Previous studies emphasize the importance of the company's competitive advantages and what is required to achieve them. What seems to be the basis for being able to compete is to constantly exceed customer expectations, which is achieved when companies are working on continuous improvement. This thesis aims to implant a model that contributes to continuous improvement by locating errors within the process, which can clarify where and what kind of maintenance is needed and thereby in a cost effective way improve the process, ensure quality and achieve customer requirements. The model is based on the PDCA model, which will consist of seven steps between P and D, in these seven steps a MFD matrix and Decision Matrix is also included. In order to increase the reliability of the model it has been tested on a case company, which provides basis for the result's outcome. The author's findings and conclusions show that the model fulfills its purpose, however, the model dependent on previous documentation and require some prior knowledge and time to implement. / Tidigare studier poängterar vikten av företags konkurrensfördelar och vad som krävs för att dem uppnå dem. Det som tycks ligga till grund för att kunna konkurera är att ständigt överträffar kundernas förväntningar, vilket åstadkoms genom att företaget jobbar med ett ständigt förbättringsarbete. Detta examensarbete har till syfte att implementera en modell som bidrar till ett ständigt förbättringsarbete genom att lokalisera fel i processen, vilket kan tydliggöra var och vilken typ av underhåll som behövs och där igenom på ett kostnadseffektivt sätt förbättra processen, säkerställa kvalitet och därmed uppnå kundernas krav. Modellen bygger på PDCA där modellen kommer bestå av sju steg mellan P och D, i dessa sju steg är även med en MFD matris och en beslut matris inkluderats. I syfte att öka modellens tillförlitlighet har den testat på ett fallföretag, vilket ger grund för resultatets utfall. Författarens resultat och slutsatser visar på att modellen fyller sitt syfte dock är modellen beroende av tidigare dokumentation och kräver en viss förkunskap och tid för att kunna genomföra.

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The main objective of the thesis “Conceptual Product Development in Small Corporations” is by the use of a case study test the MFD™-method (Erixon G. , 1998) combined with PMM in a product development project. (Henceforth called MFD™/PMM-method). The MFD™/PMM-method used for documenting and controlling a product development project has since it was introduced been used in several industries and projects. The method has been proved to be a good way of working with the early stages of product development, however, there are almost only projects carried out on large industries which means that there are very few references to how the MFD™/PMM-method works in a small corporation. Therefore, was the case study in the thesis “Conceptual Product Development in Small Corporations” carried out in a small corporation to find out whether the MFD™/PMM-method also can be applied and used in such a corporation.The PMM was proposed in a paper presented at Delft University of Technology in Holland 1998 by the author and Gunnar Erixon. (See appended paper C: The chart of modular function deployment.) The title “The chart of modular function deployment” was later renamed as PMM, Product Management Map. (Sweden PreCAD AB, 2000). The PMM consists of a QFD-matrix linked to MIM (Module Indication Matrix) via a coupling matrix which makes it possible to make an unbroken chain from the customer domain to the designed product/modules. The PMM makes it easy to correct omissions made in creating new products and modules.In the thesis “Conceptual Product Development in Small Corporations” the universal MFD™/PMM-method has been adapted by the author to three models of product development; original-, evolutionary- and incremental development.The evolutionary adapted MFD™/PMM-method was tested as a case study at Atlings AB in the community Ockelbo. Atlings AB is a small corporation with a total number of 50 employees and an annual turnover of 9 million €. The product studied at the corporation was a steady rest for supporting long shafts in turning. The project team consisted of management director, a sales promoter, a production engineer, a design engineer and a workshop technician, the author as team leader and a colleague from Dalarna University as discussion partner. The project team has had six meetings.The project team managed to use MFD™ and to make a complete PMM of the studied product. There were no real problems occurring in the project work, on the contrary the team members worked very well in the group, having ideas how to improve the product. Instead, the challenge for a small company is how to work with the MFD™/PMM-method in the long run! If the MFD™/PMM-method is to be a useful tool for the company it needs to be used continuously and that requires financial and personnel resources. One way for the company to overcome the probable lack of recourses regarding capital and personnel is to establish a good cooperation with a regional university or a development centre.

The method of moment (MoM) [1] is a widely used method in electromagnetics to solve static and dynamic electromagnetic problems on varying geometries. However, in closely spaced geometries coupled with large aspect ratios, e.g. a large parallel plate capacitor with very small separation gap, the problem exhibits several challenges. Firstly, the close proximity of the field and source elements presents problems with convergence in numerical evaluations of the interactions between them. Secondly, the aspect ratio of the geometry gives an approximation whereby to far field points, the source contributions from locations that are far apart appear to cancel each other. This leads to high condition numbers in the system matrix. This thesis explores the potential solution to these problems as well as the application of modular fast and direct (MFD) [2] solver to expedite the solution of such problems.

