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Protein stability is a property of high importance and is of interest in a variety of fields. It determines if a protein has its native fold and can be of influence in certain diseases such as Parkinson's and Alzheimer's disease. It can also be of interest in an industrial setting to optimise the stability of enzymes in certain physicochemical environments. Recent developments in machine learning have yielded novel methods able to predict protein characteristics with surprising accuracy solely from sequence information. However, few such models have been proposed for predicting protein stability. The aim of this project was to create a model able to predict protein stability from sequence information, by utilising a multiple sequence alignment based protein language model. Different models were developed to predict two quantities relating to protein stability, Gibbs free energy of unfolding and the heat denaturation temperature. Due to limited training data the performance of the models predicting Gibbs free energy was poor. One of the models predicting heat denaturation temperature, proved more promising, with higher performance than a previously published model trained on similar data. However its ability to predict conventionally obtained heat denaturation temperatures was poor., Can computers find better proteins? Finding more efficient enzymes is critical for chemical industry to become sustainable. In order to efficiently find better enzymes new tools are needed that reliably predict protein properties. The chemical industry is on a search for new green technology that can replace catalysts that are often toxic and made of scarce minerals. A promising alternative is catalytic proteins, so called enzymes, that can be produced renewably and pose no toxic threat. However, in order to be a viable alternative, the enzymes must become more effective and be able to withstand harsher conditions. To design enhanced or entirely new enzymes accurate and fast predictions regarding the protein’s properties are needed. One such highly sought after property is protein stability at high temperatures since it usually speeds up chemical reactions. A promising approach for developing predictive models are machine learning techniques, which have proved powerful in numerous fields. At the department of Biophysical Chemistry at Lund University it was tested if such a model, that predicts the thermal stability of proteins, could be created. The study concluded that the tested models could detect some features of proteins, however for the models to be more useful, they must be trained on more data of high quality. The limiting factor during development was therefore the amount of relevant and available data. This is a common problem in the machine learning field, where the models are created by training on data, the computer is taught how to make predictions by learning from a dataset. The rule of thumb is that the more data it is trained on, the better performance. But what would be the benefit of using computers over good old laboratory work? While resulting in reliable values, laboratory work is usually costly and time-consuming and requires well trained personnel. If a relatively accurate predictive model can be constructed an estimate of a protein’s stabili

Chronic obstructive pulmonary disease (COPD) is the third largest cause of death worldwide, with its most prominent risk factor being inhalation of smoke and pollutants. In this project, we studied two processes that are involved in COPD: autophagy and cellular senescence. Using primary human bronchial epithelial cells (HBECs) from healthy and COPD donors, we aimed to show that cigarette smoke extract (CSE) gives rise to an impaired autophagy flux as well as increased senescence. With multiple CSE incubation times and CSE concentrations, our data shows an impaired autophagy flux at the early time points 5h and 24h. However, the senescence data is inconclusive. Further optimization of the study design could enable the development of an appropriate in vitro assay. In the end, could continued research of this kind contribute to increased knowledge and understanding of the disease, as well as enable development of medical targets in the mission of disease treatment., Rökextrakt och dess negativa påverkan på återvinningsprocesser i lungceller från KOL-patienter Kroniskt obstruktiv lungsjukdom (KOL) är en global folksjukdom och den tredje största dödsorsaken i världen. Den kan kopplas till en mängd andra sjukdomar och tillstånd som också ofta ökar risken för att utveckla KOL, t ex hög ålder, kardiovaskulära och neurosjukdomar. Men den största och mest välkända riskorsaken för KOL är rökning och exponering för föroreningar. Vi har studerat celler från KOL-patienters andningsvägar och fokuserat på två processer som är viktiga för cellens hälsa: autofagi och cellulär senescence. Vi kan utifrån våra resultat, och i likhet med tidigare publiserad forskning, konstatera att rökningen påverkar dessa processer och ger upphov till en sjuk och skadad cell. Autofagi är ett typ av återvinningssystem i cellen, där proteiner och andra cellkomponenter bryts ned och återvinns. Det är en process som alltid pågår, men som vid cellulär skada och/eller näringsbrist aktiveras ytterligare. Detta med syfte att regenerera komponenter så som aminosyror samt ta hand om de skadade celldelarna. Cellulär senescence å andra sidan, är en process som kan liknas vid cellulärt åldrande. När en cell blir tillräckligt gammal och/eller skadad finns det olika slutdestinationer. Antingen så genomgår cellen programmerad celldöd (apoptos) eller så blir den senescent. Det är ett mer eller mindre permanent tillstånd som innebär att cellen är levande men har slutat celldela sig. Processen är viktig för att hålla vävnad frisk och för att förhindra att skadade celler utvecklas till t ex cancerceller. Samtidigt har förhöjda nivåer av senescence kunnat kopplas ihop med olika sjukdomar, bland annat KOL. Vi studerade nivåerna av autofagi och cellulär senescence i celler från friska och KOL- patienters bronchier, närmare bestämt celler från det yttersta lagret av vävnaden – epitelet. Det är dessa celler som röken kommer i direktkontakt med. Genom att utsätta cellerna för rökextrakt

