Anti-TNF alpha antibodies were among the first approved antibody drugs and now belongs to the best-selling drugs. Today, several companies are developing biosimilars to those drugs which will increase the access of medications and potentially reduce health care costs. There is a great demand for pharmacokinetic assays for anti-TNF-alpha drugs and the bridging assay format is a potential tool, mostly due to its high serum tolerance. This project at Gyros Protein Technologies AB aimed to investigate the properties of the solid phase on the Gyrolab and to utilize this to optimize the bridging assay to be used as a pharmacokinetic assay for a human antibody in the presence of serum. The solid phase was optimized by incorporating three reagents with increasing molecular weight and examining the column profiles generated. Furthermore, the capture reagent was titrated with b-BSA to avoid cross-binding of both arms of the antibody to the capture reagent. Since the background was relatively high, further optimization was done to reduce background and increase the signal to noise ratio. The performance of the optimized bridging assay was compared to alternative PK assay formats. The estimated sensitivity of the bridging assay was 5 ng/ml compared to 250 ng/ml for the indirect antibody assay and 2.5 ng/ml for the bridging assay using an anti-idiotypic antibody as detect. The optimized bridging assay performed well without dilution in buffer and was therefore used for affinity determination of Humira in neat serum. Variable concentrations of TNF-alpha were added to a fix concentration of Humira to compete with the interaction. Calculated KD-values were similar regardless of whether the measurements were performed in neat serum or after dilution in Rexxip buffer.

The innate immune system are a cooperation of many components – receptors being one of them. Both membrane-bound and cytosolic receptors play a large role in the defence system against pathogens and danger. NLRP3 is a receptor which assembles a protein complex called inflammasome in response to cytosolic stress and is responsible for many autoimmune diseases if it malfunctions. The activation of the NLRP3 inflammasome leads to secretion of inflammatory cytokines and in many cases to programmed cell death. The structure, function and activation of the NLRP3 inflammasome is still not fully understood and the urge to understand the mechanisms behind are important for future medical improvements. The aim was to anchor the NLRP3 inflammasome by the cell membrane - By Overlap PCR, the NLRP3 cDNA was fused extracellular and trans-membrane parts of the TLR4 cDNA to anchor the NLRP3 to the membrane and in turn analyse the inflammasome with LPI™ technology. Multiple primers and a TLR4 nucleotide were designed and the NLRP3 was amplified with specific overhangs by PCR. The fusion protein was successfully linked together by Overlap PCR but not confirmed by sequencing. The gene fusion demands high quality primers for amplification and further evaluation must be made to the details of the laboratory. To anchor the protein complex to the cell membrane, continue to be of full importance and can be an asset in many structural studies and biopharmaceuticals trials.

Klorat som avfallsprodukt från pappersindustrin har lett till miljöproblem på grund av klorats toxiska verkan på växter och alger, och har även lett till bekymmer för människohälsan där klorat avfallet har kommit i kontakt med dricksvatten. För att åtgärda detta så har mycket forskning gjorts på bakterier med förmågan att reducera klorat till syrgas och kloridjoner, en anaerob process som vissa naturligt förekommande bakterier kan utföra. Med ökad kunskap om regleringen av denna kloratreducerande process, kan dessa bakterier utgöra en effektiv reningsprocess av pappersbrukens avloppsvatten.  Ideonella dechloratans är en sådan bakterie, den har ett genkluster som kodar för de kloratreducerande enzymerna. Nedströms för dessa finns en arsR-sekvens som tros att koda för en transkriptionsfaktor; och ytterligare information om denna transkriptionsfaktor kan möjligen bidra till förståelse av genuttrycket hos den kloratreducerande funktionen. Syftet med detta arbete är att transformera expressionsceller med förmågan att uttrycka arsR, så framtida försök kan göras för att identifiera potentiella bindningssäten för ArsR-proteinet. arsR-sekvensen amplifierades med primrar specifika för ändarna hos arsR, sekvensen ligerades i en pET-21a(+) vektor från Novagen och transformerades med BL21 (DE3) expressionsceller. Med en IPTG inducering kunde ett stort uttryck av olösligt ArsR observeras. Komplikationer med resultatet och framtida tillvägagångsätt diskuteras. / Chlorate as a waste product from the paper industry has caused environmental problems due its toxic effect on plants and algae and is also a concern for human health where chlorate has contaminated the tap water supplies. To address this issue, a great deal of research has been carried out on naturally occurring bacteria that can anaerobically reduce chlorate to oxygen and chloride ions. With additional knowledge of how this chlorate-reducing process is regulated, these bacteria may one day provide an effective purification process of wastewater from paper mills. Ideonella dechloratans is such a bacterium that has a gene cluster which encodes the chlorate-reducing enzymes. Downstream of this cluster is an arsR-sequence believed to encode a transcription factor, which could aid in the understanding of the gene expression for the chlorate-reducing operon. The goal of this research is to transform expression cells with the ability to express the arsR-sequence so that future trials can be made to identify any potential binding sites for the ArsR-protein. The arsR-sequence was amplified with primers specific to the ends of the arsR-sequence. The sequence was then ligated into a pET-21a(+) vector from Novagen and transformed with BL21 (DE3) expression cells. By IPTG inducing these transformants it was possible to observe a significant expression of insoluble ArsR. Complications with the outcome and future approaches are discussed.