Detta projekt utfördes som examensarbete för högskoleingenjörsexamen i innovationsteknik och design, 22,5 högskolepoäng, vid Karlstads universitet. Som uppdragsgivare stod Reminiscor AB. Uppkomsten av projektet låg i en förfrågan från företaget att utveckla ett moduluppbyggt pedalbord för gitarrister.Det här produktutvecklingsprojektet genomfördes med användarkrav och användarönskemål i fokus för att definiera lämpliga funktioner för och utformning av ett modulbaserat pedalbord. Arbetet inleddes med att undersöka utbudet av olika typer av pedalbord och effektpedaler på marknaden. Intervjuer med gitarrister i olika åldrar och från olika genrer genomfördes för att skapa en uppfattning om gemensamma krav och önskemål som kunde ligga till grund för det fortsatta arbetet. Utifrån observation av pedalbordsanvändning och litteraturstudier ingick även ergonomiska avvägningar i utformningen av konceptet.Konceptet som projektet resulterade i togs fram bl.a. med hjälp av Modular Function Deployment-MFD, en metod för att finna lämplig modulindelning av produkter. Denna metod innefattar Quality Function Deployment-QFD, funktionsanalys, modulindikationsmatris-MIM, utvärdering och förbättring på modulnivå. Arbetet presenterar även hållfasthetsberäkningar och visualisering av det framtagna pedalbordskonceptet.Det framtagna konceptet består av sex olika moduler av två olika typer, främre och bakre. Dessa finns i sin tur i tre olika längder som kan kombineras och monteras samman för att utgöra pedalbord av olika storlek. Varje enskild modul är dessutom försedd med en funktion som gör att monteringsytan för pedaler kan ställas i olika inbördes vinklar. På så sätt möjliggör modulerna ett pedalbord med stora anpassningsmöjligheter för användaren. / This is a Degree Project for a Degree of Bachelor of Science in Innovation and Design Engineering, 22.5 ECTS Credits, at Karlstad university on assignment by Remiscor AB. The project originated in a request from Reminiscor AB to develop a modular pedalboard for guitarists.In order to define appropriate functions and design of a modular pedalboard, user requirements was the focus point of this product development project. The early stages of the project involved research on the range of different kinds of pedalboards and effects pedals offered on the market. Interviews with guitarists of different age and from different genres were carried out to give an understandingo f common demands and preferenses, to serve as a foundation for further work. From observation of pedalboard use and litterature studies, the design of the concept also included ergonomical considerations.One of the methods used to develop the concept that this project resulted in was Modular Function Deployment-MFD. This method helps defining an appropriate modular structure in a product. It involves Quality Function Deployment-QFD, function analysis, Module Indication Matrix-MIM, evaluation and improvement on a modular level. This work also present calculations on Solid Mechanics and visualisation of the developed pedalboard concept.The presented concept consists of six different modules divided into two types, front and back. Each of these include three different lengths that can be combined to constitute pedalboards of different sizes. Each individual module contain a function to enable different angle settings of the pedal mounting surface, independent of adjacent modules. With these properties, the modules make a pedalboard with considerable customization options for the user possible.