Biotin is an essential co-factor in various metabolic processes and is crucial for the growth and maintenance of living organisms. The market need for biotin is multifaceted and driven by its importance in human health, beauty and cosmetics applications, pharmaceuticals, animal nutrition, and other industries. Current methods of industrial biotin production are unsustainable and generate environmentally hazardous waste, fueling the demand for new, greener strategies. The production of biotin through microbial fermentation has thus become an attractive alternative. Biotin biosynthesis is a complex and energy-intensive process that requires several enzymatic reactions, and biotin titers in microbial production have not reached economically viable levels. Biotin Synthase (BioB), the enzyme that catalyzes the last step of this process in E. coli, the conversion of dethiobiotin to biotin, has been identified as the bottleneck for this pathway. Overexpression of the enzyme generates oxidative stress and inhibits growth, though the exact mechanism has not yet been elucidated. This thesis employed a multiplexed engineering approach via high-throughput genetic engineering, selection, and screening methods to explore whether creating E. coli strains more resistant to oxidative stress would lead to higher biotin production capabilities. Using the expression of a DNA methylase to introduce controlled genetic mutations in Biosyntia's proprietary biotin-producing E. coli strains and selecting strains with improved resistance to oxidative stress yielded a selection of strains with increased resistance, which were screened for their biotin production. The improved resistance to oxidative stress and BioB induction in the strains did not lead to higher biotin production levels., The global need for biotin in the food, feed, and cosmetics industries is increasing steadily. Because current production methods use petrochemicals as precursors for synthesis, they are unsustainable and generate environmental waste. This has fueled the demand for alternative, more sustainable strategies. Biotin production via microbial fermentation could be a greener alternative but has not reached economically viable levels and cannot compete with current production methods. E. coli can naturally produce biotin but does so in minute amounts. This thesis aims to improve biotin production levels in biotin-producing E. coli strains to contribute towards a greener, more sustainable process. A bottleneck in the biosynthetic pathway, which has limited production levels, has been identified in previous research: the enzyme BioB, which catalyzes the last step of biotin synthesis. This enzyme creates oxidative stress in the cells and thereby inhibits cell growth. It was hypothesized that creating strains more resistant to oxidative stress and higher levels of intracellular BioB could lead to higher biotin production capabilities. By generating a controlled level of genetic diversity or introducing new genes into the strains and then selecting those with higher oxidative stress resistance, this thesis aims to find a strain that can produce higher levels of biotin. By nature, the randomness of the mutagenesis process generates a high number of strains that need to be tested for their biotin production. In this thesis, the number of strains that need to be tested is systematically reduced by selecting strains with a higher oxidative stress resistance by exposing them to various stressor concentrations. Only the fittest, most resistant strains survive this and are subsequently tested for their biotin-production capabilities. The work revealed that strains with higher resistance to oxidative stress and BioB production did not produce higher levels of biotin, indicating other l

Development in sequencing technologies has made the analyses of genetic material much more accessible. Processing sequenced data for an accurate analysis comes with its challenges, especially with the studies in microbial in clinical in vivo samples where difficulties in the collection of these samples for sequencing could lower the quality and contamination from the human host which might affect the accuracy of downstream analysis. In this project, we use RNA-seq and different reference genomes to look at the differential gene expression of Pseudomonas aeruginosa (PA), one of the most prevalent species of bacterial pathogens in the progression of chronic pulmonary diseases such as cystic fibrosis, due to its resistance to antimicrobial treatment. In this project, we created a pangenome from 21 strains of PA and explored the use of this, its subsets (core and soft-core gene sets) and a commonly used PA genome (PAO1) as reference genomes. We compared some of the differences and similarities in the results using the four gene sets, including mapping transcripts while developing a feasible pipeline to process raw sample reads from human sputum samples for differential expression and gene ontology enrichment analysis. From the analyses, we have found that differentially expressed genes upregulated in in vivo samples were related to biofilm, which plays a role in the difficulties in the treatment of PA infections, across most of the various genome reference-based results., How a “pan-genome” can help discover which genes that bacteria use to survive inside the human body Have you ever wondered about the microscopic world that exists in our bodies? Would they attack us at our moment of weakness? For people who are affected by cystic fibrosis, a disease that affects the lungs by causing a buildup of fluids, this can become