Ribosomes are large macromolecules responsible for protein synthesisand they consist of both RNA and proteins. Each ribosome is made of one large and one small subunit. Even though the ribosome is one of the most studied machineries in the cell there is a gap in our understanding of how this macromolecule functions in vivo. In this project we aimed to develop a method for tracking a specific subset of ribosomes using super-resolution fluorescence microscopy. This was achieved by using the MS2 coat protein (MS2CP) fused to a fluorescent marker and by modifying ribosomes to have the RNA loop to which theMS2CP binds with high affinity. We were able to obtain the most promising results when the MS2CP was fused to a Halotag with the dye JF549 attached to it. The JF549 has good cell permeability which allows simple and efficient labelling of ribosomes. To be able to observe translation of specific mRNAs we used this labelling strategy to track orthogonal ribosomes which do not recognise mRNA normally produced in cells but can translate mRNAs with a modified 5’-UTR.Orthogonal ribosomes were tested with several different 5´-UTRs. With the construct for which we obtained the highest expression level we observed that up to 43% of the labelled orthogonal ribosomes were engaged in translation of the specific mRNA. The system will make it possible to determine how the sequence of a particular mRNA will affect its in vivo translation.

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1. Abstrakt:Bakgrund: Malaria är en av världens viktigaste infektionssjukdomar och det beräknas vara ca300 miljoner drabbade varje år, därför är metabolismen av läkemedel som används för attbehandla malaria såsom kinin och artemisinin värt att lägga fokus på. Cytokrom P450enzymerna har en viktig roll i metabolism av malarialäkemedel och dessa uppvisar variationinterindividuellt samt mellan olika populationer på grund av polymorfism.Syfte: Denna studie har fokuserat på att undersöka tre polymorfa gener (CYP3A4*1B,CYP3A5*3 och CYP2B6*6) hos både friska och malariasmittade barn i Uganda för attjämföra resultaten med en population i Mwanza, Tanzania. Dessa polymorfa alleler påverkarmetabolismen av artemisinin och kinin, vilket i sin tur kan förorsaka minskad/ökad ellermisslyckad klinisk effekt.Metod: Genotypning av individernas blodprov gällande dessa genvarianter undersöktesgenom laboratoriestudier med PCR som huvudsaklig metod. DNA sekvensering utfördes vidUppsala Genome Center.Resultat: Resultaten visade att allelfrekvensen i Mwanza för CYP3A4*1B var 78%respektive 16% för CYP3A5*3, medan de var 72 % respektive 50% hos populationen iUganda. Allelfrekvensen för CYP2B6*6 i Uganda var 72 % och 36 % i Mwanza, Tanzania.Sammanfattning: De flesta malariamediciner uppvisar skillnader i kinetik och dynamikvilket kräver terapeutisk läkemedelsmonitorering. Sammanfattningsvis finns det skillnaderoch variationer bland de studerade polymorfa CYP enzymer interindividuellt och mellanolikaetniska grupper.Resultatet av denna studie visade både små skillnader mellan de två studerade populationernamen även skillnader mellan individer i den studerade gruppen i Uganda.

The use of molecular chaperones can increase the yield of correctly folded proteins. This is especially needed in the expression of proteins non-native to the host organism. This study set out to investigate the function of the chaperone GroES; a component in the GroE-system. The function of this chaperone has only been studied alone in vitro. Here we lay ground to further studies on GroES and its ability to act alone in vivo. GroES was expressed from a plasmid and characterized through its potential to increase the amount of correctly folded proteins. Characterization was mainly done by fluorescence spectroscopy with hard-to-fold proteins linked to fluorescent probes. Results show a very clear increase in fluorescence for most of the substrate proteins tested, indicating that GroES has a significant role in the GroE-system and perhaps outside of it.

Approximately 30 million years ago, ancestors of fungus-growing termites started an obligate mutualistic relationship with a Basidiomycete fungus Termitomyces. The success of this obligate relation is the division of labour and reliance on termite caste gut microbial symbionts. Termites workers maintain Termitomyces fungal garden with their workforce and dual gut passage while the soldier caste protects the colony from predators. The fungal garden concurrently provides enough food for the colony members. Royal pair (a king and a queen) is the centralised caste in the colony, and they control the colony population by their massive reproduction, but their gut community composition remains unexplored. This project aimed to characterise the gut microbes associated with royal pairs of a fungus‐growing termite species Macrotermes natalensis. Four colonies were explored using high throughput sequencing of 16S rRNA gene amplicon dataset. The high-throughput sequence result showed that royal gut microbiotas were comprised of a lower number of bacterial taxa than sterile caste (workers and soldiers). This less number of bacterial taxa suggested that the royal pair gut was completely decoupled from the sterile castes gut, which indicates that the royal pair were possibly provided with a unique diet. The study also showed diversity in bacterial genus-level OTUs of royal pairs in all four colonies which indicated that there is a diet variation between the king and queen. The media predicting strategy could facilitate future cultivation efforts for targeted royal pair gut bacterial strains.