The City of Cape Town is the most congested city in South Africa, with Johannesburg coming in second. Capetonians are spending 75% more time in traffic because of the congestion during peak hours, thus reducing time spent on leisure and other activities. Due to population growth, increasing car ownership and declining capacity of rail infrastructure, Cape Town's road infrastructure will continue to be under severe pressure if the status quo is maintained. Research shows that congestion levels in urban areas are key factors in determining the effectiveness and productivity of the transport system. Traffic congestion poses a threat to the economy and the environment. Increasing corridors' capacity by increasing the number of lanes does not necessarily solve the problem. Effective urban traffic management and efficient utilization of existing infrastructure are critical in creating sustainable solutions to congestion problems. To achieve this, it is important that appropriate urban-scale models and monitoring strategies are put in place. Effective traffic management and monitoring strategies require accurate characterization of the traffic state of an urban-scale network. Several approaches, including kinetic wave theory and cell transmission models or macroscopic traffic simulation models, have been proposed and developed to describe the traffic state of an urban-scale network. However, these approaches are limited and require significant amounts of computational time and effort. The application of macroscopic fundamental diagram (herein referred to as MFD) to characterize the state of an urban-scale network has thus far proven to be more effective than other approaches. MFD represents the state of urban traffic by defining the traffic throughput of an area at given traffic densities. It describes the characteristics and dynamics of urban-scale traffic conditions, allowing for improved and sustainable urban scale traffic management and monitoring strategies. Against this backdrop, the existence of MFD for the City of Cape Town (CoCT) urbanscale network is yet to be established and the implications yet to be understood, as in other parts of the world. The main aim of this research was, therefore, to empirically estimate the macroscopic fundamental diagram for the CoCT's freeway network and analyse its observed features. To achieve this, observed data of 5 minutes periods for the month of May 2019 was used to estimate the MFD. The results confirmed that when the chaotic scatter-plots of flow and density from individual fixed loop detectors were aggregated the scatter nearly disappeared and points grouped neatly to form a clearly defined free-flow state, critical state and the formation of hysteresis loops past the critical density corresponding with the network observed maximum flow. Further analysis of the MFDs showed that a single hysteresis loop always forms past the critical density during the evening peak in a weekday MFD. However, it was inconclusive during the morning peak period in weekday MFDs. Lastly, an explicit hysteresis loop seldom appears in a Saturday MFD when the peak of traffic demand is lower than on weekdays. In order to understand the dynamics of the congestion spread, the freeway network was partitioned into penetrating highways network and the ring highway network. The results showed that the maximum flows observed for the two sub-networks were significantly different (943 veh/hr/lane for the penetrating highways network and 1539 veh/hr/lane for the ring highway network). The penetrating highways network's MFD indicated the presence of congestion in the network whereas the ring highway network indicated only the free-flow state (no indication of congestion) during peak periods. The congestion seen on the penetrating highways network was found not to be sufficiently spread on those highways. On the 24th May, congestion on the penetrating highway network was observed during both the morning and evening peak periods, whereas on the 31st May congestion was observed mainly during the evening peak period, with hysteresis-like shape. These observations confirmed that congestion during peak periods is not homogenously spread across the entire network, certain areas are more congested than others, hence the observed formation of hysteresis loops and slight scatters. Lastly, the hysteresis loops observed in the penetrating highways network's MFD was further characterized in terms of their shape and size. First, the results showed that the slight scatter and hysteresis patterns observed in penetrating highways network MFD's vary in size and shape across different days. The shapes of the hysteresis loops observed during both the morning and evening peak periods, were type H2 hysteresis loops, signifying a stable recovery of the network with the average network flow remaining unchanged as average network density decreases during the recovery. Characterization of the size of the observed hysteresis loops showed that the drop of the hysteresis (an indicator of network level of instability during recovery phase) was smaller, signifying a more stable network traffic and homogenous distribution of congestion during the recovery phase.