Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 72-93).

As an important chemical raw material, alcohols can be used as fuels, solvents and chemical feedstocks to produce a variety of downstream products. With limited fossil fuel resources, alcohol synthesis from syngas reactions can be a potential alternative to the traditional petroleum based alcohol synthesis. Among many catalysts active for syngas to alcohol processes, alkali promoted Mo2C has shown promising performance. More interestingly, the alkali promoter was found to play an important role in shifting the reaction selectivity from hydrocarbons to alcohols. However, limited understanding of the mechanism of this alkali promoter effect is available due to the complexity of syngas reaction mechanism and low content of alkali added to the catalysts. In this thesis, we performed a comprehensive investigation of the alkali promoter effect with density functional theory (DFT) calculations as our primary tool. We first examine various Mo2C surfaces to determine a representative surface structure active to alkali adsorption. On this particular surface, we develop a syngas reaction network including relevant reaction mechanisms proposed in previous literature. With energetics derived from DFT calculations and a BEP relation, we predict the syngas reaction selectivity and find it to be in excellent agreement with experimental results. The dominant reaction mechanism and selectivity determining steps are determined from sensitivity analysis. We also propose a formation mechanism of alkali promoters on Mo2C catalysts that shows consistency between experimental IR and DFT computed vibrational frequencies. Finally, the effect of alkali promoters on the selectivity determining steps for syngas reactions are investigated from DFT calculations and charge analysis. We are able to rationalize the role of alkali promoters in shifting the reaction selectivity from hydrocarbons to alcohols on Mo2C catalysts.

Bok/Mtd (Bcl-2-related ovarian killer/Matador) is considered a pro-apoptotic member of the Bcl-2 family. Though identified in 1997, little is known about its biological role. We have previously demonstrated that Bok mRNA is upregulated following E2F1 over-expression. In the current work, we demonstrate that Bok RNA is low in quiescent cells and rises upon serum stimulation. To determine the mechanism underlying this regulation, we cloned and characterized the mouse Bok promoter. We find that the mouse promoter contains a conserved E2F binding site (-43 to -49) and that a Bok promoter-driven luciferase reporter is activated by serum stimulation dependent on this site. Chromatin immunoprecipitation assays demonstrate that endogenous E2F1 and E2F3 associate with the Bok promoter in vivo. Surprisingly, we find that H1299 cells can stably express high levels of exogenous Bok. However, these cells are highly sensitive to chemotherapeutic drug treatment. Taken together these results demonstrate that Bok represents a cell cycle-regulated pro-apoptotic member of the Bcl-2 family, which may predispose growing cells to chemotherapeutic treatment.

Organische-Anionen-Transporter (OATs) sind maßgeblich an der Ausscheidung von körpereigenen und körperfremden Substanzen über die Niere beteiligt. In Ratten, einem häufig verwendeten Tiermodell in präklinischen Studien, ist bekannt, dass die basolateral lokalisierten Organischen-Anionen-Transporter 1 (Oat1) und 3 (Oat3) in männlichen Tieren stärker und darüber hinaus Testosteron abhängig exprimiert werden. Beide Transporter sind an der Ausscheidung von organischen Anionen, einschließlich negativ geladener Medikamente wie zum Beispiel Adefovir, Furosemid oder Penicillin, beteiligt. In den menschlichen Nieren zählen der OAT1 und der OAT3 zu den klinisch relevanten Transportern, deren Funktionen im Laufe neuer Medikamentenentwicklung berücksichtigt werden sollten. Für das Antibiotikum Penicillin wurde bei Frauen ein vermehrtes Auftreten von Nebenwirkungen im Vergleich zu Männern gezeigt. Dieses erhöhte Risiko könnte möglicher Weise auf einer geschlechtsabhängigen Expression des OAT1 und OAT3 zurückzuführen sein. Ziel der vorliegenden Arbeit war es, den molekularen Mechanismus, der für die höhere Oat1 und Oat3 Expression in den männlichen Rattennieren verantwortlich ist, zu identifizieren. Mit Hilfe von Luciferase assays wurde die Aktivierung von Ratten und menschlichen Oat1/OAT1 und Oat3/OAT3 Promotoren