This thesis is based on studies, described in four papers, in which the folding energy landscape of MerP was investigated by various techniques. MerP is a water-soluble 72 amino acid protein with a secondary structure consisting of four anti-parallel β-strands and two α-helices on one side of the sheet in the order β1α1β2β3α2β4. The first paper describes the use of CD and fluorescence analysis to examine the folding/unfolding process of MerP. From these experiments it was found that the protein folds according to a two-state model in which only the native and unfolded forms are populated without any visible intermediates. With a rate constant of 1.2 s-1, the folding rate was found to be unusually slow for a protein of this size. The studies presented in the second and third papers were based on measurements of native-state amide proton exchange at different temperatures (Paper II) and GuHCl concentrations (Paper III) in the pre-transitional region. In these studies partially unfolded forms were found for MerP which are essentially unrelated to each other. Thus, in the folding energy landscape of MerP, several intermediates seem to occur on different folding trajectories that are parallel to each other. The slow folding rate of MerP might be coupled to extensive visitation of these conformations. Hydrogen exchange in MerP did also reveal structure-dependent differences in compactness between the denatured states in GuHCl and H2O. In the last paper multivariate data analysis was applied to 2-dimensional NMR data to detect conformational changes in the structure of MerP induced by GuHCl. From this analysis it was suggested that regions involved in the most flexible part of the protein structure are disrupted at rather low denaturant concentrations (< 2.1 M GuHCl) while the native structures of the most stable parts are still not completely ruptured at 2.9 M GuHCl. Finally, the stability, kinetics, contact order and folding nuclei of six proteins with similar topology (MerP, U1A, S6, ADA2h, AcP and HPr) were compared. In this analysis it was found that their folding properties are quite diverse, despite their topological similarities, and no general rules that have been formulated yet can adequately predict their folding behaviour.

Bacterial antibiotic resistance is an increasing global health problem, leaving few therapeutic options available for the treatment of pathogenic infections. The development of new antibiotics has been slow since their discovery more than 8 decades, therefore, monitoring the extent and distribution of antibiotic resistance is of great importance. The aim of this study was to determine the presence of antibiotic resistance genes in sludge samples obtained from three wastewater treatment plants (WWTPs) in Sweden. Samples were collected and analyzed for the presence of nalidixic acid (NA), chloramphenicol (CHL), and tetracycline (TC) resistance genes using polymerase chain reaction (PCR). The DNA extracted from Eskilstuna and MälarEnergi sludge showed the presence of NA and TC resistance genes, whereas Örebro sludge was found to have resistance for TC antibiotic genes. To validate the results, PCR detection for resistance genes was performed on Escherichia coli isolates from the sludge samples. Antibiotic susceptibility testing was used to confirm the genetic analysis for antibiotic resistance genes detection in these E. coli. The PCR results for TC resistance genes correlated between sludge PCR analysis and bacterial isolates for all 3 WWTPs. Based on the results obtained from the genotypic analysis of sludge and E coli, incomplete compatibility in regards to NA, and CHL were observed. However on the basis of antibiotic susceptibility testing, E coli isolates from MälarEnergi sludge samples unveiled the majority presence for antibiotic resistance genes. The results suggest that extra monitoring for the wastewater treatment facilities are vital to minimize the rising incidence of antibiotic resistant bacteria.

