culture and one chitinase-like gene in spruce xylem were cloned, after which the chitinases and chitinase-like proteins were produced in Pichia pastoris yeast. The total proteins of the culture medium, the purified chitinases isolated from the medium and the chitinases and chitinase-like proteins produced in P. pastoris were used to examine their substrate alternatives with the carbohydrate microarray method. The connection between apoplastic lignin and the chitinolytic enzymes in culture medium was not found and obvious candidates for the endogenous substrates were not detected. However, the mannan degradation in the presence of the chitinases was strong enough to give reason to further analyses.

The thesis explores possibilities for mental health promotion in urban planning trough a case study of the community space in Lapinlahti, Helsinki. Lapinlahti is a former psychiatric hospital, and the area has in the 2010’s been developed through community efforts into a center for mental wellbeing and culture in Helsinki, a “Lapinlahti for all”. The future use of the area has been contested for the past years, with the City of Helsinki and the organizations at Lapinlahti having different views on how the area and it’s cultural and historical mental health legacy should be preserved and developed. In the discussions, statements and visions, the area’s mental health value has also been translated into urban planning, taking many forms. Mental health is a value that has traditionally not been prioritized or regarded as a value of its own in urban planning, and although the relationship between urban form and wellbeing is well known, urban (mental) health is seldom tied to cities physical- and land-use planning (Kim et al, 2022; Corburn 2004). The thesis approaches this topic by analyzing mental health as a planning objective, discussing how different understandings and approaches to mental health have affected the planning visions surrounding Lapinlahti. The thesis uses a theoretical framework of urban governance and critical discourse analysis (CDA) to seek an understanding to the different approaches to the area’s development, and identify the different understandings, connections and visions that surround Lapinlahti. The study identifies three discursive constructions of Lapinlahti: Lapinlahti as a site for cultural heritage, Lapinlahti as a place for mental health, and Lapinlahti as a site for development. The results show that all actors in their development schemes have considered the area’s mental health value from a cultural-historical perspective, viewing the area as a site for mental health history. This history is however understood and manifested in different ways for the actors, influencing different visions for how the area should be developed and what interests and/or values that should guide the development. The thesis continues with presenting three approaches for mental health promotion in urban planning, concluding that planning should be attentive of how the space is governed, the relationship between mental health and the space, and the activities and meanings embedded in space.

Prostate cancer is one of the most common cancers diagnosed in men. Somatic copy number alterations (SCNA), such as the deletion of PTEN or NKX3.1 and the amplification of MYC, have been associated with prostate cancer progression and could serve as potential biomarkers during diagnosis. One approach to utilize this information would involve screening a large number of prostate tissue sections for SCNAs and subsequently validating the findings using a secondary method. This process could enable more personalized treatment options for cancer patients. This thesis aimed to create a robust and reproducible workflow for SCNA identification. This was achieved by optimizing a chromogenic immunohistochemistry (IHC) protocol using immunostaining chambers and open-source 3D-printed laboratory hardware. The optimized protocol was then transferred to an automated liquid handling robot, and a panel of three antibodies for PTEN, NKX3.1, and MYC was developed for SCNA screening with IHC. Additionally, a chromogenic in situ hybridization (CISH) protocol was optimized to validate the results of the IHC. The immunostaining chambers required a lower antibody dilution to perform comparably to the manual IHC stainings. The automated protocol using the liquid handling robot produced high-quality stains with optimized dilutions. The optimized CISH protocol successfully identified the presence of the target gene, but unclear signals and merging of the signals obstructed detailed analysis. While complete deletion of PTEN was detectable, determining the number of gene copies per cell proved challenging due to signal variability and sample-dependent problems. Further optimization of the CISH protocol or development of an automated analysis workflow tailored to address these challenges is needed for more accurate analysis.

