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Escherichia coli ribosomal RNA (rRNA) is post-transcriptionally modified by site-specific enzymes. The role of most modifications is not known and little is known about how these enzymes recognize their target substrates. In this thesis, we have structurally and functionally characterized two S-adenosyl-methionine (SAM) dependent 23S rRNA methyltransferases (MTases) that act during the early stages of ribosome assembly in E. coli. RlmM methylates the 2'O-ribose of C2498 in 23S rRNA. We have solved crystal structures of apo RlmM at 1.9Å resolution and of an RlmM-SAM complex at 2.6Å resolution. The RlmM structure revealed an N-terminal THUMP domain and a C-terminal catalytic Rossmann-fold MTase domain. A continuous patch of conserved positive charge on the RlmM surface is likely used for RNA substrate recognition. The SAM-binding site is open and shallow, suggesting that the RNA substrate may be required for tight cofactor binding. Further, we have shown RlmM MTase activity on in vitro transcribed 23S rRNA and its domain V. RlmJ methylates the exocyclic N6 atom of A2030 in 23S rRNA. The 1.85Å crystal structure of RlmJ revealed a Rossmann-fold MTase domain with an inserted small subdomain unique to the RlmJ family. The 1.95Å structure of the RlmJ-SAH-AMP complex revealed that ligand binding induces structural rearrangements in the four loop regions surrounding the active site. The active site of RlmJ is similar to N6-adenine DNA MTases. We have shown RlmJ MTase activity on in vitro transcribed 23S rRNA and a minimal substrate corresponding to helix 72, specific for adenosine. Mutagenesis experiments show that residues Y4, H6, K18 and D164 are critical for catalytic activity. These findings have furthered our understanding of the structure, evolution, substrate recognition and mechanism of rRNA MTases.

The objective of this research was to develop high performing polymer modified calcium sulfoaluminate (CSA) cement materials for use in applications requiring superior adhesion characteristics. Little information is available describing interactions of CSA cement containing minor phase tri-calcium aluminate (C3A) with commonly used admixtures. Given the scarcity of information, a basic approach for developing cementitious materials was followed. The basic approach consisted of four tasks: cement design, admixture design, polymer design and testing developed materials. The iterative, time consuming process is necessary for understanding the influence of specific constituent components on overall system behavior. Results from the cement design task suggest calcium sulfate type influences microstructural characteristics and strength development for materials based upon the experimental CSA cement. Results from the admixture design task suggest lithium carbonate and tartaric acid are effective accelerating and retarding admixtures for hydration reactions including reactants yeelimite, calcium sulfate and water. Results from the polymer design task suggest vinyl acetate / ethylene (VAE) dispersible polymer powders (DPP) are compatible with systems containing the experimental CSA cement and other commonly used admixtures. Additionally, results from the polymer design task highlight a method for specifying the ductile behavior of materials containing the experimental CSA cement as majority hydraulic binding agent. Finally, results from the testing of developed materials task suggests adhesion performance for materials containing the experimental CSA cement can be influenced by adjusting the ratio of polymer to hydraulic binding agent in material formulations. Polymer modified CSA cement mortars demonstrated bond strength resulting in substrate failure when cast over porous concrete substrates. Developed mortars demonstrated consistent bonding performance when applied to non-porous substrate materials, metal and glass. Select polymer modified mortars displayed adhesion bond performance such that the glass substrate materials fractured during pull off testing.

This work familiarizes readers with the issues of slot antennas. It presents design and simulation of slot antenna for X band in CST Microwave Studio program. The simulation procedure is described here, including all the settings required for proper operation of the simulation. Then there is the description of the principle of the Half-Mode Substrate Integrated Waveguide - HMSIW. In the end the designed structure of HMSIW and the slot antenna are assembled and measured. The results of the simulation are compared with the results acquired by measurements. The designed antenna at the frequency 10 GHz achieves the impedance bandwidth 255 MHz, and the gain 8,81 dBi (the simulated values in CST Microwave studio).