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21618号 / 医博第4424号 / 新制||医||1033(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 大森 孝一, 教授 松田 秀一, 教授 安達 泰治 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Cells dedicate tremendous amounts of energy to express essential genes for survival. During transcription, RNA polymerase (RNAP) actively scans the template strand of DNA, stalling when it meets DNA damages. Stalled RNAP prevents repair by the nucleotide excision repair pathway (NER); a sub-pathway of NER named transcription-coupled repair (TCR) resolve this problem by removing RNAP and recruiting repair proteins. In Escherichia coli, a TCR protein named “Mutation Frequency Decline” (Mfd) couples removal of RNAP through its motor activity with recruitment of the NER repair proteins. Mfd can be divided into two functional halves; the N-terminal region (MfdN, domains 1-3) is essential for NER protein recruitment, and the C-terminal region (MfdC, domains 4-7) is responsible for RNAP-interaction and motor activity. Data suggest Mfd undergoes large conformational movement to activate RNAP removal and repair protein recruitment. To study the activation mechanism of Mfd, we created several full-length “hyperactive” mutants by perturbing interactions between MfdN and MfdC. In all mutants, residue 79 in domain 1 is changed from aspartic acid to arginine (D79R), disrupting a key salt bridge interaction with arginine 804 in domain 6. The linker connecting MfdN and MfdC was made cleavable to allow separation of MfdN and MfdC, which enable us to study activities in equal molar concentration. We have studied the effect of the D79R mutation in vivo (cytotoxicity and UV sensitivity) and in vitro (enzyme activity and thermal stability), and demonstrate that this single residues change render the enzyme “hyperactive”. This confirms our model of activation: activation of Mfd results from breaking communication between MfdN and MfdC

For over a century, the railway system has been gradually designed and adapted to serve the corresponding demands under variations of given budgets. However, recent developments indicate that the railway systems of many European countries gradually come to their limits, as the national infrastructure managers declare an increasing share of their network tracks as congested. Consequently, the capabilities of each railway system are getting more into focus, to adequately serve the recent intention of shifting more demand to rail to encounter climate change. The system’s capacity is thereby of particular interest, i. e. whether the system already has the ability to serve increasing traffic loads by leveraging existing reserves, or otherwise needs significant extensions to serve the increasing demand. We thus need to quantify the current capacity of the railway system to identify its current capabilities and to deduct corresponding measures to leverage capacity reserves and relieve saturated network parts. Only the appropriate measure selection, i.e. deciding where to apply traffic reorganization and optimization or infrastructural extensions and restructuring, allows to achieve the goal of shifting more demand to rail under limited resource constraints. The main contributions of this thesis are in the design, optimization and application of a network capacity assessment approach for large-scale railway networks, which incorporates the perspectives of infrastructure, operations and demand by using the number of trains per time window and scheduled waiting times as capacity metric. Hence, this thesis provides a new definition of network capacity, and develops petri net (PN)-based capacity assessment models for railway networks with the use of mixed integer program (MIP) and row generation. The capacity is then determined by assessing the maximum utilization and the scheduled waiting times of the railway network with respect to infrastructure, railway operations and demand. We first introduce the definition of railway network capacity, which extends the concept of railway capacity from stations and corridors to entire networks. This new utilization-based and demand-centric definition of practical railway network capacity defines railway network capacity as the maximum number of departing trains in the network over a given time period, regarding the given infrastructure, operations and demand. This definition allows to accurately determine the interplay of infrastructure, operations and demand, with a combined measure of traffic flow and scheduled waiting times. In the context of this new definition on network capacity, different assessment approaches for the capacity of railway stations, corridors and networks are reviewed with regard to their spatial scope, the used approach and the applied capacity metric. Second we propose the railway network utilization model (RNUM), which extends an existing PN based approach from single line to entire network operations. This model builds upon individual lines, which are then connected to more complex structures. The analysis of the maximum utilization is based on the network’s elementary circuits. Furthermore, token modifications are introduced to characterize relevant process circuits and introduce interline separation places to model and assess complex networks. By additionally considering rolling stock circulations and imposed train orders, the utilization is determined for given operation scenarios of a line system, which operates at heterogeneous frequencies. The resulting timetable independent