untersucht. Hierzu wurden zunächst Oat1/OAT1 und Oat3/OAT3 Promotorkonstrukte generiert, welche unterschiedlich lange Promotorregionen enthielten, und diese anschließend transient in OK oder LLC-PK1 Zellen transfiziert. Mittels Co-Transfektion potentieller transkriptioneller Regulatoren konnte deren Einfluss auf die Promotoraktivität von Oat1/OAT1 und Oat3/OAT3 untersucht werden. Zur Identifikation geschlechtsabhängig exprimierter Gene in der proximalen Tubuluszelle der Rattennieren wurden von vier männlichen und vier weiblichen Tieren je eine Niere präpariert und deren RNA mit Hilfe eines microarrays und real-time PCR analysiert. Im Rahmen dieser Arbeit konnte gezeigt werden, dass die bereits bekannte männlich dominierende Expression von Oat1 und Oat3 in Rattennieren nicht durch den klassischen Testosteron/Androgenrezeptor vermittelten, transkriptionellen Mechanismus reguliert wird. Vergleichbar zu den Ratten Oat1 und Oat3, zeigten auch die menschlichen OAT1 und OAT3 Promotoren keine Aktivierung durch den Testosteron/Androgenrezeptor-Komplex. Während der Suche nach geschlechtsabhängig exprimierter transkriptioneller Regulatoren in der Rattenniere, konnte die Expression des Transkriptionsfaktors B-cell CLL/ lymphoma 6 (BCL6) erstmalig als männlich dominierend identifiziert werden. Die bereits bekannten Aktivatoren der Oats/OATs Expression, hepatocyte nuclear factor 1α (HNF1α), HNF1β und HNF4α zeigten keine geschlechtsabhängige Expression. Zudem konnte gezeigt werden, dass BCL6 die Promotoren der Ratten und menschlichen Oat1/OAT1 und Oat3/OAT3 aktiviert. Die BCL6-vermittelte Aktivierung von Oat1/OAT1 und Oat3/OAT3 erfolgt nicht über die bislang vorhergesagten BCL6-Bindungsstellen, aber möglicher Weise über Protein-Protein Interaktionen mit den Transkriptionsfaktoren HNF1 oder cAMP response element binding protein (CREB). Zusammenfassend konnte gezeigt werden, dass der Transkriptionsfaktor BCL6 einen vielversprechenden Regulator der geschlechtsabhängigen Expression von Oat1 und Oat3 in Ratten darstellt. Es ist anzunehmen, dass BCL6 ebenso die humane OAT1 und OAT3 Expression reguliert.

Over a decade after the completion of the human genome, researchers around the world are still wondering what information is hidden in the genome. Although the sequences of all human genes are known, it is still almost impossible to determine much more than the primary protein structure from the coding sequence of a gene. As a result of that, the need for recombinantly produced proteins to study protein structure and function is greater than ever. The main objective of this thesis has been to improve protein production, particularly using Escherichia coli. To improve protein production in Escherichia coli there are a number of different parameters to consider. Two very important parameters in the process of protein production are transcription and translation. To study the influence of differences in transcription rate, target proteins with different characteristics were produced under control of three promoters of different strength (lacUV5, trc and T7). Analyzing the total amount of target protein as well as the amount of soluble protein demonstrated the benefits of using a strong promoter such as T7. However, protein production is also highly dependent on translational efficiency, and a drawback associated with the use of Escherichia coli as host strain is that codons rarely used in this host can have a negative effect on the translation. The influence of using a strain supplied with genes for rare codon tRNAs, such as Rosetta(DE3), instead of the standard host strain BL21(DE3), was therefore evaluated. By using Rosetta(DE3) an improved protein yield for many of the poorly produced proteins was achieved, but more importantly the protein purity was significantly increased for a majority of the proteins. For further understanding of the underlying causes of the positive effects of Rosetta(DE3), the improved purity was thoroughly studied. The cause of this improvement was explained by the fact that Rosetta(DE3) has a significantly better read through of the full sequence during translation and thereby less truncated versions of the full-length protein is formed.  