a lifetime warfare against microbes such as Pseudomonas aeruginosa (PA). This tricky species of bacteria can change its growth form, making it difficult to treat patients who are infected. Thanks to a large set of genes in its chromosome, PA can change its growth mode from free-living cells in a liquid to forming a thick layer of cells known as a biofilm, by switching on or off various genetic materials. Since different strains of PA have different sets of genes, it is difficult to study common traits between strains and the importance of each gene. Hence, we want to use a more inclusive approach to explore their gene expression. Here we create a pan-genome, a complete set of genes of different strains to use as a reference when studying how different PA strains use their particular set of genes. We used this to explore what kind of genes are more expressed in human samples from people with PA in their lungs, compared to PA grown in a lab. Improvement in sequencing technology has made the analyses of genetic material more accessible and the use of software tools has become essential in processing these data. We created a pan-genome from 21 strains of PA. From this, we identified a gene set that was shared among all these strains, i.e., the core gene set. While exploring the pan-genome, we found most genes that support their survival are found more commonly in their core gene set. To highlight the importance of which gene set that is used as a reference, we examined how the results from the analysis changed depending on which gene set we used as a reference. We did this by comparing sequenced RNA from the samples by ps

Recent technological advancements have revolutionized tree inventory methods for the forest industry. The development of terrestrial laser scanning (TSL) and automatized tree recognition software to estimate crucial tree parameters such as diameter at breast height (DBH) has made the inventory work faster and more reliable. Forest managers can quickly acquire large amounts of data to safely estimate timber yield and effectively use the resources of the forest. This study assesses the Hough transform algorithms (TreeLS) performance to acquire DBH and tree height in the Rumperöd mixed forest in Scania, Sweden, with continuous cover forestry management. Few studies have been made evaluating the Hough transform script under these challenging conditions with uneven terrain and irregular spatial tree density and dense understory vegetation. The result showed large difficulties for the Hough transform algorithm to correctly identify the trees in the plot due to stones, boulders, and uneven terrain. Only 25% of the trees in the plot were identified correctly. The algorithm also returned artefacts that further impaired the results of the TLS measurements to traditional field measurements. The mean difference in DBH between TLS measurement and field measurement in the plot was 115 mm and for tree height, the mean difference was 7.35 m. This difference in DBH and tree height would have overestimated the timber yield and made this algorithm unsuitable for the forest industry in the conditions present in the Rumperöd mixed forest.

Bryophytes play a significant role in various ecological processes, including soil succession and colonization after disturbances. Although they are commonly believed to take up nutrients from soil solutions rather than the soil itself, the influence of soil on their growth and distribution is evident from previous studies. In order to examine the impact of soil conditions on bryophyte species composition and abundance, samples of soil and vegetation were collected from industrially disturbed sitesin Skåne. pH and phosphate concentrations were measured and compared with the identified bryophyte species and their coverage. Both pH and phosphate were found to be important factors influencing bryophyte diversity. Most species were associated with high pH and low phosphate conditions. Moreover, total species richness exhibited a decline with rising phosphate levels. Certain species were restricted to very specific conditions. The results indicate the potential benefits of maintaining neutral to high pH and low phosphate levels to aid bryophyte conservation efforts., Moss Matters: The First Step in Reclaiming Disturbed Soils Although frequently escaping the spotlight, bryophytes, consisting of mosses, liverworts, and hornworts, are the second largest group of land plants with a vital role in various ecological processes, such as soil formation, carbon storage and nutrient cycling. As smaller plants, they efficiently take advantage of nutrient-poor soils and recolonize soils following disturbance, thus improving the habitat, and paving the way for the eventual arrival of vascular plants. The main characteristics setting bryophytes apart from vascular plants is how they acquire nutrients. Lacking a traditional root system, they absorb water and minerals across their entire surface, allowing them to grow on various substrates beyond just soil. Despite this strategy, evidence suggests that soil chemistry has a substantial effect on their abundance and diversity. To investigate the relationship between the soil and bryophytes, a study was conducted on industrially disturbed sites of Skåne, a region in southern Sweden. By analyzing the pH and phosphate levels of the soil, as well as identifying the species composition of the populations, the research aimed to gain a deeper insight into how these soil conditions shape bryophyte vegetation. The findings have shed some light on the intricate interactions between soil and bryophytes. The majority of the species showed a clear preference for high pH and low phosphate. This affinity for phosphate-poor environments is likely an adaptive strategy. Given that most vascular plants struggle to establish under such circumstances, this provides bryophytes with a competitive advantage. Moreover, a collaborative effect was observed – when certain species deviated from their usual pH preferences (e.g. a species with a documented preference for alkaline soil was found on acidic soil), they compensated by favoring higher phosphate concentrations. Additionally, several species were confined to very spec