approach allows to fully characterize the utilization of the network. To assess the network capacity, an enumeration-based railway network capacity (RNC) framework is further introduced, which evaluates the maximum utilization over diverse operation scenarios to represent possible network demands. The resulting train flows as well as the average scheduled waiting times per train, the capacity and the corresponding network effects were finally quantified and determined in network-specific macroscopic fundamental diagram for the railway network (MFD-R). Third, we introduce the railway network utilization MIP model (MIP-RNUM) to determine the optimal capacity utilization by combining PNs with mathematical linear programming. The presented model is enabled to simultaneously assess different train locations and line orders to provide the network’s utilization, capacity-optimal train locations and line orders for given operation scenarios. The MIP-RNUM is further improved to provide the demand-centered capacity utilization, by incorporating extended demand structures, which capture the demanded flows and magnitudes as fixed proportions of trains per line. The additional incorporation of local routing and thus optimal line orders in the utilization assessment, extend the model further to provide the optimal and demand-centered capacity utilization without the correspondingly required enumeration of different line orders. The resulting fully extended MIP-RNUM comprehensively captures the interplay of infrastructure, railway operations and demand; and the resulting effects on the network capacity. Fourth, we propose the row generation MIP-RNUM (MIP-RNUM-RG) to assess the capacity of large-scale instances. The proposed approach tackles the computationally intensive enumeration of the network’s cycles of the RNUM by applying lazy-constraint generation i.e. iteratively adding violated constraints of previous solutions to the problem in a row generating manner. To assess the solution quality of intermediate solutions during the capacity assessment of large instances, a lower-bound method is presented, which combines a higher order max-plus system and a binary search algorithm. The lower-bound method allows to check the feasibility of a given solution and to quantify the optimality gap of the current results while solving the MIP-RNUM-RG. In summary, this thesis provides multiple scientific contributions to efficiently assess the capacity of complex railway networks by developing several assessment models and frameworks. By integrating the different perspectives of infrastructure, operations and demand, this thesis supports network design towards the development of demand-centric railway systems. Regarding the intended growth of the railway demand in the near future, this thesis can guide practitioners to assess the capabilities of our present railway systems and derive the necessary actions to transform them into the transport systems of our future. / Das Eisenbahnsystem wurde über ein Jahrhundert lang entworfen und angepasst, um die jeweilige Nachfrage unter einem sich verändernden Budget zu bedienen. Aktuelle Entwicklungen zeigen jedoch, dass die Eisenbahnsysteme vieler europäischer Länder allmählich an ihre Grenzen stoßen. Zeitgleich geraten die Fähigkeiten eines jeden Eisenbahnsystems in den Fokus, mit denen zur Begegnung des Klimawandels mehr Verkehr auf die Schiene verlagert werden kann. Die Systemkapazität ist dabei von besonderem Interesse, d. h. ob das System bereits in der Lage ist, wachsende Verkehrsmengen durch die Nutzung existierender Reserven zu bewältigen, oder ob es zur Bedienung der steigenden Nachfrage einen deutlichen Ausbau braucht. Aus diesem Grund muss die Kapazität des Eisenbahnsystems bewertet werden, um damit seine aktuellen Möglichkeiten zu identifizieren und durch entsprechend abgeleitete Maßnahmen Kapazitätsreserven nutzbar zu machen und saturierte Netzteile zu entlasten. Der wesentliche Beitrag dieser Arbeit liegt im Entwurf, der Erweiterung und Anwendung eines Ansatzes zur Untersuchung der Netzwerkkapazität für großräumige Eisenbahnnetze unter Einbeziehung der Einflussfaktoren Infrastruktur, Betrieb und Nachfrage. Als Kapazitätsmetrik kommen dabei die Zugzahlen pro Zeiteinheit und die planmäßigen Wartezeiten zum Einsatz. Diese Arbeit entwirft dafür eine neue Definition der Netzwerkkapazität und entwickelt anschließend Petri-Netz (PN) basierte Untersuchungsmodelle für die Eisenbahnnetzkapazität unter Nutzung von gemischt-ganzzahliger Programmierung und Zeilengenerierung (eng. row generation). Durch die Analyse der maximalen Kapazitätsausnutzung und der planmäßigen Wartezeiten im Netz wird die Kapazität unter Berücksichtigung der Einflussfaktoren bestimmt. Zuerst wird die Definition der Eisenbahnnetzwerkkapazität eingeführt, die das Konzept der Eisenbahnkapazität von Bahnhöfen und Streckenkorridoren auf Netzwerke erweitert. Diese neue, auf Kapazitätsausnutzung basierende, nachfragezentrierte Definition der praktischen Eisenbahnnetzwerkkapazität definiert die Netzkapazität als die maximale Anzahl der im Netzwerk abfahrenden Züge innerhalb eines gegebenen Zeitintervalls, unter Berücksichtigung der gegebenen Einflussfaktoren. Im Kontext dieser neuen Definition werden verschiedene, existierende Untersuchungsansätze für die Kapazität von Eisenbahnknoten, Streckenkorridoren und Netzwerken