Moreover, the effect of supplementation of rare tRNAs was shown to be highly dependent on the target gene sequence. Surprisingly, it was not the total number of rare codons that determined the benefit of using Rosetta(DE3), instead it was shown that rare arginine codons and to some extent also rare codon clusters had a much bigger impact on the final outcome. As a result of the increased interest in large-scale studies in the field of proteomics, the need for high-throughput protein production pipelines is greater than ever. For that purpose, a protein production pipeline that allows handling of nearly 300 different proteins per week was set up within the Swedish Human Protein Atlas project. This was achieved by major and minor changes to the original protocol including protein production, purification and analysis. By using this standard setup almost 300 different proteins can be produced weekly, with an overall success rate of 81%. To further improve the success rate it has been shown that by adding an initial screening step, prior high-throughput protein production, unnecessary protein production can be avoided. A plate based micro-scale screening protocol for parallel production and verification of 96 proteins was developed. In that, protein production was performed using the EnBase® cultivation technology followed by purification based on immobilized metal ion affinity chromatography. The protein products were finally verified using matrix-assisted laser desorption ionization time-of-flight MS. By using this method, proteins that will be poorly produced can be sorted out prior high-throughput protein production. / <p>QC 20131120</p>

There are two main purposes of this thesis. The first one is to get a better understanding of the aspects affecting customers’ loyalty in the telecommunication industry, in the context of when customers are using the services. The second purpose is to look into what the case company gains by having customers that are more loyal, where the degree of loyalty is measured by the Net Promoter Score metric. The methodology used to carry out the research is a case study with an approach that is both qualitative and quantitative. Where the quantitative approach has the largest share. Two datasets have been used in this thesis, one collected by the authors by sending out surveys and one collected beforehand at the case company. The survey created by the authors aim to let customers assess the satisfaction level with technical and non-technical aspects that can affect loyalty. The dataset that is already collected by the case company document the initial degree of loyalty of customers along with the revenue per customers over a period of years. The two datasets are used for the two different research purposes respectively. The statistical analysis for the data is conducted using the statistical tool Minitab. The findings for the first purpose are that our survey questions can be split into three categories using factor analysis. The categories are Perceived mobile multimedia quality, Perceived broadband multimedia quality and General perceptions. The first two categories are driving customer loyalty and the third category are indicators of customer loyalty. For the second purpose the findings are that the case company has different gains of more loyal customers depending on if the customers are either mobile or broadband customers. More loyal mobile customers stay longer as customers and also buy more. More loyal broadband customers only stay longer as customers. The practical implications of the findings are that the case company has to think of customer loyalty in new ways. There are more indicators of if a customer is loyal than the Net Promoter Score, these are for example customer satisfaction, perceived brand value, perceived overall quality, perceived customization etc. Therefore it would be better to measure customer loyalty not only with the Net Promoter Score Metric but to pick out 2-3 indicators to ask the customer and create an average index for all the questions that can represent the customers’ loyalty. Furthermore there are not a specific variable that drives customer loyalty more or less, several aspects are acting together in two high level groups. Another practical implication is that the gains of more loyal customers are higher for mobile customers since they buy more from the case company and stay longer as customers. However, for broadband customers, they only stay longer. Therefore the Net Promoter Score is not as useful to track for broadband customers. Either the broadband customers should have more opportunities to buy more or another metric should be used for broadband customers.