Although microalgae have been considered for the biological treatment of wastewater since the 1950’s, their potential to efficiently remove pollutants from various streams remains largely untapped and is yet to be utilized at large scale. The production of algal biomass and extraction of high-value compounds has, however, become increasingly popular with large scale farms and biorefineries around the world producing many promising alternatives to petroleum-based products and processes. While microalgae systems rival traditional production in terms of environmental sustainability and health benefits, the economic viability remains a challenge. This study aimed to investigate the potential of a biorefinery concept using wastewater as growth medium for the production of natural pigments by cyanobacterium, Arthrospira platensis. Using effluent streams as a growth media drastically cuts costs of production and with this circular approach, we are able to address challenges facing the wastewater treatment industry while providing a sustainable alternative to petroleum-based products. During phase one, the growth of A. platensis was monitored on different amounts of wastewater supplemented with standard growth media. Biomass productivity and growth rate ranged from 233,12 – 2000 mg.L-1.d-1 and 0,19 – 0,37 d-1, with 50% FWW supplemented with 50% Zarrouk media resulting in the highest values and thus proving to be the preferred growth media. However, cultures grown on 75% FWW supplemented with 25% Zarrouk media resulted in the highest PC content and thus was chosen as the growth media for further investigation. Phase two investigated the effect of different photoperiods (14h:10h and 16h:8h) on the production of PC, while assessing the scale-up potential of the system and monitoring nutrient removal. Photoperiod had no significant effect on PC content, however, a decrease in total PC production was seen between phases, suggesting further optimization for scale-up to be viable., Harnessing Microalgae: Transforming Wastewater into Valuable Pigments Innovative solutions are constantly sought to address the challenges of wastewater treatment and the increasing demand for sustainable products. One promising approach involves utilizing microalgae in a biorefinery system that not only cleans wastewater but also extracts valuable pigments from the biomass. This concept presents an intriguing solution that combines environmental remediation with the production of high-value products. Microalgae are microscopic organisms that harness the power of photosynthesis to convert sunlight and carbon dioxide into organic matter. They are incredibly efficient at this process, exhibiting high growth rates and accumulating various valuable compounds, including pigments. Their ability to thrive in diverse environments, including wastewater, makes them an ideal candidate for treatment and resource recovery. Traditional wastewater treatment processes consume large amounts of energy and are environmentally taxing. However, by integrating microalgae cultivation with wastewater treatment systems, we create a symbiotic relationship where the nutrients and organic matter present in the wastewater are used as a nutrient source for growth, effectively purifying the water in the process. One particularly exciting aspect is the extraction of valuable pigments from the microalgae biomass. These pigments not only provide color to the microalgae but also possess significant commercial value in various industries such as food, cosmetics, and pharmaceuticals. This study aims to investigate the potential of this biorefinery concept on local wastewater sources from the treatment facility RecoLab located in Helsingborg, Sweden. By establishing growth of a popular microalgae, Arthrospira platensis, on a food wastewater stream which is high in nutrients, we can optimize the biomass growth and assess the pigment content produced throughout cultivation. Additionally, we investigate th

Forensic sexual assault samples typically contain a mixture of a small quantity of sperm cells and a high quantity of epithelial cells. This relationship complicates the generation of a DNA profile, which prompts the need for differential lysis and extraction of the DNA. Differential extraction is a lengthy method that includes multiple tube transfers and requires a purification step. Amicon Ultra centrifugal filters are employed to purify samples; however, these filters are costly and susceptible to potential breaks in the supply chain. The objective of this project was to examine alternative methods utilizing “off-the-shelf” reagents for sperm cell lysis or sample purification, with the goal of streamlining the current differential extraction protocol. Three methods for sperm cell lysis were studied: alkaline lysis, lysis with the nonionic detergent NP-40, and lysis with a natural decondensation assay. Isopropanol precipitation was examined as an alternative purification method. Additionally, reducing the number of washing steps in the differential extraction protocol was investigated. The results showed that optimized alkaline lysis (25 µL NaOH (0.2 M), 25 µL Tris-HCl (0.2 M) and TE buffer) was comparable to the differential extraction protocol in terms of DNA recovery. Alkaline lysis was also comparable to the differential extraction when performed on mock sexual assault samples. Isopropanol precipitation likewise showed equal DNA yields, complete DNA profiles and peak heights compared to Amicon filtration. Lastly, it was shown that reducing the number of washing steps of the reference protocol produced comparable DNA profiles. In conclusion, the findings suggest that the