Mycobacterium tuberculosis has one ribosomal RNA operon. The survival of this bacillus thus depends on a transcription mechanism that can effectively couple gene expression to changes in the environment. σ factors are transcription proteins that bind to the RNA polymerase (RNAP) and dictate gene expression. Extra Cytoplasmic Function σ factors (ECF) are a subset of σ factors that coordinate environment-induced changes in transcription. The environment specific binding of ECF σ factors to the RNAP presents an effective mechanism for the bacillus to modulate gene expression. ECF σ factors, in turn, are regulated by their interaction with an anti-σ factor. The active σ factor is released from this complex upon specific cellular or environmental stimuli. The aim of this study was to understand the structural and mechanistic aspects of σ factor activation. Towards this goal, two ECF σ factors, σC and σL, were examined. Structural and biophysical studies on M. tuberculosis σC provided a novel insight into ECF σ factor regulation. Inter-domain interactions in σC were sufficient to occlude the DNA recognition regions even in the absence of an interacting protein. The structure of M. tuberculosis σL in complex with the anti-σ factor RslA provides a structural basis to rationalize the release of active σL under oxidative stress. The other chapters of this thesis include a description of the structure and biochemical features of a hypothetical protein Rv2704 that is co-transcribed with the primary σ factor σA. In an effort to understand the collaboration-competition-redundancy model of prokaryotic σ factors, we performed a computational analysis of this system compiling experimental data from the E. coli and B. subtilis model systems. These results are also presented in this thesis. Put together, the structural and biochemical characteristics of the σ factors presented in this thesis suggest substantial variations in the regulatory mechanisms of the M. tuberculosis σ factors when compared to the canonical E. coli or B. subtilis model systems. This thesis is organized as follows: Chapter 1: The introductory chapter of this thesis is organized to frame the pertinent mechanistic issues involved in the σ factor-regulatory protein interactions in the context of the underlying biology of M. tuberculosis. The first part of this chapter provides an overview of σ factors and a summary of the classification of these proteins and their roles in different prokaryotes. The latter part of this chapter is a summary of the pathogen M. tuberculosis in terms of its genetic composition, gene expression as well as aspects of virulence and pathogenecity. Chapter 2: This chapter describes the characterization of the ECF σ factor, σC. Here we report the structure of an ECF σ factor σC from M. tuberculosis. σC is essential for the lethality of M. tuberculosis in a mouse model of infection. Our studies suggest that M. tuberculosis σC differs from the canonical ECF σ factors as it has an N-terminal domain comprising of 126 amino acids that precedes the σC2 and σC4 domains. In an effort to understand the regulatory mechanism of this protein, the crystal structures of the σC2 and C4 domains of σC were determined. These promoter recognition domains are structurally similar to the corresponding domains of E. coli σA despite the low sequence similarity. Fluorescence experiments using the intrinsic tryptophan residues of σC2 as well as surface plasmon resonance measurements reveal that the σC2 and σC4 domains interact with each other. Mutational analysis suggests that the Pribnow box-binding region of σC2 is involved in this inter-domain interaction. Interactions between the promoter recognition domains in M. tuberculosis σC are thus likely to regulate the activity of this protein even in the absence of an anti-σ factor. Chapter 3 provides an account of the regulatory features of the ECF σ factor, σL. ECF σ factors are often regulated by their interactions with an anti-σ factor that can sense diverse environmental stimuli. Transcriptional responses to changes in the oxidation state are particularly important for M. tuberculosis as it adapts to the environment of the host alveoli and macrophages. Here we demonstrate that the protein RslA binds Zinc and can sequester σL in a reducing environment. Our data suggests that the cytosolic domain at the N-terminus of RslA alone is involved in binding σL. Under oxidizing conditions, the σL/RslA complex undergoes substantial conformational rearrangements that coincide with the release of the Zinc cofactor. In the absence of Zinc, the affinity of RslA for σL reduces by ca 8 fold compared to the holo form. The CXXC motif of RslA acts as a redox sensor. In response to oxidative stimuli, the proximal cysteines in this motif can form a disulfide bond with the release of the bound Zn2+ ion. This observation could be rationalized based on the crystal structure of the σL4/RslA complex. Put together, RslA is a distinct variant of the Zinc binding anti-σ factor (ZAS) family. The structural and biophysical parameters that control σL/RslA interactions demonstrate how variations in the rate of Zinc release and associated conformational changes in RslA could regulate the release of free σL in a measured response to oxidative stress. Chapter 4 is based on the biochemical and structural characterization of a hypothetical protein Rv2704. The gene for M. tuberculosis Rv2704 is located in the same operon as the principal σ factor σA. The biochemical and structural features of Rv2704 were thus examined to identify its role, if any, in the regulation of σA. This protein is a trimer in solution and adopts a chorismate mutase-like fold. The crystal structure reveals that Rv2704 is a member of the functionally diverse YjgF family of proteins. The important structural differences between Rv2704 and other YjgF proteins lie in the arrangement of secondary structural elements and the putative functional clefts between the subunit interface. Although Rv2704 does not interact with σA in vitro, the structural similarities to the YjgF family suggests that this protein could interact with a variety of metabolites, potentially influencing its function. Chapter 5 of this thesis is based on a computational analysis of σ factors. Four conformational segments of σ factors, referred to as σ1, σ2, σ3 and σ4 interact with specific regions of promoter DNA. ECF σ factors are a subset of σ factors that coordinate environment-induced transcription. ECF σ factors are minimalist σ factors with two DNA binding domains viz., σ2 and σ4 that recognize the –10 and –35 promoter elements and are unable to interact with either upstream-activating regions or the extended –10 element of the promoter. There are several ECF σ factors in a typical bacterium often characterized by substantial overlap in function. Here we present an analysis of B. subtilis ECF σ factors and their cognate promoters to understand functional overlap and redundancy in this class of proteins. As expected, conserved bases in the –10 element appear more critical for promoter selectivity than the –35 element. However, we note distinct conformational features in the –35 promoter interaction with the helix-turn-helix (HTH) motif when compared to a data-set of known HTH-DNA complexes. Furthermore, we note differences in –35 element interaction between σ factors that act alone and those that overlap in function. The σ factor promoter interactions were then examined vis-à-vis the estimated cellular concentration of these proteins and their affinity to bind the core RNAP. Put together, this analysis suggests that while the cellular protein concentration dictates the choice of an ECF σ factor to form a complex with the RNAP, conformational features of the –35 element serve to select potential collaborative members, a subset of which eventually initiate transcription. Collaborative arrangements and functional redundancy in ECF σ factors are thus possible within the limits placed by these two parameters. Chapter 6 is a summary of the work reported in this thesis and the conclusions that can be drawn based on these studies. The appendix section of this thesis comprises of technical details that were not included in the main text of this thesis. Appendix I describes the initial characterization of the M. tuberculosis σD/anti-σD complex. Appendix II provides the experimental protocols as well as some of the supplementary data to the work reported in Chapters 2-5 of this thesis.

