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LCMV Lymphocytic choriomeningitis virus is a rodent-borne pathogen belongs to Arenaviridae family. Most of the studies have referred Mus musculus as the main reservoir of the LCMV. It has been detected in pet rodents, laboratory rodents, and wild mice. Humans be infected with LCMV through the ingestion or inhalation of sources contaminated with rodent feces, urine, or both. LCMV infection can be asymptomatic, present with mild symptoms, or it can cause aseptic meningoencephalitis (AME) and teratogenic effects in infants. However, clinical cases of LCMV infection have been rarely reported, and there is only fragmental knowledge on the presence and prevalence of LCMV infections around the world. Likewise, the genetic characteristics of the circulating LCMV strains and impact of LCMV on public health have remained poorly characterized. This study was performed in the Southern Iraq, due to the lack of comprehensive information about LCMV in this area. There were three main aims in this thesis. First, to assess the prevalence of LCMV among the healthy human population in the Nasiriyah region, southern Iraq. Second, to assess whether LCMV infections can be associated with neurological manifestations. Third, to characterize the genetic variation and evolutionary history of LCMV strains circulating in southern Iraq. Serum and CSF samples were collected from patients and healthy people in Nasiriyah governorate in the Southern Iraq. Serum samples were screened for LCMV using Immunofluorescence assay (IFA) to detect IgG and IgM antibodies. Real-time PCR was used to detect LCMV genome. In order to confirm the PCR positive samples, we sequenced these samples by Next-generation sequencing. The serological assay results showed 12.22% IgG prevalence of LCMV among healthy people and 7.36% IgG prevalence among patients with neurological symptoms. The IgM prevalence was 1.25% among the patients with acute infections. From symptomatic patients, we sequenced partial L-segments of two new LCMV strains. The phylogenetic tree constructed on the basis of all known LCMV strains suggested that these new LCMV strains from Iraq are genetically distant from the previously known LCMV strains and form a novel sub-cluster within LCMV species. This study is the first survey of LCMV in the Southern Iraq. LCMV appears to be a rather common infection in Iraq. I reported new strains of LCMV that are circulating in the study site and most likely is the causative agent of the central nervous system-associated clinical manifestations in these patients. For future work, I’m aiming the detection of other Arenaviruses spreading in the Southern Iraq.

Enhancers are important regulatory elements of DNA, that are bound by transcription factors (TFs) to regulate gene expression. Enhancers control cell type specific gene expression and they can form structures called super-enhancers, that consist of multiple normal enhancers and are bound by high numbers and variety of transcription factors. These super-enhancers are important for defining cell identity and changes in the super-enhancer landscape have been linked to different cancers. In this project, characterization of super-enhancers and their transcription factors composition between primary and cancer cells were studied using genome-wide next-generation sequencing data from multiple assays, such as ChIP-seq, RNA-seq and ATAC-seq. The focus of the project was on the data processing and analysis to identify and characterize the super-enhancers. Analyses included GSEA, heatmap binding analysis, peak and super-enhancer calling and IGV analysis. This project used pancreatic HPDE cell line for primary cells and different cancers with endodermal origin as cancer cell lines. The goal of the thesis was to try show characteristic features of super-enhancers and their features in normal and cancer cells. Data analysis showed that distinct super-enhancers can be identified in cancer cells and defined super-enhancers had typical strong binding for specific transcription factor and histone modification such as histone 3 lysine 27 acetylation (H3K27ac) mark of active enhancers. Super-enhancer regions were located in highly accessible chromatin regions of the genome, and genes that were associated with HPDE super-enhancers could be shown to have association with cell identity. Peak and super-enhancer calling counts varied between cell lines for transcription factors, histone modifications and super-enhancers. Visualization of super-enhancers was successful and could show transcription factor binding and active enhancers that establish the super-enhancer structure. Comprehensive analyses allowed us to characterize typical features of super-enhancers and show differences in the numbers of super-enhancers between primary and cancer cell lines and cancer cell lines of different organ types. Analysis of the transcription factor binding showed unique peaks on some of the super-enhancers, and these peaks might have a role in inducing the super-enhancer structure.