differential extraction protocol can be modified by using alkaline lysis for sperm cell lysis or isopropanol for purification, as well as by performing only one washing step., Sperm cells are usually the most interesting biological material to analyze in forensic sexual assault samples. However, today’s method for extracting DNA from sperm is both time-consuming and requires purification with expensive filters. It is therefore relevant to investigate alternative protocols that can help streamline the process. The term “sexual offense” it the Swedish legal umbrella term for crimes of a sexual nature, with major crimes including sexual assault. Typically, the biological material of highest interest in sexual assault samples is sperm cells, as DNA can be extracted and potentially linked to a suspect. However, due to the nature of most sexual assault samples, where sperm cells are present in lower quantities in comparison to other cell types (e.g. epithelial cells), successful extraction and analysis of sperm cell DNA is difficult. Because of this, a method called differential extraction is typically performed, where the sperm cells and other cells in the mixture are treated separately. Differential extraction is a lengthy protocol that requires multiple transfers of material between tubes, which can lead to loss of DNA and contamination. On top of this, it uses the strong reagent dithiothreitol (DTT) to successfully break open the sperm cells and release the DNA. DTT interferes with downstream analysis and DNA profiling, for which reason the samples must be purified. At the National Forensic Centre (NFC), purification of samples is done with centrifugal filters called Amicon filters. As there is only one supplier of these filters, the process is susceptible to disruptions in the supply chain, which occurred during the Covid-19 pandemic. Furthermore, Amicon filters are expensive. Therefore, it was relevant to examine alternative methods for sperm cell disruption (lysis) and sample purification that could simplify the current method, preferably while using easily accessible reagents. This project examined three alternative methods for sperm ce

Although microalgae have been considered for the biological treatment of wastewater since the 1950’s, their potential to efficiently remove pollutants from various streams remains largely untapped and is yet to be utilized at large scale. The production of algal biomass and extraction of high-value compounds has, however, become increasingly popular with large scale farms and biorefineries around the world producing many promising alternatives to petroleum-based products and processes. While microalgae systems rival traditional production in terms of environmental sustainability and health benefits, the economic viability remains a challenge. This study aimed to investigate the potential of a biorefinery concept using wastewater as growth medium for the production of natural pigments by cyanobacterium, Arthrospira platensis. Using effluent streams as a growth media drastically cuts costs of production and with this circular approach, we are able to address challenges facing the wastewater treatment industry while providing a sustainable alternative to petroleum-based products. During phase one, the growth of A. platensis was monitored on different amounts of wastewater supplemented with standard growth media. Biomass productivity and growth rate ranged from 233,12 – 2000 mg.L-1.d-1 and 0,19 – 0,37 d-1, with 50% FWW supplemented with 50% Zarrouk media resulting in the highest values and thus proving to be the preferred growth media. However, cultures grown on 75% FWW supplemented with 25% Zarrouk media resulted in the highest PC content and thus was chosen as the growth media for further investigation. Phase two investigated the effect of different photoperiods (14h:10h and 16h:8h) on the production of PC, while assessing the scale-up potential of the system and monitoring nutrient removal. Photoperiod had no significant effect on PC content, however, a decrease in total PC production was seen between phases, suggesting further optimization for scale-up to be viable., Harnessing Microalgae: Transforming Wastewater into Valuable Pigments Innovative solutions are constantly sought to address the challenges of wastewater treatment and the increasing demand for sustainable products. One promising approach involves utilizing microalgae in a biorefinery system that not only cleans wastewater but also extracts valuable pigments from the biomass. This concept presents an intriguing solution that combines environmental remediation with the production of high-value products. Microalgae are microscopic organisms that harness the power of photosynthesis to convert sunlight and carbon dioxide into organic matter. They are incredibly efficient at this process, exhibiting high growth rates and accumulating various valuable compounds, including pigments. Their ability to thrive in diverse environments, including wastewater, makes them an ideal candidate for treatment and resource recovery. Traditional wastewater treatment processes consume large amounts of energy and are environmentally taxing. However, by integrating microalgae cultivation with wastewater treatment systems, we create a symbiotic relationship where the nutrients and organic matter present in the wastewater are used as a nutrient source for growth, effectively purifying the water in the process. One particularly exciting aspect is the extraction of valuable pigments from the microalgae biomass. These pigments not only provide color to the microalgae but also possess significant commercial value in various industries such as food, cosmetics, and pharmaceuticals. This study aims to investigate the potential of this biorefinery concept on local wastewater sources from the treatment facility RecoLab located in Helsingborg, Sweden. By establishing growth of a popular microalgae, Arthrospira platensis, on a food wastewater stream which is high in nutrients, we can optimize the biomass growth and assess the pigment content produced throughout cultivation. Additionally, we investigate th