rezensiert. Die Ansätze werden insbesondere hinsichtlich ihres räumlichen Umfangs, des angewendeten Verfahrens und der jeweils genutzten Kapazitätsmetrik verglichen. Als Zweites wird das Eisenbahnnetzwerkausnutzungsmodell (eng. railway network utilization model – RNUM) präsentiert, das einen existierenden PN-Ansatz von einer einzelnen Linie auf Netzwerke erweitert. Dieses Modell setzt sich aus einzelnen Linien zusammen, die zu komplexeren Strukturen zusammengesetzt werden. Die Analyse der maximalen Kapazitätsausnutzung basiert auf den Elementarkreisen des entstehenden Netzwerks. Durch die zusätzliche Berücksichtigung von Fahrzeugumläufen und vorgegebenen Zugfolgen wird die Kapazitätsausnutzung für gegebene Betriebsszenarien eines Liniensystems bestimmt, in welchem die Linien mit heterogenen Taktzeiten verkehren. Der resultierende, fahrplanunabhängige Ansatz erlaubt die vollständige Charakterisierung der maximalen Kapazitätsausnutzung unter Berücksichtigung diverser Betriebsszenarien. Die resultierenden Zugverkehrsströme und die mittleren planmäßigen Wartezeiten pro Zug, die ermittelte Kapazität und die zugehörigen Netzwerkeffekte werden schließlich in einem netzwerkspezifischen makroskopischen Fundamentaldiagram für Eisenbahnnetzwerke (MFD-R) bestimmt. Als Drittes wird das Eisenbahnnetzwerkausnutzungs-MIP-modell (MIP-RNUM) eingeführt, um die optimale Kapazitätsausnutzung durch eine Kombination von PN und linearer Programmierung zu bestimmen. Das eingeführte Modell kann simultan verschiedene Zugpositionen und Zugfolgen berücksichtigen, um auf deren Grundlage die Netzwerkausnutzung, kapazitätsoptimale Zugpositionen und -folgen für gegebene Betriebsszenarien zu untersuchen. Im Folgenden wird das MIP-RNUM erweitert, um die nachfragezentrierte Kapazitätsausnutzung zu erfassen. Die zusätzliche Berücksichtigung von variablen Fahrwegen in Knoten und den zugehörigen optimalen Zugfolgen in der Ausnutzungsuntersuchung ergänzen das Modell zusätzlich, um die optimale und nachfragezentrierte Kapazitätsausnutzung ohne die bisher benötigte Enumeration der Zugfolgen zu ermitteln. Das resultierende erweiterte MIP-RNUM erfasst das Zusammenspiel von Infrastruktur, Eisenbahnbetrieb und Nachfrage und deren umfassende Auswirkungen auf die Netzwerkkapazität. Zuletzt wird das zeilengenerierende MIP-RNUM (MIP-RNUM-RG) vorgestellt, um auch die Kapazität großräumiger Instanzen untersuchen zu können. Der vorgestellte Ansatz begegnet der rechenzeitintensiven Enumeration der Elementarkreise des RNUM mit einer sog. lazy constraint generation, d. h. der iterativen, zeilengenerierenden Ergänzung verletzter Nebenbedingungen zum Problem. Um bei der Untersuchung großräumiger Instanzen die Lösungsqualität der jeweiligen Zwischenergebnisse beurteilen zu können, wird eine untere Schranke vorgestellt, die ein max-plus System höherer Ordnung mit einem binären Suchalgorithmus kombiniert. Diese untere Schranke ermöglicht die Zulässigkeitsprüfung einer gegebenen Lösung und darüber hinaus die Quantifizierung der Optimalitätslücke der aktuellen Ergebnisse. Damit stellt diese Arbeit verschiedene wissenschaftliche Beiträge in Form unterschiedlicher Untersuchungsmodelle und -methoden bereit, um die Kapazität komplexer Eisenbahnnetzwerke zu untersuchen. Dabei werden die verschiedenen infrastrukturellen, betrieblichen und nachfragespezifischen Perspektiven integriert betrachtet, um die nachfragezentrierte Netzentwicklung von Eisenbahnsystemen zu unterstützen. Unter Berücksichtigung des Wachstums der Eisenbahnnachfrage in naher Zukunft kann diese Arbeit so Planer*innen helfen, die Fähigkeiten unserer gegenwärtigen Eisenbahnsysteme zu untersuchen und daraus die nötigen Handlungsalternativen abzuleiten, um die Verkehrssysteme unserer Zukunft zu entwickeln.

Introduction Nucleotide excision repair (NER) is a highly conserved pathway involved in repair of a wide variety of structurally unrelated DNA lesions. One of the well characterized NER systems is from E. coli which involves UvrABC nucleases. NER consists of two related sub-pathways: global genomic repair (GGR), which removes lesions from the overall genome, and transcription coupled repair (TCR), which removes lesions from the transcribed strand of active genes. Bulky DNA lesions such as cyclobutane pyrimidine photodimers (CPD) induced by UV irradiation block RNA polymerase (RNAP) during transcription. In bacteria, a gene product of mfd called transcription repair coupling factor (TRCF) or Mfd is required for TCR. Bacterial Mfd interacts with the stalled RNAP, displaces it from the DNA and recruits NER proteins at the site of damage. Mfd, thus contributes to the faster repair of the transcribed strand compared to the non-transcribed strand for similar kind of lesions. Intracellular pathogens like M. tuberculosis are constantly exposed to a variety of stress conditions inside the host, mainly due to host defense systems and antibiotic treatments. It is therefore, extremely important for bacteria to have DNA damage repair and reversal mechanisms that can efficiently counteract these effects. However, very little is known about DNA repair systems in M. tuberculosis compared to other bacteria. Sequencing of M. tuberculosis genome revealed the presence of NER associated genes including a putative mfd. Additionally, due to the high GC content of genome as well as the DNA damage prone host environment, the