The main purpose of this thesis is to research High-Order Sigma-Delta Analog-to-Digital converter for precision measurement, a PI compensator and a third-order Sigma-Delta modulator has been proposed based on a second-order Sigma-Delta modulator. In accordance with the analysis result of frequency domain and time domain of system, we use third-order model because of better response with auxiliary software to simulate and implement the system, then measure modulator output variance for input variation. This converter circuit demonstrates that it can achieve the requirements of precision and linearity which the measure instrument demands.

For the fractional-N frequency synthesizers using delta-sigma modulation (DSM) techniques, higher PLL bandwidth is highly desirable in order to achieve faster settling time. As the PLL bandwidth is increased, more quantization noises pass through the PLL so that the output phase noise performance is degraded. There is a tradeoff between phase-noise performance and PLL bandwidth. To improve the problem, the thesis studies the quantization noise cancellation technique. With this technique, the PLL bandwidth can be increased without the cost of degrading phase-noise performance. With the help of Agilent EEsof¡¦s ADS, the phase-noise performance of the studied fractional-N frequency synthesizers can be predicted. For demonstration, this research implements a 2.6 GHz fractional-N frequency synthesizer hybrid module, and compares the measured phase noises with and without the technique under considering various combinations of MASH DSM orders and PLL bandwidth. Another demonstration of this thesis is to design a PLL IC using TSMC 0.18 £gm CMOS process, and make a discussion on the testing performance of the PLL IC.