Climate change is changing the precipitation patterns around the globe, leading to more extreme weather events like severe drought and heavy rainfalls. These events are intrinsically related to soil moisture fluctuations, which strongly modulates carbon fluxes in terrestrial ecosystems. Studying the behavior of microbial communities present in agriculture soils during drying and rewetting events can help understand soil dynamics under climate change scenarios and help the knowledge gap of how perennial crops can be useful in reducing climate change consequences. In this project, I compared perennial and annual crop systems in depth, down to 90 cm, by characterizing the soils and measuring their microbial responses to a drying and rewetting event. From this study, it was possible to conclude that both soils present a sensitive response to such event, with both lag and recovery times increasing with depth. Moreover, soils exposed to perennial crops generally showed shorter lag and recovery times than those from annual crops, which suggests that perennial crops might have a higher capacity to withstand the negative effects of droughts. Based on the results obtained and the intrinsic limitations of the experiment, it is clear that further investigation is needed, namely in the form of respiration studies, more replicates and statistical analysis., Climate change is causing extreme weather events worldwide, like severe droughts and heavy rainfall, by changing precipitation patterns. These events affect water levels and have a major impact on carbon movement in soils. To understand how soil behaves under changing climate conditions, I studied how microbes in agricultural soils behave after drying and rewetting events, by comparing perennial and annual crops soils to explore their potential in mitigating climate change effects. I characterized soils from perennial and annual croplands from Skåne, Sweden and conducted drying and rewetting experiments to evaluate the microbial responses. The results showed that both soil types were sensitive to drought, with microbes taking longer to recover in deeper soils. Surprisingly, soils from perennial crops showed to be better adapted to drought conditions, with the potential to help fight climate change. Future studies should include more replicates, analyze respiration and the microbial communities by sequencing DNA, and apply statistical techniques to support the validity of the conclusions.

Rainforests are of great importance for biodiversity and several ecosystem services. In Rwanda, a considerable decline in rainforest covers have been observed during the last decades. The Gishwati-Mukura Forest is one of the rainforests in Rwanda that has experienced a substantial reduction in forest cover, 99.4 %. The aim of this research has been to investigate what the changes in forest cover of Gishwati-Mukura have been, what impacts they had on local livelihoods, biodiversity and occurrence of floods and landslides, and what the reasons for the deforestation have been. The method used to reach the aim has been a combination between field observations and interviews with local inhabitants in Rwanda, a review of literature, and analysis of changes in forest cover, land use, and hydrological data. The main reasons for the deforestation are found to be an increase of local population, expanded agricultural land use, use of wood as primary source for energy production and mining activities. The deforestation in Gishwati-Mukura has had negative impacts on biodiversity, ecosystem services and resilience of the ecosystems, as the habitats for the species have been fragmented and reduced. A correlation between the decreased forest cover and higher flow rates in Sebeya river has been found, indicating that the loss of forests is a potential cause for more frequent floods and landslides., Allmänt känt är att världens regnskogar bidrar till flertalet ekosystemtjänster som hjälper till att upprätthålla förutsättningarna för liv på jorden och som vi människor kan dra nytta av. Den höga och välutvecklade biologiska mångfald som dessa skogar inrymmer är att tacka för detta. Rwanda, ett litet land beläget i den östra delen av Afrikas tropiska zon, har under det senaste seklet varit objekt för omfattande avskogning som påverkat nationens regnskogars funktionalitet. Under samma period har landet förlorat stora delar av sin ursprungliga biologiska mångfald och årligen utsatts för naturkatastrofer i form av översvämningar och jordskred. Denna masters uppsats ämnar utforska hur avskogningen i västra Rwanda, mer specifikt i nationalparken Gishwati-Mukura, har påverkat skogens biologiska mångfald och riskerna för översvämningar och jordskred i området från år 1960 till idag. Metoderna som använts för att uppnå detta syfte är en kombination av en litteratursammanställning, datainsamling och analys av satellitbilder över området och av flödesförändringar i en av de närliggande floderna, Sebeya. Dessutom har fältstudier på plats i Rwanda genomförts och innefattat observationer från några av de avskogade områdena och intervjuer med lokalbefolkning, forskare och anställda vid statliga institutioner. Resultaten från arbetet fastslår att det totala skogstäcket av naturlig skog minskat med 89 % mellan 1960 och 2019 och att denna minskning gett upphov till förluster av den biologiska mångfalden. Något som inte påvisats är dock till vilken omfattning biodiversiteten påverkats. Studien visar därutöver på ökade flödeshastigheter i Sebeya vilket insinuerar att ökad erosion och således ökad risk för översvämningar och jordskred förekommer. Förordat är att mer forskning om de naturliga skogarnas effekter på och betydelse för biologisk mångfald och förekomst av översvämningar och jordskred genomförs.