The TTN gene encodes a giant muscle protein called titin that regulates the function of muscle sarcomere and interacts with several other muscle proteins. Mutations in TTN are associated with a broad range of skeletal and cardiac muscle disorders termed titinopathies. Previous studies have shown the importance of unusual TTN splicing events in patients with TTN-related cardiomyopathies and muscular dystrophies. In this project, we characterized eight TTN splicing variants to further expound on the pathogenesis of titinopathies and to enhance the diagnostic accuracy for patients with TTN mutations. In addition, we also made a comparative analysis of five different RNA/cDNA sequencing techniques to extrapolate on which approach is most suitable to study splicing variants in TTN gene. Skeletal muscle samples of six patients were analyzed in this study who were previously detected with TTN variants in a compound heterozygous state from a targeted next-generation sequencing assay. Our results from traditional Sanger sequencing methods, second-generation (Illumina RNA-Sequencing) and third-generation sequencing (Single-molecule real-time sequencing) methods showed distinct splicing events in the form of partial or complete exon skipping, intron retention, and in few instances showed multiple splicing effects rendered by a single variant. Complying with the guidelines of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, the splicing variants were classified as pathogenic, likely pathogenic or variant of uncertain significance primarily on the basis of our experimental data. To address which sequencing method is most promising for analyzing TTN splicing variants, Illumina RNA Sequencing is very efficient, though, the combination of Illumina RNA Sequencing with long-read sequencing could be ideal. Our results further demonstrate that a near full-length titin is vital for survival until birth, and further studies are needed to understand the pathophysiology mechanism of congenital titinopathies.

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive degeneration of upper and lower motoneurons (MN) within the central nervous system (CNS), leading to muscle atrophy and eventual paralysis. Cause of death is in most cases due to respiratory failures 3-5 years after diagnosis. ALS can occur idiopathically without any know causes or it can be associated with certain genetic mutations. One of these known factors is a point mutation in the superoxide dismutase 1 (SOD1) gene, particularly the G93A mutation is known to affect the functionality of SOD1. SOD1 is an enzyme that metabolizes reactive oxygen species (ROS) and the SOD1-G93A mutation limits this functionality and propagates endoplasmic reticulum (ER) stress signalling cascades. Mutated SOD1 cannot be broken down by the cell, and hence it is associated with activation of protein degradation (ERAD) system with a prolonged ER stress signalling, followed by apoptotic cellular response. Although SOD1-G93A mutation has been widely studied, the basic mechanisms of the disease are not fully understood. Mesencephalic astrocyte derived neurotrophic factor (MANF) is an evolutionary conserved protein with trophic properties. MANF has been researched as novel treatment in a range of neurodegenerative diseases, such a Parkinson’s. MANF has been shown to promote cell survival but has limitation as an administered drug treatment. In this study we used transgenic SOD1-G93A mouse model with male mice to study the effects of a novel MANF variant for ALS. Disease progression and histology were used to assess the treatment efficacy.

As the most common mental disorder, anxiety disorders present a major burden to healthcare worldwide and a challenging problem to overcome for the ones suffering from it. Recently, researchers have started to recognize that the relationship between sleep and anxiety disorders is bidirectional; disturbed sleep is a potential risk factor for the progression of anxiety and anxiety can lead to sleep disturbances. However, the neural mechanisms underlying anxiety and sleep problems are still poorly recognized. In this study, we used a chronic sleep fragmentation (SF) paradigm to investigate how disturbed sleep alters anxiety-like behavior in mice and what are the potential underlying neuronal mechanisms. This model was chosen because we wanted to focus on a common form of disturbed sleep in humans rather than total sleep deprivation. We measured anxiety-like behavior in the light-dark box and open field tests right after the 2-week SF period and again after a week of recovery. Additionally, we performed immunohistochemical analysis to study prolonged cell activity (transcription factor ∆FosB), parvalbumin (PV) interneurons and perineuronal net (PNN) structures in the medial prefrontal cortex (mPFC) of the mice. Changes in mPFC activity and related brain areas are associated to anxiety in humans and anxiety-like behavior in rodents alike. Similarly, changes in PV interneurons and PNNs, that regulates PV cell function, are associated to anxiety-like behavior. However, PV interneurons and PNNs have not been previously studied in a setting that combines sleep fragmentation and anxiety-like behavior. We found that chronic SF increases anxiety-like behavior in female mice and that this effect persists at least for a week. Conversely, we did not observe significant increase in anxiety-like behavior in male mice. Both female and male mice showed decrease in ∆FosB in the mPFC suggesting that SF treated mice had lower overall levels of cell activity. Similarly, we found that SF treated mice had decreased PV interneuron intensity in both sexes which could indicate changes in the cell activity. However, the pattern of changes in the IHC results was not identical in males and females. Based on the IHC results, we suggest that SF affects neuronal processes in both sexes but the disparity in them could explain the difference in the behavioral effect. This thesis shows that disturbed sleep can lead to increased anxiety-like behavior in rodent models and recognizes potential targets to study the mechanisms behind the phenomena.