Trapezius myalgia is a pain condition that usually develops in people with repetitive and stressful work tasks, which can lead to chronic widespread pain (CWP). This work compares protein expression levels in healthy women with those in women who have chronic widespread pain, including pain in the trapezius muscle, by using a proteomic approach.  Twodimensional gel electrophoresis and silver staining with a subsequent digital quantification of protein spots was used to detect spots which had significantly higher protein levels in either group. Preparative gels were made and stained with SYPRO Ruby, the protein spots that were significantly different between the groups were picked from the SYPRO Ruby gels and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF. The optical density of seven protein spots were significantly decreased in the trapezius muscle of the CWP subjects; however the standard deviations were notably high. Five of the seven proteins could be identified as desmin, creatine kinase B-type, serum albumin, heat shock protein beta-1 and slow skeletal muscle troponin T. Apart from serum albumin, all these proteins can possibly be responsible for pain in the trapezius muscle in CWP. In conclusion, this study demonstrates that two-dimensional gel electrophoresis in combination with mass spectrometry is a powerful tool to identify potential biomarkers of musculoskeletal pain in subjects with CWP. The results may provide new insights into the mechanisms and patho-physiology of trapezius myalgia.

The serotonergic system is involved in a broad range of functions in both vertebrates and invertebrates and is highly conserved across taxa. Serotonin is an important monoamine acting in the brains of humans and animals, and has large and varying influences on many aspects of an individual’s life. For example, in humans, serotonin modulates feelings of happiness and in fruit flies, higher levels of serotonin increase aggression. In humans, an abnormal serotonergic system can result in health issues, such as depression and obsessive compulsive disorders, for which medications have been developed, including selective serotonin reuptake inhibitors (SSRI). Because the serotonin system has a large influence on human health, understanding how it functions is of great interest to researchers. Using comparative studies to explore differences in the serotonin system across taxa can provide insight into the mechanistic details of the system. To investigate if the serotonin system is comparable between vertebrates and invertebrates, a literature study with particular focus on receptors and proteins involved was performed. In addition, this report takes part in an experimental study investigating the effect of the SSRI fluoxetine in Mediterranean field crickets.  Fluoxetine reduced exploration propensity of crickets, which was reversed, compared to what was anticipated and compared to effects seen in vertebrates. The literature review suggests that serotonin receptors are quite similar, but that proteins differ more when comparing vertebrates and invertebrates. This offers a likely explanation as to why results of studies on these different groups of animals may differ.

Cells are encapsulated by a biological membrane in order to separate the cell interior from the surrounding environment. Different lipids and proteins compose the membrane and present a semi-permeable barrier for the diffusion of ions and molecules across the lipid bilayer. Membrane proteins also mediate the passage of signals between the interior and the exterior of the cell.   To ensure the proper functioning of membrane proteins, it is essential that nascent membrane proteins are correctly integrated into the lipid bilayer to be able to fold and oligomerize.  In this thesis, an engineered protein containing two natural transmembrane segments followed by an additional test segment, has been used as a model protein to study (i) sequence requirements for translocon-mediated insertion of the test segment, (ii) dynamics of nascent membrane proteins undergoing translocon-mediated insertion and (iii) to carry out an extensive mutagenesis scan to identify critical residues in the mammalian arrest peptide Xbp1 that enhances translational stalling in the ribosome. This provides a toolbox of arrest peptides with different stalling strengths that will be useful for force measurements on nascent protein chains. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

