The aim of this work was to determine if the protein Majastridin found in the proteobacterium Rhodobacter blasticus has a functional relative in the hypothetical protein Q1U8S3/ B3XNV1 found in Lactobacillus reuteri. To be able to study the protein, it was overexpressed in  E. coli-cells and purified. As a starting material, the L. reuteri Q1U8S3 gene previously cloned into a pET SUMO vector from Invitrogen was used. The produced protein will be a fusion protein containing a His6-tag, a SUMO-protein and the protein of interest. A nickel column in combination with a gel filtration column was used to purify the protein and after purification, crystallization experiments were set up using standardized kits.

Mechanisms involved in the clearance of chylomicrons and aspects of the interactions at the vascular endothelium were studied in the rat. The poly-anion heparin, known to release lipoprotein lipase (LPL) from the vascular endothelium, enhanced the clearance of chylomicrons. Five minutes after heparin injection, the clearance of chylomicron triglycerides and retinyl esters was markedly accelerated. The rapid initial clearance was followed by a slower clearance of heavily lipolyzed chylomicrons. In contrast, one hour after heparin the clearance of both triglycerides and retinyl esters was retarded. This decreased removal of chylomicrons coincided with a decrease in the heparin releasable LPL activity, indicating that the previous release to plasma by heparin had resulted in net loss of functional LPL in the tissues. The poly-cation protamine released hepatic lipase and some LPL from their binding sites to plasma. One hour after protamine, plasma triglyceride levels were increased, indicating that chylomicron removal was impeded. It has been speculated that protamine inactivates LPL in vivo, but this was not the case. Ten minutes after injection of protamine normal amounts of LPL could be released by heparin. Thus, the accumulation of plasma triglycerides was not due to a rapid inactivation of LPL by protamine. LPL has specificity for sn-1,3-ester bonds. To investigate if this specificity is important in vivo, a lipid emulsion containing medium-chain fatty acids (MCFA) in the sn-1,3-position and long-chain fatty acids (LCFA) in the sn-2-position was synthesized, as well as an emulsion containing MCFA-TG mixed with LCFA-TGs (MMM/LLL). In vitro experiments showed large differences in the hydrolysis of the emulsions, but in vivo there were only small differences in the metabolism. To further study if lipid emulsions are cleared by the same mechanisms as chylomicrons, an emulsion was made by the same formulation as Intralipid® with addition of 3H-triolein and ,4C-cholesteryl ester. As measured by the removal of cholesteryl esters, the emulsion was cleared at the same rate as was chylomicrons. The triglyceride label was, however, removed more slowly from the emulsion droplets than from chylomicrons. Together with the lower recirculation of labeled free fatty acids (FFA) in plasma, this suggests that there was less lipolysis of the emulsion. The current view that removal of lipid emulsions in vivo is mainly dependent on LPL-mediated hydrolysis might thus not be correct. To further analyze the metabolism of chylomicrons, a compartmental model was developed. In this process, the distribution volume for chylomicrons was shown to be larger than the blood volume, a model for the metabolism of FFA in the rat was validated, and the full tissue distribution of injected chylomicrons was determined. According to the model, about half of the triglyceride label was removed from the circulation together with the core label while for the emulsion this number was about 80 %. In fasted rats all labeled fatty acids appeared to mix with the plasma FFA pool, while in fed rats about one-fifth of the fatty acids did not mix with the FFA but was apparently channeled directly to tissue metabolism. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 1995, härtill 5 uppsatser.</p> / digitalisering@umu.se

Apis mellifera, otherwise known as the common honey bee, is an incredibly important social animal. Their important role in the world makes studying them of great importance. Their stomachs can be divided into three parts, the foregut, the midgut and the hindgut. The mouth and crop are located in the foregut, the midgut encompasses the ventriculus and the hindgut is made up of the ileum and rectum. Each part of a honey bee intestine hosts a different community of bacteria that vary in proportion with age, caste and season. These microbiota are essential for a honey bees mood, development and overall health. No two authors agree completely as to what the a honey bee’s gut microbiota is. In this thesis study the intestinal tract microbiome of four bee colonies, two of which belonging to the Apis mellifera carnica subspecies and two to the Apis mellifera buckfast subspecies, were sequenced. All four are from the same region in Sweden, Uddevalla. Many issues were found during this project, including one sick colony, but through them a more thorough and guaranteed method to sequence these honey bee intestinal bacteria was developed. The results of the sequencing showed that there is indeed a major difference in these intestinal communities even in bees from the same region or from the same subspecies. A possible culprit for the diseased colony was found.