For biomedical electronics the compatibility to the biological environment should be well-considered. Therefore this paper evaluates dispensed carbon nanotubes (CNT's) on polyimide (PI) foil for conductive tracks and electrodes for flexible, biomedical applications. A CNT based ink is investigated regarding biocompatibility, flexibility, conductivity and suitability for electrode materials with contact to artificial body fluids. The testing methods comprise bending tests with resistance monitoring, adhesion tests and the utilization of dynamic fluidic and electrical load on dispensed structures. The CNT ink showed good bending properties up to 2653 cycles with an average sheet resistance of 32.5 Ohm/sq. A demonstration of biocompatibility using the adherent cell line HFFF2 resulted negatively. No delamination or dissolving effects occurred during exposure to 0.9 % sodium chloride solution.

The rapid development in the semiconductors industry has enabled the placement of multiple chips on a single die. This has helped boost the functionality of modernday application specific integrated circuits (ASICs). Thus, digital circuits are being increasingly placed along-side analog and RF circuits in what are known as mixed signal circuits. As a result, the noise couplings through the substrate now have an increased role in mixed-signal ASIC design. Therefore, there is a need to study the effects of substrate noise and include them in the traditional design methodology. ∆Σ analog-to-digital converters (ADCs) are a perfect example of digital integration in traditionally analog circuits. ADCs, used to interface digital circuits to an analog world, are indispensable in mixed-signal systems and therefore set an interesting case study. A ∆Σ ADC is used in this thesis to study the effects of substrate noise. A background study is presented in the thesis to better understand ∆Σ modulators and substrate couplings. An intensive theoretical background on generation, propagation and reception of substrate noise is presented in light of existing researches. System and behavioural level models are proposed to include the effects of substrate noise in the design stages. A maximum decay of 10dB is seen due to injection of substrate noise system level simulations while a decay of 12dB is seen in behavioural simulations. A solution is proposed using controlled clock tree delays to overcome the effects of substrate noise. The solution is verified on both the system and behavioural levels. The noise models used to drive the studies can further be used in mixed-signal systems to design custom solutions. / Den snabba utvecklingen inom halvledarindustrin har möjliggjort placering av flera marker på en enda dö. Detta har hjälpt till att öka funktionaliteten hos moderna applikationsspecifika integrerade kretsar. Sålunda placeras digitala kretsar i allt högre grad parallella och RF-kretsar i de så kallade blandade signalkretsarna. Som ett resultat har bullerkopplingarna genom substratet nu en ökad roll i ASICdesign med blandad signal. Därför finns det behov av att studera effekterna av substratbuller och inkludera dem i den traditionella designmetoden. ∆Σ analog-till-digital omvandlare är ett perfekt exempel på digital integration i traditionellt analoga kretsar. ADC, som används för att gränssnitta digitala kretsar till en analog värld, är oumbärliga i blandningssignalsystem och är därför en intressant fallstudie. A ∆Σ arkitektur används i denna avhandling för att studera effekterna av substratstörning. En bakgrundsstudie presenteras i avhandlingen för att bättre förstå ∆Σ modulatorer och substratkopplingar. En intensiv teoretisk bakgrund på generering, förökning och mottagande av substratbuller presenteras i ljuset av befintliga undersökningar. Systemoch beteendemodellmodeller föreslås inkludera effekterna av substratbuller i konstruktionsstadiet. Ett maximalt förfall på 10dB ses på grund av injektion av substratbuller på systemnivå medan ett förfall av 12dB ses i beteende simuleringar.En lösning föreslås med hjälp av kontrollerade klockträdfördröjningar för att övervinna effekterna av substratbuller. Lösningen är verifierad på både system och beteendenivåer. De brusmodeller som används för att driva studierna kan vidare användas i blandningssignalsystem för att designa anpassade lösningar.