Circular economy (CE) is often offered as a solution to mitigate climate change and more efficient resource use. However, the socio-cultural side of transformation to CE is widely overlooked in the academic literature (Kirchherr et al., 2018) and in the context of CE, consumer-citizens are often framed as “consumers”, “users” and in terms of “acceptance” of new products and modes of provision (Hobson & Lynch, 2016). In fact, taking part in CE can be quite laborious and the notion of consumption work highlights the time, skills and access needed to participate in circular consumption (Hobson et al., 2021). Existing research on CE skills are scarce, outdated and focused on only one practice at a time. The research gap of citizens’ CE skills has been identified by several researchers (e.g. Hobson et al., 2021; Wieser, 2019) and this thesis aims to fulfil the gap by adopting a qualitative approach. The data on which this research is based on, consists of semi-structured interviews with 20 Finnish citizens who have been active in implementing zero waste lifestyles and responsible consumption principles that are relevant for CE. By exploring their everyday practices related to CE, I identify six skill categories that the active citizens utilise to take part in CE. Particularly (1) manual skills were identified by the interviewees as central to performing circular activities. They include skills such as sewing and technical skills that enable repair and repurposing materials. The interviewees possess (2) divergent thinking skills and abilities to think creatively, for example about the ways you can use a certain item. They are also skilful in questioning consumption related social norms. (3) Research and communication skills are central for active citizens as they are trying to figure out the most sustainable options and inspire others with humour and positivity to take part in the circular economy. The interviewees describe often utilising (4) organising and prioritising skills that revolve around time management. They need to make decisions and prioritise certain actions that preferably are quite influential in terms of their carbon footprint. Moreover, when buying products second hand they should start looking for the items early and with rental options, the need should be anticipated and planned. Another identified set of skills are (5) household skills. They include maintenance skills of household goods and clothes, cooking skills to avoid food waste by using creativity and planning as well as recycling skills on sorting different fractions. The respondents also described (6) skills brought by experience. Knowledge on different second hand marketplaces and the skills to recognise good quality on materials and items enable circular practices. One of the main contributions of this thesis is consolidation of various sets of citizen skills relevant for the CE into a single framework. The findings further illustrate that consumer-citizens are doing a multitude of CE activities that require consumption work and certain skills. The findings provide information on how citizens engage and coordinate CE practices on the household level by prioritising and planning, a topic on which research has been lacking (Hobson et al., 2021). The skills of “thinking outside the box” are also a new set of skills that emerged from the interviews and it has a clear connection to the “unlearning” of noncircular consumption practices (Wieser, 2019). The identified skills could be taught more through formal and informal education channels, but it should be considered, how infrastructure, companies and services can ease people’s participation in CE. Findings of the thesis offer insight on the domestic reality of CE and how it could be improved in the Finnish context.

As the effects of climate change have become increasingly more visible in recent years, interest in climate adaptation has grown in both research and policy contexts. However, although Southeast Asia is one of the regions most vulnerable to climate change impacts, there has not yet been an effort to comprehensively track how Southeast Asian countries and communities are adapting to climate change. I apply a systematic review methodology developed for adaptation research to map adaptation responses identified in the Asian Development Bank’s (ADB) projects in Southeast Asia in 2016-2020. My results show that close to a fifth of the ADB’s adaptation projects in Southeast Asia is implemented in Cambodia, while Thailand and Timor-Leste are the least covered countries. In general, the characteristics of my examined projects are relatively similar to global adaptation trends. Flooding, drought, storms, and other heavy rainfall events are the most frequently addressed climate hazards by both the projects I examined as well as by UNFCCC climate fund projects and by adaptation responses documented in scientific papers. The sectors addressed and actors targeted by ADB projects were also typical to multilateral funding institutions, focusing on the agricultural and water sectors as well as national and local governments and farmers. Capacity building was the most frequent adaptation response category, indicating that adaptation implementation as delivered by the ADB is still in a relatively early phase in most Southeast Asian countries. In addition to results related to climate adaptation in Southeast Asia, I also demonstrate the applicability of a systematic review methodology for tracking climate change adaptation responses implemented by multilateral development banks, given sufficient information is made available on relevant projects.