The Sigma-54 Promoter Database contains computationally predicted sigma-54 promoters from over 60 prokaryotic species. Organisms from all major phyla were analysed and results were made available online at http://www.sigma54.ca. This database is particularly unique due to its inclusion of intragenic regions, grouping of data by COG and COG category, and the ability to summarize results either by phylum or database-wide. ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and nonribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has over 200 gene clusters from over 185 compound families. It also features a unique sequence repository containing over 10,000 PKS/NRPS domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. This database will be a useful resource for members of the PKS/NRPS research community enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information.

In present day, digital signal processing (DSP) is a popular technology and widely used in many fields. There have increasing number of applications that need high resolution converters. Therefore, analog-to-digital converters play a major role in DSP, and a well-performed ADC will enhance the performance of a certain system. Different types of ADCs are available for various functions. Delta-sigma  converters are famous for high resolution. Dynamic parameters can be used to judge the performance of an ADC, this paper will focus on the critical parameters of spectrum analysis, which contains Signal-to-Noise-and-Distortion Ratio (SINAD), Effective Number of Bits (ENOB) and Spurious-free Dynamic Range (SFDR). The theory and test method of these critical parameters are proposed in this paper using the Evaluation Module and Matlab. The results we acquired from the Evaluation Module are SINAD=86.15dB, SFDR=109.2dB, ENOB=14.177bits; and the results we calculated from MATLAB are: SINAD=86.14dB, SFDR=108.8dB, ENOB=14bits.

Köpingsföretaget GETRAG All Wheel Drive AB utvecklar, tillverkar och levererar komponenter för drivteknik till personbilsindustrin. Genom projektet 580-9 planerar företaget att införa en monteringsbana för en nyutvecklad produkt. Till denna önskar företaget skapa en materialhantering som är kostnadseffektiv, lever upp till kundernas krav på hög kvalitet samt utesluter hantering av träemballage vid monteringsbanan. Syftet med examensarbetet är därför att ge förslag till en kostnadseffektiv materialhantering där emballage som avger restprodukter inte hanteras vid monteringsbanan. För att undersöka examensarbetets frågeställningar har vi utrett hur materialförsörjningen till banan bör skötas. Studien bygger främst på teorier om lean produktion och förpackningslogistik. Utredningen innefattar en analys av nuläget och ger förslag till förbättringar utifrån denna. Vidare har vi studerat effekterna av och kostnaderna för alternativ till trä- och kartongemballage samt gjort en kartläggning av marknaden för alternativa emballage. Resultatet av studien visar att för att skapa en effektiv materialhantering är det viktigt att eliminera de slöserier som finns i materialflödet, till exempel överproduktion, onödiga lager och onödiga transporter. För att skapa en jämn materialhantering bör mängden artiklar som fylls på vid banan motsvara förbrukningen under en bestämd tidsperiod, eller multiplar av denna period, för samtliga produkter. Vidare bör inte montörerna ansvara för påfyllnaden av artiklar vid monteringsbanan, detta bör istället skötas av en materialhanterare. Studien visar även att olika förpackningar bör användas för olika artiklar beroende på produktens egenskaper samt varifrån den levereras. Att utesluta trä- och kartongemballage medför kostnader som måste vägas mot kundernas krav. Om det är alltför kostsamt att leverantören skickar i emballage som inte avger damm eller flisor finns det möjlighet till en ompackning. Denna bör för det specifika projektet ske internt i form av en manuell dukning. Utifrån de slutsatser som dragits av arbetet är vår rekommendation att GETRAG All Wheel Drive AB bör arbeta för en mer kostnadseffektiv materialhantering genom lean produktion och sex sigma samt satsa mer på förpackningsutveckling. / GETRAG All Wheel Drive AB is situated in the city of Köping, Sweden. The company develops, manufactures and supplies transmission components for the auto¬motive industry. Through project 580-9 the company is planning an assembly line for a newly developed product. For this project GETRAG wants to create a materials handling that is cost efficient, lives up to the customer demands on high quality and excludes handling of wooden pallets near the assembly line. The purpose of this thesis is therefore to suggest a cost efficient materials handling where packaging materials that give off dust or splinters are not used near the assembly line. To examine the questions in the thesis a study on how the support of materials to the assembly line should be handled has been made. It is based on theories of lean production and packaging logistics. The study includes an analysis of today’s flow and gives suggestions for improvements. We have also evaluated the costs and effects of replacing wooden packaging with alternative packaging materials. In addition, a survey of the market for alternative packaging materials has been made. The results show that to create an efficient handling of materials it is important to eliminate waste like over production, unnecessary storage and unnecessary transportations. To assure a constant flow of articles brought to the assembly line the replenishment should be equivalent to the consumption during a certain period of time, or multiples of this time, for all articles. Furthermore, the assembler should not be the one bringing materials to the assembly line; this should be done by a material handler. The study also shows that different packaging should be used for different articles, depending on product characteristics and where the supplier is situated. Excluding packaging material made out of wood or cardboard results in costs that must be weighed against customer demands. When it is too expensive to let the supplier deliver the articles in a packaging that does not give of dust or splinters, a repacking station is a possible solution; in the case of project 580-9 in the form of an in-house manual unpacking before the assembly. Our recommendation is that GETRAG All Wheel Drive AB should try to achieve a more cost efficient materials handling through lean production and six sigma and at the same time put more resources in to packaging development.