Elevated postprandial triacylglycerol concentrations ([TAG]) are associated with the development and progression of atherosclerosis, and are established as an independent risk factor for future cardiovascular disease. Considering the majority of the daytime is spent in a postprandial state typically, and the paediatric origins of atherosclerosis are well established, lifestyle interventions including manipulations of exercise energy expenditure and dietary energy intake should be initiated early in life. Therefore, this thesis aimed to investigate the postprandial metabolic responses to different exercise and energy intake manipulations in boys and girls, with concentrations of circulating TAG representing the primary outcome of interest. To achieve this, a total of 60 healthy 11 to 13 year old boys and girls were recruited into five experimental studies. The first experimental study (Chapter 4) demonstrated that a single session of high-intensity interval running (HIIR) involving 10 x 1 min intervals at 100% maximal aerobic speed (MAS) resulted in a moderate reduction in postprandial plasma [TAG] in 11 to 12 year old boys. In the second experimental study (Chapter 5), immediate replacement of the moderate-intensity exercise-induced energy deficit negated the reduction in postprandial plasma [TAG] in 11 to 13 year old boys. Furthermore, an exercise-induced energy deficit was required to promote an increase in whole-body fat oxidation. The importance of the associated energy deficit was explored further in Chapter 6, which demonstrated that a moderate-intensity exercise-induced energy deficit elicited a greater reduction in postprandial plasma [TAG] than an isoenergetic diet-induced energy deficit in 11 to 13 year old girls (21% vs. 10% respectively). Chapter 7 compared the effect of 10 x 1 min interval runs at 100% MAS (HIIR) and 5 x 1 min interval runs at 100% MAS combined with a mild reduction in habitual energy intake by 0.82 MJ (195 kcal; HIIR-ER) on postprandial metabolism in 11 to 13 year old girls. Acute manipulations of low volume HIIR and ER reduced postprandial plasma [TAG] and increased resting whole-body fat oxidation, with the magnitude of effect marginally, although not meaningfully, greater following HIIR than HIIR-ER. The final experimental chapter (Chapter 8) compared directly healthy 11 to 13 year old boys and girls postprandial TAG responses to acute HIIR. Although postprandial plasma [TAG] was substantially lower in boys compared with girls, the magnitude of reduction following HIIR was similar between the sexes (11% vs. 10% respectively). Collectively, these studies demonstrate the efficacy of acute moderate- and high-intensity exercise, and to a lesser extent energy-intake restriction, to reduce postprandial plasma [TAG] and increase resting whole-body fat oxidation in boys and girls. Furthermore, the beneficial effect of exercise on postprandial metabolism appears dependent on the maintenance of the associated energy deficit. These lifestyle interventions have the potential to provide a practical, effective and engaging stimulus to promote a healthier cardiovascular risk profile in early adolescence.