I takt med att allt mer antibiotika används och att världen blir allt mer globaliserad ökar och sprids antibiotikaresistensen. Djurhållningen i världen kantas av stressgivande miljöer som för små utrymmen och för många djur per yta. Det får djuren att drabbas av infektioner som vi botar med antibiotika. Antibiotika används även inom djurhållning i tillväxtfrämjande syfte och för att förebygga sjukdom och minska stress. Denna fel- och överbehandling av antibiotika i kombination med att vi använder samma sorts antibiotika inom human sjukvård som inom djurhållning gör att våra livsmedelsproducerande djur utgör en smittorisk för resistenta bakterier som hotar att nå oss via bland annat livsmedelskedjan. I och med att djuren medicineras via tillägg i foder och vatten och att upp till 90% av antibiotikan följer med fekalierna ut, sprids resistensen i naturen då stor del av fekalierna distribueras på jordbruksåkrar i fertiliserande syfte. Det ökar på spridningsrisken samt utgör ytterligare en risk för oss när vi äter grödorna. Från akvakulturer hamnar ungefär 80% av antibiotikan i det omgivande vattnet och i sedimentet och kan därifrån spridas till havets mikrober, vidare till fisk- och skaldjurspatogener och sedan till terrestra bakterier. Åtgärder till dessa problem innefattar att minska spridningen och förhindra uppkomsten av resistenta bakterier. Man bör forska fram fler antibiotika exklusivt för en sektor, i första hand vaccinera och när man måste använda antibiotika bör det vara en smalspektrumsvariant. Man måste också förbättra den globala djurhållningsstandarden, så att risken för spridning minskar vid resor och handel. Det krävs också ett ökat kunskapsläge och ett gemensamt internationellt samarbete för minskad och mer restriktiv antibiotikaanvändning. / As more antibiotics are being used in the world, and as the world gets more globalized, antibiotic resistance is a problem that is growing and spreading. Animal husbandry all over the world provides animals with stressful environments such as too small spaces and too many animals per area. The stress makes the animals suffer from infections that we cure with antibiotics. Antibiotics are also used in animal husbandry as a growth promoter and to prevent illness and decrease stress. This mis- and overuse of antibiotics and the fact that we are using the same type of antibiotics for human health care as well as for animal husbandry, makes our livestock a threat - we can get infected with antibiotic resistant bacteria through the food chain. As a result of us medicating the animals by putting antibiotics in their feed and water (where up to 90% of the antibiotics ends up in the faeces), the resistance is spread in nature, since the faeces often are used as fertilizers in agriculture. This increases the risk of spreading and is another threat for us when we eat the crops from the fields. From aquacultures about 80% of the antibiotics ends up in the nearby water and sediment and can spread through the microbes of the ocean, via fish and shellfish pathogens to terrestrial bacteria. Measuring steps includes decreasing the spread and preventing the rise of resistant bacteria. More research is needed to find new antibiotics, that should be used exclusively for one sector. We should also vaccinate more and when antibiotics are needed, use narrow spectrum antibiotics. Another step is to improve the global animal husbandry standards, so the risk for spreading decreases when travelling and importing/exporting. More education and international teamwork for reduced and more strict antibiotic usage is also needed.

DNA methylation is an epigenetic modification in which a methyl group is covalently added to the DNA. In vertebrate genomes methylation occurs almost exclusively at cytosines immediately followed by a guanine (CpG dinucleotides). Two important aspects of DNA methylation have inspired several recent scientific investigations including those in this dissertation. First, methylated cytosines are hotspots of point mutation due to a methylation-dependent mutation mechanism, which has caused a deficiency of CpGs in vertebrate genomes. Second, DNA methylation in promoters is linked with transcriptional silencing of the associated genes. This dissertation presents the results of four studies in which I investigated the impacts of DNA methylation on the neutral and functional evolution of vertebrate genomes. The results of the first two studies demonstrate that DNA methylation has profound impacts on both inter- and intra-genomic neutral substitution rate variation. The third and fourth studies demonstrate that DNA methylation has played critical roles in shaping the evolution of vertebrate promoters and gene regulation.