Background: There is a need to develop methods of determining concentration and purity for two new affinity ligands, protein T and protein H, in order to ensure the quality of an industrial production of said proteins. Aims: To develop a High Performance Size Exclusion Chromatography, HPSEC, method to determine concentration and purity of protein T and to improve an existing HPSEC method for concentration and purity determination of protein H that show selectivity, display linearity between peak area and injection amount and give repeatable results. Methods: For protein T, Xbridge Premier Protein and Superdex Increase columns were used of the lengths 15 and 30 cm together with 50mM and 0.3M Sodium phosphate buffers and PBS and mobile phases. For protein H, only a 15 cm Superdex Increase column was used with 0.3M Sodium phosphate buffer. Different reducing conditions during sample preparation were tested. The linearity and measuring ranges were determined by injecting different volumes of reference standard and evaluating . Repeatability was tested with three triplicates of reference standards across three occasions with the same equipment and running conditions. Results: For protein T the 15 cm Xbridge column with 50mM Sodium Phosphate buffer was selected. Little difference between reduction conditions with exception of reduction at high temperature which resulted in degradation or aggregation for both proteins. Acceptable selectivity and separation between main peak and impurities was demonstrated for both methods. Both methods were linear and gave repeatable results in the measuring ranges 2.43 – 16.98µg, 4.85 – 16.98µg and 2.56 – 15.37µg for purity determination of protein T, concentration determination of protein T and both purity and concentration determination protein H, respectively. Conclusion: Two methods, one for protein T and one for protein H, were developed which met qualification criteria use in quality control., An important part of pharmaceutical production is the purification of the active ingredient which can be done, in part, using proteins called affinity ligands which selectively bind specific targets. Just like the active ingredients in drugs, companies must be sure that these affinity ligands don’t contain harmful impurities and fulfil product specifications in order to protect patient safety. A common efficient method for determining protein concentration and purity is called high performance size exclusion chromatography, HPSEC. HPSEC is a method where a solution flows through a tube filled with porous particles called a column, which separates compounds according to how fast they travel through the column. How fast something travels depends on the size of the compound. Different affinity ligands have different properties which may impact how they interact with the column which may distort results. Therefore suitable parameter conditions must be determined for each affinity ligand to be measured. The aim of this study is to develop to methods by finding suitable HPSEC parameter conditions for determining purity and concentration of two affinity ligands, here called protein T and protein H. Both methods should be separate the affinity ligands well from impurities and be linear and repeatable. To this end, four columns were tried; two different sizes for the porous particles, and two different tube lengths. Solutions with different salt concentrations were used to pass through the column as well as different times and temperatures of preparing the samples were tried so that the ligands were in their active states. Once suitable parameters had been selected, different protein amounts were used to see for what sample concentrations the method would be linear. The concentration and purity of a sample were determined on three different days using the final selected parameters to test if the method was repeatable. The results showed the column with smaller particles were

The concept of mussel farming as a mitigator to nutrient pollution is steadily spreading. The southernmost part of Sweden borders the Baltic Sea where the water quality differs between the costs, however, all are affected by eutrophication. The study presents a suitability analysis using GIS to find potential locations for blue-mussel farm establishment, and the outcome was produced as maps. A multi-criteria analysis (MCA) was done based on the environmental conditions needed for mussel growth (chlorophyll a, salinity, dissolved oxygen, temperature, currents, and water depth), possible disturbances (pipelines, cables, shipping, and nature reserves) and a short discussion on the spatial availability considering potential variations of eutrophication levels in the water based on adjacent land cover. The difference in salinity had a great effect on the location suitability, and adjustments showed that with lower salinity, the area availability increased, marginally along the west coast but to a pronounced degree along the east coast.