transcription in M. tuberculosis may encounter the problems, which are not apparent in other bacteria. Therefore, the gene like mfd may play very important role in physiology of M. tuberculosis. In the present study, we describe the biochemical and functional characterization of Mfd from M. tuberculosis (MtbMfd) and discuss its unusual properties. Biochemical characterization of MtbMfd Genome analysis of M. tuberculosis as well as the sequence alignment studies revealed that MtbMfd is 1234 amino acids long multifunctional protein having various domains specialized for different functions. Cloning of Mtbmfd was carried out by reconstructing the full length gene from three PCR amplified fragments using genomic DNA as a template. Complementation study using Mtbmfd suggested that the gene of interest complements E. coli counterpart and increases survival of UV irradiated cells. To further characterize the function of Mtbmfd, a road block reporter assay was performed, which indicates that the MtbMfd interacts with stalled E. coli RNAP and displaces it from the site of transcription resulting in low reporter gene activity. The MtbMfd protein was expressed and purified by using various chromatographic techniques, and confirmed by mass spectrometry. In addition to full length protein, a number of truncated MtbMfd constructs were generated and purified to homogeneity. Mfd is a motor protein and requires ATP hydrolysis in order to translocate along DNA. The signature motifs of superfamily 2 helicases / ATPases are present at the C-terminal of Mfd along with translocase motif which is highly homologous to motif present in RecG helicase. To analyze the kinetics of ATP hydrolysis of MtbMfd and its truncated proteins, ATPase reactions were carried out using γ32P-ATP as a tracer. Wild-type MtbMfd exhibited ATPase activity, which was stimulated ~1.5 fold in presence of dsDNA. The mutant MtbMfd (D778A), which harbors mutation in one of the key residues of Walker B motif of the ATPase domain showed negligible ATPase activity indicating the importance of residue D778 for ATP hydrolysis. While the C-terminal domain (CTD) comprising amino acids 600 to 1234 showed elevated ATPase activity, the N-terminal domain (NTD) containing the first 500 amino acid residues was able to bind ATP but deficient in hydrolysis. Deletion of 184 amino acids from the C-terminal end of MtbMfd (MfdΔC) increased the ATPase activity by ~10-fold compared to full-length MtbMfd. The translocase activity of MtbMfd was measured by an oligonucleotide displacement assay and it was found that full length MtbMfd and CTD have a very weak translocase activity whereas, MfdΔC exhibited efficient translocation along DNA in ATP dependent manner. These results provide a direct correlation between translocase and ATPase activity of MtbMfd, and suggest possibly an auto-regulatory function for the extreme C-terminus of MtbMfd. Oligomeric status of MtbMfd was determined using various techniques including gel filtration chromatography and it was found that MtbMfd exists as monomer and hexamer in solution. The monomer showed increased ATPase activity and susceptibility to proteases compared to the hexameric form. MfdΔC, on the other hand, was predominantly monomer in solution implicating importance of the extreme C-terminal region in oligomerization of protein. Taken together, the biochemical evidence suggests that monomeric MtbMfd is an active form and oligomerization provides stability to the protein. One important finding of the present study is the binding of ATP to NTD of MtbMfd. All Mfd NTDs resemble UvrB and possesses the degenerate ATPase motifs. Indeed, on the basis of sequence and structural similarities, it has been suggested that Mfds have evolved from UvrB incorporating an additional translocase activity. UvrB has a cryptic ATPase activity while the NTD of Mfd may have lost the activity as it possesses degenerate Walker motifs. In contrast, NTD of MtbMfd binds ATP but is hydrolysis deficient. A closer comparison of the amino acid sequences in the Walker A motif reveal that conserved K 45 of UvrB has been replaced by R in case of NTD of MtbMfd. It has been shown previously that mutation of K 45 to A, D and R led to a loss of ATPase activity of UvrB. Thus, MtbMfd seems to be a natural mutant of UvrB. Since NTD harbors an intact UvrA interacting domain, when it is expressed it may sequester the cellular pool of UvrA leading to dominant negative phenotype. When UV survival assays were carried out, cells expressing NTD showed hyper-sensitivity to UV light – a typical characteristic of NER deficiency. In addition, in vitro NER assay clearly suggested that NTD sequesters pool of UvrA inside the cell and blocks both GGR and TCR which further affects the mutation frequency of bacterial cells. Influence of MtbMfd on elongation state of RNAP The movement of RNAP along the template during transcription elongation is not uniform and is interrupted due to various factors. To overcome transcription elongation interruptions, a number of proteins viz. Mfd, Gre and Nus act on RNAP and modify its activity. RNAP displacement and transcript release experiments showed that MtbMfd influenced the elongating RNAP by more than one way. MtbMfd displaced stalled RNAP, which was blocked by NTP starvation on T7A1 promoter based template in a concentration and time-dependent