Abstract The Profitability of Lean Six Sigma: A Study of National Grain Producers Inc. describes the different actions taken by NGP to take advantage of Lean Six Sigma and increase the company’s profitability. These actions are reviewed as investments to aid in assessing how beneficial they have been. This approach helps to quickly determine if what has been done within NGP so far as part of Lean Six Sigma has been successful which helps in deciding whether or not to continue the use of the LSS system.

Pseudomonas syringae pv. syringae strain B728a (P.s.s. B728a) is an economically significant plant pathogen that is capable of successful epiphytic colonization of leaf surfaces. Although the virulence factors associated with this pathogen’s ability to cause disease have been well studied, the transition from epiphyte to pathogen is not well understood. The research described in this dissertation utilizes high throughput sequencing transcriptome analyses to define an iron regulatory network that is predicted to be utilized during the epiphytic portion of the P.s.s. B728a lifecycle. This dissertation also describes a collaborative microarray analysis that analyzes the P.s.s. B728a transcriptome at a global level. An iron associated sigma factor, AcsS, encoded within a peptide synthesis rich region of the P.s.s. B728a genome is shown to regulate the citrate siderophore achromobactin. RNA-seq transcriptome analysis reveals that this sigma factor regulates expression of genes predicted to be involved in functions that are important during the epiphytic stage of P.s.s. B728a, including genes involved in iron response, secretion, extracellular polysaccharide production, and cell motility. As part of a collaboration, the transcriptomes of the P.s.s. B728a genome and nine deletion mutants in regulatory genes were analyzed by microarray analayses using seven treatment conditions, including epiphytic and in planta conditions. As part of these microarray analyses, results are described for the global regulator, GacS, and a downstream transcription factor, SalA. This study confirms the role of GacS and SalA in the regulation of major virulence components of P.s.s. B728a such as phytotoxin production and Type III secretion. This study also elucidates a role for GacS and SalA regulation of genes important for epiphytic survival and function, including the Type VI secretion system, iron acquisition, and EPS production.