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第23914号 / 工博第5001号 / 新制||工||1781(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 阿部 竜, 教授 安部 武志, 教授 作花 哲夫 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Dunaliella, a genus of unicellular, biflagellate green algae, is one of the most studied microalgae for mass culture and is of commercial importance as a source of natural -carotene. Dunaliella species have the desirable properties of halotolerance and photoautotrophy that makes their large-scale culture simple and cheap using resources unsuitable for conventional agriculture. The ease and cost-effectiveness of culture makes Dunaliella a desirable target for increased production of natural compounds by metabolic engineering or for exploitation as biological factories for the synthesis of novel high-value compounds. However, the lack of efficient genetic transformation systems has been a major limitation in the manipulation of these microalgae. In chapter four we describe the development of a nuclear transformation system for Dunaliella tertiolecta. The gene encoding the phleomycin-binding protein from Streptoalloteichus hindustanus, was chosen as the selectable marker as this protein retains activity at high salt concentrations. To drive expression of the chosen selectable marker, two highly expressed Dunaliella tertiolecta RbcS genes and their associated 5' and 3' regulatory regions were isolated and characterised (chapter three). Dunaliella transformation cassettes containing the RbcS promoter and terminator regions flanking the ble antibiotic resistance gene were constructed. These expression cassettes were tested in Chlamydomonas reinhardtii cells and found to drive expression of the ble gene in this heterologous system. This study also demonstrated that truncation of both the D. tertiolecta RbcS1 and RbcS2 regulatory regions significantly increases the expression of the ble gene in C. reinhardtii cells. To determine if the foreign DNA could stably integrate into the Dunaliella genome, four transformation methods: microprojectile bombardment, glass bead-mediated transformation, PEG-mediated transformation and electroporation were tested and a number of parameters varied. Southern blot analysis revealed that the plasmid DNA transiently entered the Dunaliella cells following electroporation but was rapidly degraded. Following electroporation, one stably transformed Dunaliella line was recovered. This is the first demonstration of the stable transformation of this alga. Chloroplast transformation is becoming a favoured method for the production of recombinant proteins in plants, as levels of heterologous protein are often higher than those achieved by transforming the nucleus. The Dunaliella chloroplast genome has not been genetically characterised, and thus there were no existing promoter and terminator sequences or sequences of intergenic regions that could be used for vectors in transformation of the chloroplast. Therefore, this study aimed to isolate and characterise promoters of highly expressed genes and matching terminators capable of driving transgene expression, and also to characterise intergenic regions that would be suitable insertion sites for the vector construct (chapter five). The complete gene sequence of two highly expressed Dunaliella chloroplast genes psbB and rbcL including the promoter and terminator regions as well as the coding sequence of the psbA gene were cloned and sequenced. In addition, the psbA gene is useful as a selectable marker as introduced mutations confer resistance to the herbicide 3-(3,4-Dichlorophenyl)-1,1-Dimethylurea (DCMU). Two homologous transformation constructs based on mutated psbA genes were developed and tested using microprojectile bombardment. A number of parameters were tested including: the size of the gold microprojectile particle, the distance of the plates from the point of discharge, plating onto membranes or filter paper, helium pressure, addition of an osmoticum to the medium and recovery time. Although no chloroplast transformants were recovered in this study, these homologous recombination constructs should prove useful in the development of a chloroplast transformation protocol. The other major component of this study was to investigate the use of microalgae as an expression system for the production of recombinant proteins. Transformation of Chlamydomonas reinhardtii, a species related to Dunaliella, is well developed. In chapter six, this study examined the expression of two human proteins, -lactalbumin and IGF-1 in Chlamydomonas reinhardtii. Plasmids containing the C. reinhardtii RbcS2 promoter upstream of the cDNAs of these two proteins were introduced into C. reinhardtii cells using glass-bead mediated transformation. Transgenic C. reinhardtii lines were generated and shown to contain the transgenes by PCR and Southern hybridisation. RT- PCR and northern hybridisation were subsequently used to demonstrate that the transgenes were transcriptionally active. The transcripts however, could only be detected by RT-PCR indicating that the genes were transcribed at low levels. Accumulation of the -lactalbumin protein could not be demonstrated, suggesting that although the transgenes were transcribed, they were either not translated or translated at levels below the sensitivity of western blot analysis or that any protein produced was rapidly degraded. Previous studies have indicated that in microalgae codon usage is vital in translation of the foreign protein. Codon modification of the IGF-I and -lactalbumin genes should lead to higher levels of protein accumulation. This study reports the first successful stable nuclear transformation of Dunaliella tertiolecta. Therefore it is now feasible that Dunaliella can be examined as a bioreactor for the expression of recombinant proteins. In addition, two chloroplast genes (psbB and rbcL) and their corresponding promoters and terminators have been characterised and a selectable marker cassette based on the mutated psbA gene constructed.