With warming in soils due to climate change, a series of secondary factors arise, which have multifaceted effects on soil microbial communities. Of these, alterations to soil moisture are among the most crucial to understanding how microbial functions will change in the face of climate change. As living organisms, microbes must adapt to their environment, and their adaptations are reflected in their response to contemporary events. How they respond can determine the fate of soil organic matter and have relevant feedback to climate systems. In this thesis, I address how the legacy effects of a soil microbial community affect its response to a drying and rewetting event in terms of resilience and resistance, as well as how these strategies can affect carbon dynamics in subarctic ecosystems. I achieved this by taking soil samples from study sites that have undergone two-year warming in Abisko, Sweden. I then subjected them to a drying and rewetting cycle, assessing the samples as they dried down and subsequently responded to being rewet. During this time, I measured bacterial and fungal growth via stable isotope probing as well as respiration via gas chromatography. I found that while moisture was affected, microbial resistance was unaffected by warming treatments. However, resilience was affected by warming treatments. Responses also differed primarily based on NDVI, possibly indicating the importance of plant inputs of carbon to the microbial response. Possible conceptual frameworks are then used to explain the observations, notably the YAS framework. Implications for carbon budgeting and models are inferred from these findings. I conclude that interactions between microbes and moisture and plant inputs impact microbial response to moisture stress in warming experiments and that future experiments may want to examine the vegetation relationship with more focus., Alterations to the carbon cycle have caused climate change to warm the planet. The arctic is warming at nearly triple the rate as the rest of the globe. Most of the world’s biologically relevant carbon is below ground in the arctic and subarctic. This is a result of the cold climate reducing decomposition below annual production, for policy to adapt to upcoming climate changes which may affect the stability of this carbon. In this study, I examined how temperature alterations to soil microbial communities alter their response to moisture alterations such as drought and drying then rewetting. I used warmed sites near the Abisko research station in the subarctic birch forest that had five treatments of warming. The treatments consisted of a control plot, a summer warming plot, a winter warming plot, a chronic (year-round) warming plot and an extreme warming plot. I sampled soil and took field measurements of these treatments. I then dried the soil down, and then rewet it. During these alterations, I used isotopic methods to measure the growth of microbes. I also measured their respiration during this time. I found that microbial communities did not stay active during the drought period and that treatments had no effect on this. However, microbial communities that had a higher amount of photosynthesis had a more robust response, while microbial communities that had experienced dryer conditions had a more efficient response. I associate this response with the microbes adapting to both the stress of the moisture deficit as well as potential stress of carbon availability. I theorized that this might be because of microbes have to shift their activities in plots without plants. Plants provide carbon which microbes can use as an energy source and without it, there is a possibility that the ability to respond to stress may have been impaired. The carbon dynamics described in this study could be used in models and carbon budgeting for future warming. Additionally, understandi

Introduction: In Bio-pharmaceutical production, peristaltic pump tubing is considered one of the factors that influence protein aggregation. Background: Protein particles present challenges for the control and analysis of various manufacturing processes in the biopharmaceutical industry for their significant effects on safety and quality. Aim(s): This research aims to study the effect of different peristaltic pump tubing on particle formation as well as the Characterization of the particles and investigate the effect of surfactants on particle formation. Methods: The study was conducted using a dynamic image analysis instrument (QICPIC) to characterize particles formed by Lipase protein samples while pumping through Silicone and PVC tubing using a peristaltic pump. Lipase samples concentration of 1mg/ml were investigated with and without polysorbate 20, Poloxamer 188, and SDS surfactants, while Lipase 10 mg/ml samples were investigated without using the surfactants. Results: Pumped of all Lipase protein samples resulted in particle formation with varying degrees between Silicone and PVC tubing. The presence of Poloxamer 188 and Sodium Dodecyl Sulfate (SDS) surfactants reduced pumping-induced particles except for Polysorbate 20. Conclusion: Silicone and PVC tubing generate particles even in the presence of surfactants and a great level of reduction the particle formation was achieved with Poloxamer 188 and SDS surfactants., Protein aggregation is a high molecular weight protein content cluster. Their presence in finished therapeutic protein products is considered risky for their significant effects on the quality of the medicine and the safety and health of the patient as it can induce adverse effects. Therefore, it is critical to identify the process that contributes to its formation and address the presence of particles in the development of therapeutic proteins. From a formulation perspective, having profound knowledge of particle development mechanisms and identifying the causes and factors affecting particle formation is important. Knowing the factors that influence particle formation is advantageous to adopt control measures to mitigate risks associated with particles beginning from the initial production steps, through storage life duration. This project was done to investigate the effect of pump tubing, Silicone, and PVC tubing, used for transporting protein during the production process, tubing of a peristaltic pump, on protein particle formation for lipase protein using Silicone and PVC tubing, and characterize the particle formed. Moreover, investigate the effect of using different surfactants on the formation of the particles. The surfactants, a commonly used compound in bio-pharmaceutical formulations to prevent aggregation, used were Polysorbate 20, Poloxamer 188, and Sodium Dodecyl Sulfate (SDS) surfactant. This was done by using a QICPIC instrument for particle analysis and Silicone and PVC tubing for pumped Lipase. The lipase samples with or without surfactant were pumped in through the tubing for thirty minutes and measurements were taken every minute. Particles were characterized using ferret diameter and Sphericity. The results were compared to see the effect of tubing type and surfactants. The results obtained from this investigation showed that peristaltic pumps can induce protein aggregation which depends on the tubing type and the presence of the surfactant. It