A new low power, wideband wireless transmitter able to convert any RF signal into a constant envelope signal enabling the use of a nonlinear and efficient power amplifier is presented. In the transmitter architecture, two normalized phase signals and the envelope are separated and processed separately. A 1-bit 2nd order SD modulator codes the envelope. Quantization noise is attenuated by a S&H interpolator introducing notches at multiples of the sampling frequency. Phase and Envelope signals are recombined and upconverted directly to radio frequencies using a novel full-digital, wideband quadrature modulator. This mixer takes advantage of the 1-bit SD output. As both LOs and envelope signals are represented by two-level signals, the product of these signals (XOR function) leads to a two-level signal, which can be used as command signal in the multiplexors. Phase signals or theirs complements that are generated by a simple Inversion Block are passed through this multiplexor at the rate of driving signals. This enables to implement a high frequency, wideband mixer instead of a more complex three-input modulator. This IQ mixer is very simple to implementate as it uses only CMOS logic gates. The generation of the quadrature clock signals in the mixer is obtained by carefully design of two paths to avoid mismatch to assure an error less than 1º (only demonstrated in simulation) and the use of SR flipflops to generate correctly the complementary signal prior to the divide-by-two circuit. Two asynchronous 9-bit DACs eliminate the 10-bit high-speed digital adder at the output of the IQ modulator and the 10-bit DAC before the PA, saving power and relaxing adder design constraints. Each DAC is divided into two full binary-weighted DACs of 4 and 5 bits. This topology enables to reduce the size ratios between the most and least significant bits related to a classic 9-bit binary-weighted structure (16 instead of 256). To test the speed and the gain control of the standalone DAC over 45 dB, a prototype DAC is designed in 0.13 ;m BiCMOS technology from STMicroelectronics together with a 1.4 GHz 9-bit CMOS ROM-less direct digital frequency synthesizer (DDFS). Over the output power range, measurements show a SFDR>25 dB with a power dissipation of 25 mW at the maximum differential output power of -3 dBm (RL=50 @). The whole transmitter is designed and implemented and a prototype transmitter is built in 0.13 μm BiCMOS STMicroelectronics process. This low cost single chip digital radio transmitter demonstrates a data rate of 1.8 GHz. The image level is measured to be -12 dBc at this sampling frequency. Dynamic range in the transmitter is 35 dB for sampling frequencies lower than 800 MHz and 25 dB for higher sampling frequencies up to 1.8 GHz. For a two-tone signal, the maximum single-ended output power is -31dBm for each tone and the power dissipation is about 35 mW. This architecture enables flexible and software-defined transmitter. Sampling frequency in the SD coder can be varied to adapt to different communications standards in terms of in-band and outof-band noise requirements and variable LO frequencies can be used. Moreover, the transmitter can adapt dynamically the output power to the power amplifier depending of the required transmitted power at the output of the PA. The transmitter has demonstrated its potential for use as a universal transmitter for applications targeting any frequency band and modulation schema up to 900 MHz (carrier frequency) and occupies a die area of 300x320 ;m2. The generated differential signal can be easily amplified by a switched-mode Power Amplifier (PA) in an efficient way because it presents constant-envelope and the PA can work in the saturation zone, which represents its optimal operation point.

Denna rapport syftar till att undersöka hur Siemens Industrial Turbomachinery AB i Finspång har valt att arbeta med processförbättringsmetoden Six Sigma, som är en mycket populär metod för att genomföra processförbättringsprojekt och mycket attraktiv för företag som ska arbeta med sådana.   Metoden bygger på statistik och att fatta välinformerade beslut. Detta görs genom att samla team-medlemmar från den process som ska förbättras och genom att göra mätningar inom sagda process.  Man börjar ett projekt genom att definiera problemet, går vidare med att mäta den aktuella processen, analyserar sedan de data man fått in, försöker komma på lösningar och slutligen implementerar man den lösning man bedömt som bäst.   Vi gjorde en kvalitativ fallstudie på företaget och intervjuade över ett dussin personer som hade olika grader av bekanthet med Six Sigma, för att få utsagor från personer med olika perspektiv på metoden.  Av detta fick vi veta att de som har varit med i ett förbättringsprojekt eller har utbildat sig inom Six Sigma var begränsade till en knapp tiondel av de anställda på företaget, men att de som var insatta i metoden var ganska väl insatta.   Vi går igenom ett antal faktorer inom Six Sigma och projekt baserade på metoden och ställer dessa mot relaterade teorier så att vi kan dra slutsatser.   Slutligen tar vi upp våra slutsatser och avslutande reflektioner där vi kommer fram till att mycket av problemen med metoden ligger i om man inte använder den fullt ut utan försöker klara sig utan att ge de resurser som krävs men att metoden annars ger ett stabilt ramverk för processutveckling.