<p>The goal of this work was to contribute to the fed-batch process optimisation task by deriving parameters that have considerable impact on productivity as well as product quality The chosen parameters were I) the design of the glucose feed profile, II) the choice of induction strategy, with respect to the method of addition, and III) the time of the induction, with respect to the specific glucose consumption rate. </p><p>The present fed-batch experiments using the lacUV5-promoter, for production of b-galactosidase, have shown that a high glucose feed rate gives a specific production rate, q_p, that is twice as high, after induction, compared to a feed rate that is 2.5 times lower. The constant accumulation of lacZ-mRNA indicates that the translational capacity is initially limiting the synthesis machinery, but after four hours of maximum specific production and a corresponding drop in lacZ-mRNA production, the cultivation is likely to be transcription limited. The high feed-rate system resulted in high accumulation of β-galactosidase, corresponding to 40% of total cellular proteins.</p><p>By design of feed profiles in a fed-batch process the detrimental effects of overflow metabolism, giving acetic acid formation, can be avoided. However, the results show that a one-dose addition of isopropyl-β-D-galactopyranoside (IPTG), provokes a non-growth associated production of acetic acid. This response can be alleviated by; lowering the inducer concentration (in this case to below 165 μM), by further reducing the feed rate of glucose or by using alternative induction methods. The use of a stepwise addition or a feed of IPTG thus delayed and reduced the level of acetic acid accumulation. It was also shown that a small change in the time-point of induction lead to large variability, regarding both productivity and acetic acid accumulation, in a fed-batch cultivation, </p><p>In order to further investigate the protein quality two additional proteins were studied in fed-batch cultivations using high and low glucose feed. The aim was to prove the hypothesis that the feed related change in the rate of synthesis of the nascent polypeptide controls the product quality. For the two proteins: Zb-MalE (wt) and Zb-MalE31 (mutant), the transcription rate, in terms of amount of IPTG, and translation rate, in terms of changes in feed rate, influences the percentage of inclusion body formation and degradation of nascent polypeptide. The data show a higher rate of inclusion body formation for the model protein Zb-MalE31 during high feed rate cultivations, as well as at high levels of inducer. Furthermore, the rate of proteolysis was significantly higher for a high feed rate. The high feed rate thus results in a higher rate of synthesis but a lower corresponding quality, for the model proteins studied.</p><p>In the present investigation of fed-batch cultivations using several different expression vectors, it was found that the central alarmone guanosine tetraphosphate (ppGpp) was formed at both high and low feed rates upon induction. It could be shown, however, that by secretion of Zb-MalE to the periplasm, the stringent response could be avoided. This might be due to the decreased burden on the host where the secretion of product further seems to make the cell able to redirect the carbon flux from overflow metabolism, since no acetic acid was produced. The secretion also demonstrates that the growth arrest could be aborted, which is otherwise gained in the P_malKproduction system.</p><p>A novel fed-batch process based on the promoters for the universal stress proteins A and B (P_uspA, P_uspB) was designed to make use of these powerful promoters in an industrial production context. It was concluded that the process had to start from a high specific growth rate and induction was performed once a limiting feed started. This was done to purposely induce the stringent response and/or acetic acid accumulation since this was required for induction. In the suggested system, induction has to be performed and maintained at continuous substrate feeding, whilst avoiding exceeding the cellular capacity, since the stationary phase starvation alone did not lead to production. In conclusion, a new stress induction based production system was achieved resulting in high accumulations of product protein without any detected metabolic side effects.</p>

Viral proteases are important targets for anti-viral drugs. Discovery of protease inhibitors as anti-viral drugs is aided by an understanding of the interactions between viral protease and inhibitors. This thesis addresses the characterization of protease-inhibitor interactions for application to drug discovery and model system development. The choice of a relevant target is essential to molecular interaction studies. Therefore, full-length NS3 protein of hepatitis C virus (HCV) was obtained, providing a more relevant target and a better model for the development of HCV protease inhibitors. In addition, resistance to anti-viral drugs, a serious problem in the treatment of AIDS, prompted the investigation of resistant variants of human immunodeficiency virus (HIV) protease. Drug resistance was initially explored by characterization of the interactions between a series of closely related inhibitors and resistant variants of HIV protease, using an inhibition assay to determine the inhibition dissociation constants (Ki). The relationship between structure, activity and resistance profiles was not clarified, indicating that the effect of structural changes in the inhibitors and the protease are not predictable and must be analyzed case wise. It was proposed that additional kinetic characterization of the interactions was required and a biosensor-based method allowing for determination of affinity, KD, and interaction rate constants, kon and koff, was adopted. The increased physiological relevance of this method was confirmed, and the affinity data have better correlation with cell culture data. In addition, interactions between clinical inhibitors of HIV protease and enzyme variants indicate that increased dissociation rates (koff) are associated with the development of resistance. Thermodynamic characterization of the interactions between HIV-1 protease and clinically relevant inhibitors revealed distinct energetic characteristics for inhibitors. The resolution of the energetics of association and dissociation identified an inhibitor with unique interaction characteristics and confirmed the validity of using this method for further characterization of molecular interactions. This work resulted in the development of model systems for the analysis of kinetics, resistance and thermodynamic characteristics of protein-inhibitor interactions. The results give increased understanding of the biomolecular interactions and can be applied to drug discovery.