Messenger RNAs are transcribed and co-transcriptionally processed in the nucleus, and transported to the cytoplasm. In the cytoplasm, mRNAs serve as the template for protein synthesis and are eventually degraded. The removal of intron sequences from a precursor mRNA is termed splicing and is carried out by the dynamic spliceosome. In this thesis, I describe the regulated splicing of two transcripts in Saccharomyces cerevisiae. I also describe a study where the mechanisms that control the expression of magnesium transporters are elucidated. The pre-mRNA retention and splicing (RES) complex is a spliceosome-associated protein complex that promotes the splicing and nuclear retention of a subset of pre-mRNAs. The RES complex consists of three subunits, Bud13p, Snu17p and Pml1p. We show that the lack of RES factors causes a decrease in the formation of N4-acetylcytidine (ac4C) in tRNAs. This phenotype is caused by inefficient splicing of the pre-mRNA of the TAN1 gene, which is required for the formation of ac4C in tRNAs. The RES mutants also show growth defects that are exacerbated at elevated temperatures. We show that the temperature sensitive phenotype of the bud13Δ and snu17Δ cells is caused by the inefficient splicing of the MED20 pre-mRNA. The MED20 gene encodes a subunit of the Mediator complex. Unspliced pre-mRNAs that enter the cytoplasm are usually degraded by the nonsense-mediated mRNA decay (NMD) pathway, which targets transcripts that contain premature translation termination codons. Consistent with the nuclear retention function of the RES complex, we find that NMD inactivation in the RES mutants leads to the accumulation of both TAN1 and MED20 pre-mRNAs. We also show that the cis-acting elements that promote RES-dependent splicing are different between the TAN1 and MED20 pre-mRNAs. The NMD pathway also targets transcripts with upstream ORFs (uORFs) for degradation. The ALR1 gene encodes the major magnesium importer in yeast, and its expression is controlled by the NMD pathway via a uORF in the 5’ untranslated region. We show that the ribosome reaches the downstream main ORF by a translation reinitiation mechanism. The NMD pathway was shown to control cellular Mg2+ levels by regulating the expression of the ALR1 gene. We further show that the NMD pathway targets the transcripts of the vacuolar Mg2+ exporter Mnr2p and the mitochondrial Mg2+ exporter Mme1p for degradation. In summary, we conclude that the RES complex has a role in the splicing regulation of a subset of transcripts. We also suggest a regulatory role for the NMD pathway in maintaining the cellular Mg2+ concentration by controlling the expression of Mg2+ transporters.

Fish has for a long time been a very important source of protein for human kind and with the world population at an all-time high, 7.5 billion and rapidly growing, the demand for fish as a food source is also at an all-time high and rapidly increasing. This has in turn led to overexploitation of many of the fish stocks of the world ocean’s and in many cases to depletion of fish stocks. The demand for sustainable food sources and sustainable usage of the world ocean’s fish stocks is therefore a subject with great deal of interest today. Much of the fish caught today are used for production of fish meal for usage as fish food at fish farms, which also increases the depletion of fish stocks around the globe. One way of dealing with this problem is to replace the fish meal as protein source in fish feed with protein from agricultural crops which in many cases are done today by usage of soy bean protein. This however poses another problem as the agricultural crops take up vast amount of land, in many cases obtained by diminishing the rainforests in the area. Another usage for the soybean would be as a direct human food source. Agricultural products are also dependent on environmental conditions to ensure reasonable production. The problems related to production of fish meal and soy has sparked the idea of using microorganisms for production of Single cell protein for usage as protein source in fish feed. Single cell protein can be produced in closed fermentation vessels and can be produced at a controlled rate and under controlled manners, while taking up negligible land space. During this thesis, the production of single cell protein from spent sulfite liquor using the filamentous fungi Paecilomyces variotii was examined. The aim of the project was to examine the effect of cultivation parameters (i.e., pH, temperature and nutrients) on the production of biomass as well as the protein content of the biomass. The correlation of the biomass growth and protein content have also been examined. The project was carried out by performing several experiment cultivations using spent sulfite liquor provided by Domsjö Fabriker in Örnsköldsvik. This process enables the utilization of a residual stream from the pulp industry which gives this process a huge environmental upside compared to similar processes as for example the commercial production of Quorn (a Single cell based food product) which utilizes pure glucose. The results showed that the protein content will steadily decrease as the biomass production increases hence it is desirable to keep the cultivation time at a minimum while maximizing biomass production during that time frame. It also points towards that the highest protein content is present in the young cell mass. The key conclusion from this thesis is however that it is possible to lower the pH of the cultivation from pH 6 down to pH 4.5 while still maintaining the biomass production and increasing the protein content. The highest obtained protein content was 62.7% at pH 4.5. The high protein content might be due to a slightly longer lag phase in the beginning of the cultivation which yields a higher number of younger cells in the final broth thus increasing protein content. Running the process at a lower pH is a huge advantage for industrial implementation as this on large scale means significant lower amounts of chemicals needed for pH adjusting of the spent sulfite liquor which renders the process much more economical. This is because pH adjustment today is one of the most costly process steps in the production of bioethanol from spent sulfite liquor.