Concern about global warming can lead to climate change anxiety, a form of anxiety characterized by excessive worry about the climate crisis and associated consequences on the natural world and human society. It has been suggested by previous research that humor can be used to manage feelings of anxiety. This study seeks to determine if this phenomenon can be applied specifically to climate change anxiety. The research combines a comprehensive literature review with an online survey that leveraged climate change themed internet memes as a proxy for humor to gather opinions about the intersections between these two topics. The survey data supplemented claims made by existing literature, indicating that climate change themed internet memes and humor in general can be useful coping mechanisms to mitigate feelings of climate anxiety. The survey was completed by 93 respondents; most of these participants were women, located in the US, and/or between the ages of 20 and 29. Results from the survey showed that people tend to feel best about their environmental anxiety when they are taking active steps to solve the problem. Conscious decisions such as reducing waste or participating in activist movements are easier to recognize and self-report than more passive coping skills. Reliance on humor was reported as a supplementary coping skill, but many respondents indicated that looking at humorous climate change themed memes did influence their feelings about climate change overall. The scope of this study was relatively small in scale, therefore the results presented in this thesis may not be indicative of broader social trends and likely require further research.

Static floating chamber (FC) measurements of CH₄ and CO₂ fluxes from northern boreal river Kitinen were analyzed for this thesis. Measurements were carried out in summer 2018. Spatiotemporal variability was measured in the fluxes by comparing three chamber measuring locations: the opposite river banks and the middle of the river. Mean CO₂ flux estimate was 0.83±0.54 μmol CO₂ m⁻² s⁻¹ (mean ± SD, n = 73), consistent with other estimates for similar systems, with a corresponding k₆₀₀ CO₂ gas transfer velocity estimate of 17±9 cm h⁻¹ . Nonlinear modelling of CO₂ flux was found useful for analyzing floating chamber data from a river. The mean CH₄ flux was 0.0084±0.0047 μmol CH₄ m⁻² s⁻¹ , slightly lower than the median for different river systems in literature. The flux estimates were compared with eddy covariance measurements (EC). FC measurements are expected to give larger results, but additionally chambers are known to overestimate fluxes in flowing water. The comparison yielded chamber fluxes 3.3 and 2.9 times the EC median values for CO₂ and CH₄ respectively. Fluxes were similar between the three locations, and they peaked in late July for both gases in all loca- tions. Some differences over the river cross-section were observed. Discharge was significantly correlated to fluxes in the middle of the river, which could be explained by inhomogeneous flow. On two measuring days in early August, the mid-river CO₂ fluxes were three times those observed near the banks. The difference was also measured in methane. No clear cause was determined, but measuring spatial variation in surface water gas concentrations and flow could clarify the causes of similar observations in further studies.

Both microplastics (MPs, size 0.1 to 5 mm) and pharmaceuticals and personal care products (PPCPs) are ubiquitous in aquatic environments globally. Polystyrene microplastic (PS-MP) and diclofenac (DCF) are among the most widespread and commonly occurring MPs and PPCPs in the environment. Exposure to these chemicals in single has been reported to cause oxidative stress, immobilization, changes in growth and reproduction and even mortality in Daphnia magna. Moreover, MPs have the ability to act as a vector for PPCPs, and several laboratory studies have reported that PS-MP is able to absorb DCF. However, the combined toxicity of MPs and PPCPs remains largely unknown, especially as is the case for the combined toxicity of PS-MP and DCF in D. magna. In this study, D. magna was exposed to PS-MP and DCF, both in single and combined, at a concentration of 0.5 mg/L each. The aim was to assess the combined toxicity of the two, and determine whether they had a synergistic, additive, or antagonistic effect in D. magna. Whole organism endpoints monitored included mortality, immobilization, and moulting. Physiological endpoints monitored focused on oxidative stress and antioxidant defence, including reactive oxygen species (ROS), superoxidase dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST). The results indicated that both PS-MP and DCF in single were able to significantly alter D. magna antioxidant and biotransformation enzyme activities by inhibition of SOD and GST, while there were no observed impacts on the monitored whole organism endpoints or ROS and CAT. However, similar significant inhibition of SOD and GST was not observed in the combined exposure, which indicates that the combined toxicity of PS-MP and DCF in D. magna was most likely antagonistic. These results highlight that the combined toxicity of MPs and PPCPs is a complex topic that still needs further investigation to fully understand the complex interactions between MPs and PPCPs.