Hepatitis C is a serious disease that affects about 200 million people worldwide. No anti-HCV vaccine or specific anti-viral drugs are available today. Non-structural protein 3 (NS3) of HCV is a bifunctional serine protease/helicase, and the protease has become a prime target in the search for anti-HCV drugs. In this work, the complete HCV NS3 gene has been cloned and expressed, and the protein has been purified using affinity chromatography. An assay for measuring the protease activity of full-length NS3 protease has been developed and used for inhibition studies. A series of peptide-based inhibitors of NS3 protease varying in length, the composition of the side-chain and the N- and C-terminal groups have been studied. Potent tetra-, penta- and hexapeptide inhibitors of the NS3 protease were discovered. Hexapeptides with an acyl sulfonamide C-terminal residue were the most potent inhibitors of the NS3 protease, having nanomolar Ki-values. The selectivity of the inhibitors was assessed using other serine and cysteine proteases. NS3 protease inhibitors with electrophilic C-terminal groups were non-selective while those comprising a C-terminal carboxylate or acyl sulfonamide group were selective. All inhibitors with a small hydrophobic P1 side-chain residue were non-selective for the NS3 protease, being good inhibitors of human leukocyte elastase. This result highlights the importance of the P1 residue for inhibitor selectivity, which stems from the major role of this residue in determining substrate specificity of serine proteases. Electrophilic inhibitors often cause slow-binding inhibition of serine and cysteine proteases. This was observed with other proteases used in our work but not with NS3 protease, which indicates that mechanism of inhibition of NS3 protease by electrophilic inhibitors may not involve formation of a covalent bond. The structure-activity relationships obtained in this work can be used for improvement of peptide-based inhibitors of HCV NS3 protease towards higher inhibitory potency and selectivity.

A variety of HIV-1 protease inhibitors and their interactions with the enzyme have been characterized in order to identify novel and improved drugs against AIDS. The investigated inhibitors were represented by clinical and non-clinical inhibitors, active site and allosteric inhibitors, transition-state analogues and metal-ions. In addition, different enzyme variants were used to investigate the contribution of different amino acid residues to the interaction with different ligands. The problem of resistance has been addressed by exploring novel types of inhibitors, and resistant mutants of HIV-1 protease. A study resolving the inhibition of HIV-1 protease by Cu2+ showed that the enzyme can be allosterically inhibited and that copper inhibition is a result of an interaction with His-69 and a subsequent conformational change. Several types of transition-state analogues were analyzed with respect to their inhibition of wild-type and resistant mutants of HIV-1 protease. Unfortunately cyclic compounds were not found to be better than linear compounds. Moreover, it was not possible to identify structure-activity relationships that clearly correlated with efficacy towards mutants and a biosensor based method for more detailed kinetic studies was therefore adopted. By cross-linking the immobilized enzyme on the biosensor matrix, a stable surface was obtained and kinetic rate constants could be determined for the interaction between the enzyme and inhibitors. Additional improvements in the methodology involved identification of a more representative interaction model, allowing more detailed studies of interactions with resistant mutants and varying conditions. Finally, absorption to lipid membranes and interaction with human serum albumin and α1-glycoprotein by clinical drugs were studied in a simplified ADME model system for improvement of the earlier stages of drug development. These studies have revealed important characteristics of these drugs that can potentially be modeled into new compounds that have improved efficacy of both wild-type and resistant mutants of HIV-1 protease.