manner. RNAP displacement activity of MtbMfd was shown to depend on ATP or dATP hydrolysis. On the other hand nucleotides like ADP, GTP, CTP and ATPγS did not support the RNAP displacement activity. However, in presence of ATPγS, MtbMfd was able to bind stalled complex but unable to displace RNAP suggesting that ATP or dATP hydrolysis is important for MtbMfd function. On the other hand, MtbMfd did not affect initiating RNAP when σ factor was still bound suggesting that upstream DNA is necessary for Mfd function. To assay RNA or transcript release activity of MtbMfd after transcription complex disruption, immobilized transcription complex assay was carried out. Immobilized stalled complex was generated by UTP and CTP starvation on biotinylated T7A1 promoter based template which can be affixed to temporary pellet in presence of streptavidin beads. It was found that MtbMfd released RNA into a supernatant fraction in a concentration-dependent manner suggesting that MtbMfd releases transcript after ternary complex disruption. MtbMfd released transcript in an energy-dependent manner and both ATP and dATP supported the activity, which allows the complete separation of RNA release from RNA synthesis inside the cell. An ATPase mutant of MtbMfd (MfdD778A) failed to release transcript, which further supported that ATP hydrolysis is important for MtbMfd function. Since both Mfds and RNAPs are evolutionary conserved proteins, to analyze the effect of MtbMfd on other bacterial RNAPs, displacement and release assays were carried out. Stalled complexes were generated using EcoRNAP (E. coli), MsRNAP (M. smegmatis) and MtbRNAP (M. tuberculosis) on T7A1 promoter based template. It was observed that MtbMfd was able to displace all the three RNAPs from stalled elongation complex as well as released transcript with varying efficiency. MtbMfd showed optimal displacement and release activity in presence of mycobacterial RNAPs. Transcription elongation complexes adopt various conformations and exist as different isomerized states during elongation. In an active elongation complex the 3'-OH polymerizing end of transcript aligns with an active centre of the RNAP. However, one of the most common and intrinsic properties of RNAP is backtracking or reverse translocation, which leads to misalignment of 3'-OH polymerizing end from an active centre of the polymerase. It is of interest to know if backtracking affects MtbMfd function. It is likely that complexes blocked by lesions inside the cell might tend to backtrack, and different translocational isomers possibly have different sensitivities to MtbMfd action which may illuminate the overall mechanism of MtbMfd. Backtracking of RNAP was induced on +20 and +39 stalled complexes and the effect of MtbMfd was analyzed in presence of NTPs in the reaction. It was found that arrested or backtracked complexes were restored to the forward position by the activity of MtbMfd in presence of NTP resulting into productive elongation. These results suggest that arrested RNAP again resumes transcription if conditions are favorable; otherwise, MtbMfd further assists RNAP to dissociate which leads to release of transcript. Anti-backtracking activity of MtbMfd might have important function in cellular metabolism and it has been speculated that Mfd could play more general role during transcription apart from repair. To explore the role of MtbMfd as a transcription factor and effect of MtbMtb on transcription processes in the mycobacteria, a variety of T7A1 promoter based templates were generated. These templates were derived from genes of M. tuberculosis and E. coli having varying GC content (39-81 %). The rationale behind this experiment is that the high GC content of mycobacteria and the template derived from mycobacterial genes may pose as sequence dependent structural constraints and hence block the RNAP during transcription. By anti-backtracking activity of MtbMfd these paused complexes may get relieved, leading to efficient transcription by RNAP which may lead to the formation of more full length transcript. To analyze the effect of MtbMfd, purified templates of different GC content were incubated with RNAP and MtbMfd to carry out in vitro transcription. Although, in case of multiple rounds of transcription, multiple pauses were observed even in presence of MtbMfd. However, in presence MtbMfd around 1.5 - 2 fold increased full-length transcripts were observed suggesting that MtbMfd assisted RNAP during elongation to overcome sequence dependent pause. To avoid multiple pauses that are likely to occur due to the initiation of multiple round of transcription, and trailing effect of RNAP itself, single round of transcriptions were carried out in presence of heparin. Sequence specific pauses were observed with increasing GC percentage in template suggesting that indeed high GC content contributes to transcription pause. At the same time, MtbMfd in the reaction increased the amount of full length transcript by 1.5 - 2.0 fold probably by pushing paused RNAP forward to resume elongation. Taken together, this study investigates the biochemical properties of MtbMfd and its mechanism of action. In addition, it explores the importance of the coupling of transcription to repair in M. tuberculosis as well as the overall proof reading mechanism of transcription elongation in the GC rich genome of mycobacteria.