Grasslands occur on every continent except Antarctica and are a key part of agricultural and urban landscapes in many parts of the world. In Finland, many of the grassland species are threatened nowadays. Fragmentation, worsening quality and shrinking area of habitats are the biggest threats to grassland species. Many grassland plants, however, can be found in urban habitats such as road verges, different meadows and rocky outcrops. Suitable urban habitats could be important for these species if the degradation of their habitats continues elsewhere. Indicator species could provide information about the ecological quality of urban habitats and thus the suitability for grassland specialists. My aim for this thesis was to determine how indicator species can be used to assess the ecological quality of urban grasslands by answering the following research questions: 1. Does habitat type affect the abundance and occurrence of known quality indicator species of semi-natural grasslands? 2. Which species are characteristic to different urban grassland habitat types? 3. How different sites relate to each other in terms of vegetation? 4. How do the measures used to answer the other three questions compare together? I collected vegetation data from 28 study sites in the cities of Espoo, Helsinki and Vantaa, southern Finland. In addition, a dataset consisting of 116 sites from these cities, collected by another person, was included here. The study sites were divided into eight habitat types: dry and mesic landscape grasslands, dry and mesic road verges, dry and mesic valuable grasslands, rocky outcrops and valuable rocky outcrops. From all study sites, I collected a list of plant species observed within a standardized time frame by doing an on-site vegetation inventory. In addition, I observed the frequencies of plant species within 1 x 1 m vegetation quadrats. I used one-way ANOVA and Tukey-Kramer test as well as Welch’s ANOVA and Games-Howell test to study the effect of habitat type on abundance and occurrence of semi-natural grassland indicator species. I used IndVal to identify which species are indicators for the habitat types and their combinations. I used NMDS to study the grouping of different habitat types and their species. Habitat type affects the abundances and occurrences of semi-natural grassland indicator species in urban settings and these species can be used in evaluation of the ecological quality of urban grasslands. Indicator species produced from observed data seem to have a limited potential in evaluating the ecological quality of urban grasslands, but they provide a good method for classifying urban grassland habitats, especially valuable rocky outcrops and valuable grasslands. Study sites do form groups according to their vegetation, but these groups do not entirely follow the habitat type division used in the study. With right standardization for the use, indicator species can be a valuable tool in assessing the ecological quality of urban grasslands.

The antibiotic resistance of pathogenic bacteria is becoming a major problem in treating bacterial infections and development of new antibiotics is very challenging. In traditional phage therapy the bacteriophages, viruses that infect bacteria, are being used as an optional treatment to eliminate infectious agents. Methicillin resistant Staphylococcus aureus (MRSA) is resistant to several currently used antibiotics and is one of the most common antibiotic resistant bacteria causing infections. Therefore, it is a potential target for the phage therapy. Some of the Staphylococcus aureus strains produce several different enzymes and toxins which can be harmful to patients. Products developed for phage therapy purposes need be free from the material originated from host bacteria. In this study, three different methods were tested for the purification of bacteriophages infecting S. aureus. The main goal was to produce phage lysates with purity and phage concentration suitable for therapeutic purposes using a fast and aseptic procedure upgradable for large volumes. The tested methods were ultrafiltration with filter tubes from two different manufacturers (Sartorius Vivaspin 6 ja Merck Millipore Amicon Ultra 4), polyethylene glycol (PEG) precipitation and ion exchange chromatography. Three different bacteriophage strains were used. One was isolated from a commercial Russian phage therapy product (vB_SauM_fRuSau02) and the other two from feces of pigs (vB_SauS_fPf-Sau02 and vB_SauS_fPfSau03). Host bacteria strains for the first bacteriophage were S. aureus strains TB4 and 13KP originally isolated from human infections. Two host strains for the latter two phages were MRSA strains isolated from healthy pigs. Purification of the phage lysates was evaluated by measurement of enterotoxins produced by S. aureus bacteria, measurement of free double stranded DNA (dsDNA), and by cytotoxicity test in cell cultures. All evaluation methods were commercially available tests. To determine how much of the bacteriophages were lost in the process, the phage concentrations of the lysates were determined before and after the purification and recovery rates were calculated for the viruses. After two separate ultrafiltrations, the recovery rates of the bacteriophages were mainly good, but there was a lot of variation in the results. The lowest recovery rate calculated was 5%, the highest 57%, and the mean of all the rates 24%. In this study the ion exchange chromatography was combined with ultrafiltration which was used in pre-cleaning of the lysates and changing the phages in a buffer suitable for the chromatography. The recovery rates from the ion exchange chromatography varied between 14-26% but the results may be affected by the ultrafiltration steps performed before and after, since a lot of variation was seen in ultrafiltration processes. PEG precipitation was performed for one phage lysate only in order to compare the laboriousness of the method and the rates of the recovery to the other methods used. The rate of recovery from the PEG precipitation was 9,5% which was fairly low. The purity of this lysate was not evaluated since the method was estimated to be too laborious compared to the other methods. Ultrafiltration turned out to be an efficient method in the removal of small protein molecules, such as enterotoxins from bacteriophage lysates. With two sequential ultrafiltrations 96-99% of the enterotoxins in the lysates were removed. The removal of the free dsDNA was also successful but there was variation between the phage lysates. Approximately 67-93% of the free dsDNA was removed but it is possible that some of the measured DNA originated from lysed bacteriophages as their genome also consists of dsDNA. Ion exchange chromatography produced extremely well purified phage products. The fractions had no enterotoxins left or the amount was below the detection limit of the test (<0,5-1 ng/g). Ion exchange chromatography was able to remove 96-99% of the free dsDNA of the lysates. It is possible that some of the DNA left in the lysates originated from the bacteriophages lysed during the process or in storage after that. When comparing how simple and fast the methods were, the ultrafiltration turned out to be superior. It can be used in fast production of bacteriophage products for the treatment of S. aureus infections. The purification achieved with the ultrafiltration should be adequate for a topical use of the product. When higher purity products are required, e.g. for administrating the product intravenously, ion exchange chromatography might be a safer option.