The present study has focused on characterising protease-ligand interactions in the context of drug discovery. The proteases that have been studied are human matrix metallopeptidase 12 (MMP-12), HIV-protease and Hepatitis C virus (HCV) NS3/NS4A protease. These studies have involved kinetic characterisation of protease-inhibitor interactions using biosensor technology, as well as determination of inhibition and activity regulation by using activity assays. The regulation of MMP-12 activity by calcium was proposed, based on the study of the calcium dependence of MMP-12 activity. Furthermore, it was shown that the high affinity of hydroxamate-based inhibitors of MMP-12 were due to slow dissociation of the enzyme-inhibitor complex by using a new biosensor assay for the study of interactions between MMP-12 and ligands. A study of the pH-dependency of protease-inhibitor interactions revealed that the interaction kinetics of HIV-protease inhibitors differed with pH in a way that could be related to the inhibitor structures. This suggested that the forces of interaction are different in the association and dissociation phases of an interaction. Furthermore, it demonstrated the usefulness of pH as a variable in characterising protein-ligand interactions. Results applicable in the discovery of drugs against Hepatitis C were obtained, with the analysis of structure-activity relationships of novel inhibitors. Furthermore, the mode of binding imposed by key functional groups of the inhibitors was explored by investigating the effect of pH on the interactions with NS3. The results show the importance of using appropriate model systems for drug discovery by selecting relevant targets and assay conditions. Furthermore, the usefulness of kinetic rate information in drug discovery is demonstrated. Thus, by contributing to the knowledge of protease-ligand interactions, applicable to both protease inhibitor interactions and protease activity regulation, this thesis is expected to have an impact on the field of protease inhibitor development and drug discovery in general.

<p>Mantle cell lymphoma (MCL) is a non-Hodgkin B-cell lymphoma with very bad prognosis. The genetic hallmark of MCL, is the translocation t(11;14)(q13;q32) which leads to overexpression of cyclin D1, a D-type cyclin that is not usually expressed at high levels in normal B lymphocytes.</p><p> </p><p>Previous studies indicate that cannabinoid receptors are expressed in lymphoma and have shown that lymphoma cell death is induced as a result of exposure to cannabinoids (ligands).</p><p> </p><p>The aim of this diploma work was to combined cytostatics with the cannabinoid receptor ligand R (+)-Methanandmide (R-MA). Our data suggest that combination treatment with cytostatics and R-MA induces synergistic effects in most cases.</p>

<p>Extracellular matrix degrading proteases from the plasminogen (plg) activator (PA) and the matrix metalloproteinase (MMP) systems have been implicated as important mediators of ovulation and corpus luteum (CL) formation and regression. The aim of this thesis was to investigate the expression and regulation of PAs and MMPs in the ovary and to examine their functional roles for CL formation and function. </p><p> The expression of membrane-type MMP-1 (MT1-MMP) and its substrate gelatinase A (MMP-2) mRNAs was studied during pregnant mare serum gonadotropin (PMSG)/human chorionic gonadotropin (hCG)-induced ovulation in immature rats. These proteases were coordinately regulated so that both were highly expressed in the theca cells of large preovulatory follicles. This suggests that MT1-MMP activates gelatinase A in preovulatory follicles to degrade the follicular wall during ovulation. </p><p> In pseudopregnant (psp) rats, MT1-MMP mRNA was expressed in the CL throughout the luteal phase. Tissue inhibitor of metalloproteases type-1 (TIMP-1) mRNA was expressed during CL formation and regression. MMP-2 and collagenase-3 mRNAs were expressed during CL formation and regression, respectively. When the luteal phase was artificially prolonged or shortened, TIMP-1 and collagenase-3 mRNAs were induced only after the serum progesterone levels had decreased, indicating a close association with luteolysis in the rat. </p><p> In psp mice, the expression of mRNAs coding for both PAs, seven MMPs, and five protease inhibitors was studied. Most of the studied molecules were coordinately expressed during formation or regression of the CL. However, uPA, MT1-MMP, and TIMP-3 mRNAs were expressed throughout the luteal phase. The role of uPA was examined in psp uPA deficient mice. These mice displayed no abnormalities in luteal function or vascularity. The role of uPA is thus either not essential or can be compensated by other proteases in the absence of uPA. </p><p> In order to control the timing of the CL formation, a mouse model for PMSG/hCG-induced CL formation was developed. Five different protocols were evaluated. One of them provided CL that were stable for six days. In that protocol the mice were treated with prolactin (PRL), twice daily from day 2 of CL life onward. The expression of the steroid acute regulatory protein (StAR) mRNA in the psp CL was also characterized to assess its use as a molecular marker for CL development and regression. It was highly expressed in the forming and functional CL and downregulated at a late stage of CL regression.</p><p> The functional role of plg and MMPs for CL formation and function was investigated in plg deficient mice treated with the MMP inhibitor galardin (GM6001). Both psp mice and PMSG/hCG +PRL-induced CL formation were used. Several molecular markers for CL development and regression were used to evaluate the health status of the CL. Our data showed that healthy and vascularized CL formed even in plg deficient mice treated with the inhibitor. However, serum progesterone levels were significantly reduced in these mice, an effect that was mainly attributable to the plg deficiency. In conclusion, neither plg nor MMPs, alone or in combination, seem to be essential for the development of a functional CL.</p>