Many regions of the world are facing the problem with arsenic toxicity. Arsenic contamination has become a considerable threat to the environment triggering various big health issues for every life in that contaminated environment. Lysinibacillus sphaericus (B1-CDA) is an arsenic tolerant strain of bacteria that has been reported and characterized before by the researchers of the University of Skövde, Sweden. The bacteria were found to contain many arsenic responsive genes such as arsB, arsC, and arsR which are responsible for arsenic tolerance in the bacterium. The main focus of the current study was to characterize one of the arsB genes (gene-4251) of Lysinibacillus sphaericus B1-CDA by in silico and in vitro analyses in order to determine the molecular function of this gene. The in silico studies conducted by using the Iterative Threading Assembly and Refinement (I-TASSER) server predicted the tertiary structure of the ArsB protein and suggested that this protein is an intrinsic component of the membrane which primarily helps in the binding of metal ions and liberation of metabolic energy. To validate this predictive results, several in vitro experiments were performed. For complementation studies, the arsB gene was cloned from L. sphaericus B1-CDA and transferred to an arsB knock-out mutant of Escherichia coli JW3469-1. Both, the transgenic and mutant strains were grown under the arsenic stress of 50 mM for 96 hrs followed by measuring their growth and arsenic tolerance after every 24 hrs. Statistical analysis confirmed that there was a significant difference in growth between the transgenic and the mutant E. coli strains. The ICP-MS (Inductive Coupled Plasma-Mass Spectroscopy) analysis revealed that after 24 hrs of culture, the arsenic content in the cell-free broth of transgenic strain was reduced from 50 mM to 9.10 mM (81.8%), whereas the reduction in arsenic content by the mutant strain was from 50 mM to 9.80 mM (80.2%). These results suggest that the arsB gene is partly involved in the accumulation of arsenic inside the cells and this feature could be used for a large scale removal of arsenic from the contaminated environment.

Hair is important for thermoregulation, physical protection, sensory activity, seasonal camouflage and social interactions. Hair is produced in hair follicles (HFs), complex mini-organs in the skin devoted to this task. HFs are formed during embryonic development (morphogenesis) and new hair is continuously generated throughout life since the postnatal HF goes through cycles of regression (catagen), quiescence (telogen) and growth (anagen). The transcriptional regulation of this process is not well understood. The LIM-homeodomain transcription factor Lhx2 has previously been shown to be critically involved in epithelial-mesenchymal interactions during development of various organs and a potent regulator of stem cell function. We therefore elucidated the expression pattern and function of Lhx2 during hair formation. Lhx2 is expressed during both morphogenesis and anagen in cells scattered in the outer root sheath and in a subpopulation of the matrix cells in the proximal part of the hair bulb. Matrix cells are proliferating progenitor cells that differentiate into the components of the HF including the hair shaft. Expression is turned off during telogen, however Lhx2 expression reappears in the secondary hair germ immediately prior to initiation of the anagen stage. In contrast to previously published results Lhx2 appears to be expressed by progenitor cells distinct from those in the stem cell niche in the bulge region. The developmental-, stage- and cell-specific expression pattern of Lhx2 suggests that Lhx2 is involved in the generation and regeneration of hair. To test our hypothesis we used different genetically modified mouse strains. First we studied the effect of over-expression of Lhx2 in the HFs using a mouse model where transgenic Lhx2 expression could be induced in dorsal skin. Using this model we could show that Lhx2 expression is sufficient to induce anagen. To analyze the consequence of lack-of-function of Lhx2 we developed a mouse model where it is possible to conditionally inactivate Lhx2 and a mouse strain harbouring a hypomorphic allele of Lhx2. Mice where Lhx2 was conditionally inactivated in postnatal HFs were unable to regrow hair on a shaved area whereas all controls did regrow their hair. The mutant HFs initiated anagen but were unable to produce normal hair shafts. Thus Lhx2 is required for postnatal hair formation. We used the mouse strain carrying a hypomorphic allele of Lhx2 to study the role of Lhx2 during HF morphogenesis. Embryos homozygous for the hypomorphic allele form significantly less HFs compared to control embryos, and the HFs that do form in the mutant embryos appear to be developmentally arrested. These results suggest that Lhx2 is also important during HF morphogenesis. Thus, Lhx2 is an essential positive regulator of hair generation and regeneration.