Jäkälät ovat sieniosakkaan ja yhteyttävän levän muodostamia symbiooseja, joista suurin osa elää maaekosysteemeissä ympäri maapalloa. Jäkälät toimivat ekosysteemeissä tärkeinä indikaattorilajeina, sillä ne ovat usein hyvin herkkiä elinympäristössä tapahtuville muutoksille, esimerkiksi ilmanlaadun huononemiselle. Sticta-suvun syanojäkäliä on tähän mennessä kuvattu noin 200 lajia erityisesti subtrooppisilta ja trooppisilta alueilta. Todellisuudessa lajimäärän arvioidaan olevan paljon suurempi. Afrikan jäkälistä tiedetään vielä suhteellisen vähän, ja tietomme Itä-Afrikan Sticta-lajeista pohjautuvat pääasiassa 1980-luvulla tehtyyn tutkimukseen. Tässä tutkimuksessa tavoitteenani oli tuottaa DNA- analyysiin perustuva selvitys Sticta-suvusta Kenian Taitavuorilla. Tutkimuksessa selvitin myös Sticta-lajien symbioottisten syanobakteerigenotyyppien levinneisyyttä Taitavuorten eri metsäsaarekkeissa ja eri Sticta-lajeissa. Tutkimukseni aineistona oli 176 jäkälänäytettä, jotka ovat kerätty Taitavuorten alueelta sekä Elgonvuoren rinteeltä Länsi-Keniasta Jouko Rikkisen ja Ulla Kaasalaisen toimesta vuosina 2009- 2017. Alustava lajinmääritys morfologian perusteella tapahtui mikroskopoimalla. Neljänkymmenenkahdeksan näytteen tarkempi lajinmääritys tehtiin DNA-menetelmin, selvittämällä jokaisesta näytteestä sienen sekä syanobakteerin genotyyppi. DNA-eristyksen, PCR:n sekä elektroforeesin tein Helsingin luonnontieteellisen museon laboratoriossa kesällä 2018. DNA- sekvensointi tehtiin Sanger-menetelmällä Saksassa GATC Biotech-yrityksen toimesta. Laboratoriotöiden tuloksena sain sieniosakkaan DNA-sekvenssin kaikkiaan 48 jäkälänäytteistä. Sekvenssien perustella 46 näytettä voitiin määrittää ennestään tunnetuiksi Sticta-lajeiksi, ja kaksi näytettä osoittautui Sticta pseudosylvatica -lajille sukua olevaksi, toistaiseksi kuvaamattomaksi lajiksi. Näytteistä löytyi kaikkiaan 21 erilaista syanobakteerigenotyyppiä. Eri metsäsaarekkeista kerättyjen näytteiden syanobakteerikoostumus ei näyttänyt poikkeavan toisistaan, mutta Sticta- lajien syanobakteerikannat poikkesivat toisistaan.

Havsekosystemen runt om i världen lider av antropogen inverkan såsom näringsutsläpp och utfiske. Speciellt utfiske av högre trofiska nivåer dvs. stora rovfiskar, anses ha ändrat dynamiken i flera näringsvävar. Ändringarna har lett till kraftiga trofiska kaskader som ökat eller minskat primärproduktionen speciellt vid kustliga vattenområden. Speciellt mesopredatorer har ökat i antal, och i Östersjön är storspiggen (Gasterosteus aculeatus) en art som börjat dominera samhället. Storspiggen konsumerar växtavbetare av trådalger, och kan därmed ha en effekt på trådalgstillväxten i Östersjön. Undersökningens syfte är att granska vilken roll storspiggens predation har i trådalgsbältet, och hur ändringarna syns i näringsväven. Undersökningen bestod av ett mesokosmexperiment och en fältundersökning vid Tvärminne zoologiska station. Mesokosmexperimentet bestod av två behandlingar: 10 mesokosm med två trofinivåer (utan storspigg), och 10 mesokosmer med tre trofinivåer (med storspigg). Trofinivåerna bestod av trådalger (Cladophora sp.), märlkräftor (Gammarus sp.) och storspigg. Experimentet pågick 4 veckor, vartefter mesokosmerna tömdes och innehållet analyserades. Med en veckas mellanrum gjordes fältbesök till den närbelägna ön Långskär, för trådalgsprovtagning, observation av storspiggstäthet och magsäcksanalysering av fångade storspiggar. Trådalgsproverna analyserades under mikroskop. Fältundersökningens resultat visade att mängden storspiggshanar och fångade storspiggar minskade längs med säsongen, medan trådalgsbiomassan ökade. Antalet vuxna storspiggar korrelerade negativt med märlkräftor. Mesokosmexperimentets resultat visade att mesokosmen med storspigg hade i medeltal högre trådalgs-biomassa (24%), högre epifytmängder (72%), färre märlkräftor (79%) och lägre färgintensitet än mesokosmerna utan storspigg. I Mesokosmerna utan storspigg hade trådalgsbiomassan inte ökat nämnvärt, men trådalgen var tydligt grönare i färg och saknade epifyter. Av resultaten framgår att storspiggen påverkar primärproduktionen i ekosystemet, genom en trofisk kaskad, då växtavbetarna regleras kraftigt. Primärproduktionen ökar mest i form av epifyter och mikroalger, vilket leder till att trådalgen kvävs och börjar föråldras. Trådalgen och växtavbetarna har därmed ett mutualistiskt förhållande. För att minska mängden skadliga algblomningar i Östersjön, borde näringsvävarnas stabilitet och mångfald tas i beaktande vid fiskeriförvaltningen för att effektivera Östersjöns rehabilitering.

Faculty: Faculty of Biological and Environmental Sciences Degree programme: Master’s Programme in Neuroscience Study track: Neuroscience Author: Emma-Helka Erkkilä Title: The brain physiology of stress and the effects of burnout on executive functions Level: Master’s thesis Month and year: 08/2022 Number of pages: 35 Keywords: executive functions, emotion, cognition, stress, burnout Supervisor or supervisors: Docent Kaisa Hartikainen and Lic.Med. Mia Pihlaja Where deposited: Helsinki University Library Additional information: Abstract: BACKGROUND- Burnout as a result of prolonged and excessive stress may impair higher order cognitive functions of the brain such as executive functions and their efficiency. This Master's thesis examines the effects of chronic stress on the brain, more specifically the effects of burnout on executive functions. The aim of this study was to specifically research the effects of burnout on executive and emotional functions and their interaction. The research was conducted at the Behavioral Neurology Research Unit, Tampere University Hospital as part of Sustainable Brain Health project funded by the European Social Fund. MATERIAL AND METHODS- 54 voluntary examinees of whom 51 were analyzed. The examinees were divided into two groups based on BBI-15 survey (27 suffering from burnout and 24 control subjects without burnout). The examinees performed a computer-based Executive reaction time (RT) test, during which a 64-channel electroencephalogram (EEG) was recorded. In additions all examinees received alternating transcutaneous vagus nerve stimulation (tVNS) and placebo stimulation. From the Executive RT test, we obtained objective measures reflecting the efficiency of executive functions (RT and total errors) and specific executive functions such as working memory, inhibition and attention. Additionally, the emotional stimulus included in the test enabled the assessment of the emotional functions and the interaction between emotional and executive functions. The EEG and tVNS results were not in the scope of this master’s thesis, and they will be reported later on. RESULTS- The results of this thesis are preliminary. Distinct positive correlation was observed between burnout assessment based on the BBI-15 survey and the results of the BRIEF-A self-report which measures the subjective experience of challenges in executive functions in daily life. There was no statistically significant (p<0.05) difference between the groups in RTs or errors made in the Executive function RT test. Instead, the groups differed on how the threatening emotional stimulus affected the accuracy of responses. Subjects suffering from burnout made less errors with a threatening emotional stimulus compared to a neutral stimulus and vice versa the control subjects made more errors with the threatening emotional stimulus compared to neutral. This difference was statistically significant (p=0,025). DISCUSSION- Challenges experienced in everyday executive functions were linked with burnout. However, RTs and errors in the Executive reaction time test did not correlate with the severity of the burnout nor were the self-evaluated problems in executive functions depicted in the test performance. Instead, the subjects suffering from burnout differed from the control group in how the threatening stimulus affected the accuracy of responses in the test. It is possible that the subjects suffering from burnout benefit from the increase in arousal caused by the threatening emotional stimulus which was shown as improved accuracy of responses when there was a threatening stimulus, whereas the control group's accuracy of responses was disrupted by the threatening stimulus. We speculate that if the control group’s baseline level of arousal was optimal then the threatening emotional stimulus may have increased arousal to suboptimal level causing decrease in performance. Subjectively experienced challenges in executive functions and objective changes in the interaction between emotions and the executive functions were observed in the study. In conclusion, burnout causes changes in executive functions.