Large-scale culturing of algae with the aim of production of economically valuable substances is a growing industrial sector. A common problem of such industrial algae cultures is that they are prone to suffer from fungal infections causing growth inhibition of the algae and reduced production of the target substances. Having sensitive and target specific methods for the early detection of these infections are of great economic importance since in later stages infections may be very hard to treat. There are several potential methods that can be used for infection detection such as visual detection through microscopy or DNA amplification based methods like PCR. This report presents a novel protocol for the early detection of the parasitic fungi Paraphysoderma sedebokerense infecting the green micro algae Haematococcus pluvialis. DNA from infected frozen algae cultures collected from the Gustavsberg production plant of Astareal AB was extracted using ZR Fungal /Bacterial DNA MiniPrep kit. Conventional PCR and SYBR Green quantitative PCR were further compared to each other and optimized to be more sensitive in detecting parasitic DNA. The annealing temperature and primer concentration were optimized. In addition, two different SYBR Green PCR kits and the use of fresh versus frozen algae cultures were compared. The quantitative PCR method was able to detect as low as 300 DNA copies accurately but occasionally was capable to give a signal corresponding to as little as 4 DNA copies in a reaction. Meanwhile the conventional PCR method could accurately detect as low as 600 DNA copies and occasionally 60 DNA copies. This report shows the possibility of improving the detection of P. sedebokerense infection in industrial H. pluvialis cultures by PCR technique, emphasizes the differences between conventional PCR and quantitative PCR and presents a working protocol for the quantitative PCR based monitoring of P. sedebokerense infections.

The natural occurrence of the non-mevalonate (also called MEP after the compound methyl-erythriol phosphate) pathway in the model cyanobacterium Synechocystis sp. PCC 6803 allows for biosynthesis of various high-value terpenoid compounds. An important co-factor of this pathway is thiamine pyrophosphate (TPP), coenzyme to the 1- deoxy-D-xylulose-5-phosphate synthase (DXS) reaction in the initial step of the MEP pathway. Concurrently, TPP biosynthesis derives partially from 1-deoxy-D-xylulose phosphate, the product of DXS. This makes TPP a potentially significant measure of MEP pathway activity, and thus terpenoid productivity. The implementation of a molecular biosensor for TPP could be a promising approach towards on-line assessment and feedback regulation of MEP pathway activity and this application is therefore investigated in this work. Riboswitches have been suggested as versatile RNA-based tools for biotechnological applications in bacteria, including various cyanobacterial species. However, TPP-responsive riboswitches have not been addressed in cyanobacteria thus far. This project therefore aims at the evaluation and implementation of TPP-responsive riboswitches in Synechocystis, using a yellow fluorescent reporter protein as quantitative readout of translational regulation. Native putative OFF-switches from two cyanobacterial species are investigated along with one synthetic ON-switch, originally based on the native riboswitch from E. coli. The induction effects are assessed on both RNA and protein level for both TPP and its precursor thiamine. The synthetic riboswitch is found to be effective in Synechocystis and is further examined for its dynamic range. Several protocols for fluorescence and transcript level experiments are developed. Several continuation experiments are suggested, including further investigation of the cyanobacterial OFF-switches.

SAD-C, a gene belonging to the small short-chain alcohol dehydrogenase-like protein (SAD) gene family, is up-regulated in Pisum sativum (pea) when the plant is exposed to UV-B (280-320 nm) radiation. SAD-C has a molecular weight of about 28 kDa and adopts a tetrameric structure. The aim of this work was to purify the protein SAD-C from Pisum sativum when overexpressed in E. coli strain BL21 StarTM (DE3) One Shot®. The purification was facilitated by the presence of a His-tag consisting of six histidine residues at the C-terminal end of the protein. The purification trials of SAD-C were faced with problems since the sample fractions contained several other proteins as well. Several purification steps seem to be necessary for future trials. A crystallization trial was still set up and crystals were formed, but the crystals formed were probably not of SAD-C.