During the last decades marine aquaculture has steadily expanded and diversified to include a wider range of commercial species. Despite the intense effort towards understanding the biological requirements of farmed species, several issues remain to be addressed. Mariculture success is restricted by a number of production bottlenecks including limited seed supply, caused mainly through a combination of compromised productivity in broodstock paired with high mortalities during the early life stages. Productivity and survival success is often dependent on the successful recreation of natural environmental conditions. While in a commercial setting a concerted effort is generally made to simulate key environmental stimuli there remains a lack of understanding of the significance of many potential signals. The overarching aim of this thesis was to investigate the effects of some of the overlooked environmental stimuli on fish performance in enclosed facilities and where possible relate this to the natural setting from which the species have been removed. The studies contained in this text are focused on the effects of anthropogenic noise, light spectral composition and substrate on the performance of broodstock and juvenile development of two valuable commercial marine species Atlantic cod (Gadus morhua) and turbot (Scophthalmus maximus). The aim of Chapter 3 was to test if artificial sound can act as a stressor in Atlantic cod and thereafter to examine if chronic sound disturbances can compromise broodstock spawning performance in land-based facilities. Results showed that anthropogenic noises in a land-based marine farm are within the auditory thresholds of cod and other fish species. Juvenile cod exposed to 10 min of artificial noise (100-1,000 Hz) from 10 to 20 dB 1 re µPa above background sound levels presented a typical acute stress response with a 4 fold elevation of plasma cortisol levels within 20 min, with a return to basal levels after 40 min, while the intensity of the stress response (in terms of amplitude and return to normal levels) appeared to be correlated to the noise level applied. When a similar artificial noise of 35 dB 1 re µPa above background sound level was applied to a broodstock population daily on a random schedule during the spawning season, it significantly impacted on reproductive performances in comparison to a control undisturbed population with notably a reduction in fertilisation rate that correlated with increased egg cortisol contents. Overall, these studies confirmed, for the first time, that artificial noise mimicking anthropogenic sounds generated in marine land-based facilities trigger a typical acute stress response if a similar sound exposure is then applied in a chronic manner it resulted in reduced broodstock spawning performances. Overall this work provides novel evidence on the potential of anthropogenic noise to act as stressor in fish. The possible implications for both captive and wild stock are discussed. In chapter 4 the effects of light spectrum and tank background colour on Atlantic cod and turbot larval performance from hatch until the end of metamorphosis were investigated. In both species larvae exposed to shorter wavelengths (blue and green spectrums) showed significantly enhanced growth in terms of standard length, myotome height, eye diameter and condition factor in comparison to larvae exposed to longer wavelengths (red). Larvae performances in the colour background experiment differed between species. Atlantic cod larvae reared in a red tank background displayed the best growth and survival, while larvae in blue tank background had a significant positive effect on final survival rate. In contrast, turbot larvae survival rates were the highest in the red tank background colour with the lowest growth parameters, while larvae in the blue tank background displayed the best growth. In both species, white tank background colour resulted in the lowest final survival rate. These results highlight the biological relevance of light spectrum and background colour in marine larvae performance and survival, demonstrating the importance of considering the light composition of the light units used in the hatcheries for larval rearing. Subsequently in chapter 5 the effects of light spectrum in juvenile turbot growth, appetite, stress response and skin pigmentation were investigated. Two sets of experiments were performed with post-metamorphosed (1 g) and on-growing (100 g) turbot. Results demonstrated that short wavelength treatments had a significant positive effect on growth parameters (total length and wet weight), food intake and feeding response. Light treatments caused a positive correlation between plasma glucose and cortisol levels with significant differences between the short and long wavelength treatments. Skin pigmentation was affected by the light treatments, showing a relationship between wavelength and brightness (negative) and darkness (positive). Blue light treatment resulted in brighter and lighter skin colouration, while red light had the opposite effect: darkening of the skin. Overall these results confirm that turbot juveniles performance is enhanced by exposing them to a similar photic environment than the one from the natural ecological niche. Light spectrum intervenes in skin pigmentation and the possible mechanisms behind the variations are discussed. In general chapter 5 provides background knowledge of the possible implications of light spectrum in fish juveniles performance and possible commercial applications. The final two experimental chapters turned focus back on the optimisation of broodstock environmental management and subsequent effects on their productivity. In Chapter 6 the importance of crepuscular light simulation was investigated in Atlantic cod broodstock spawning performance. No significant impact could be observed in terms of egg production and quality in association with dawn/dusk simulation compared to abrupt lights on/off. This suggests, at least for Atlantic cod, that crepuscular light simulation is not a key factor affecting spawning performance during the spawning window. The possible implications of twilight on gamete quality prior ovulation are discussed. In Chapter 7 the effect of a “breeding nest” containing a substrate (i.e. sand) in turbot broodstock spawning performance was investigated. Behavioural observation recorded active occupancy of the nests with the suggestion of social structuring as specific individuals (females) occupied the nest preferentially. However no fertilised, naturally released eggs were collected from the overflow during the spawning seasons. This would suggest that the presence of a nest is not enough to induce natural spawning behaviour in turbot in itself however the elective occupancy suggests that nests and/or their substrate was a physical enrichment that was valued by the fish which should be explored further. Overall the studies contained in this thesis highlight further the importance of considering noise and light as crucial environmental factors in marine aquaculture. Results from the different chapters offer a possible application within the enclosed facilities that might contribute to the success of the industry. Present findings contribute towards the understanding of the effects of environmental signals in fish and provide further insight to guide further lines of research on the involvement of light spectrum on fish physiology.

The objective of this thesis is to introduce novel procedures and guidelines to design bandstop microwave filters for modern terrestrial and satellite wireless communication systems. Among all available microwave filter technologies, planar structures of microstrip and substrate integrated waveguide (SIW) are chosen, due to ease of fabrication, low profile, weight and manufacturing cost. Particularly, SIW structures are more attractive because they have a better insertion loss, quality factor, and power handling capability in comparison to their microstrip counterparts, and can also be easily integrated into other planar circuitries. A comprehensive hybrid analytic-optimization method is developed to synthesize any single-band as well as multi-band bandstop coupling matrix. In this method, the location of reflection zeros (RZs) and the attenuations in stopbands can be determined in advance. Several novel single-band, dual-band, and triple-band bandstop filters are designed using regular and ridged SIW resonators, in-line coupled singlet resonators, cross-coupled resonators, and bandstop stubs. The designed filters have fractional bandwidths up to 23% . Moreover, a tunable ridged SIW bandstop resonator and a tunable CPW resonator, etched into the top plate of the SIW transmission line, are introduced. Combining these two resonators, a dual-band SIW filter is designed that permits one of its stopband to be tuned while another stopband is fixed. All introduced filters in this thesis are verified by commercial electromagnetic software, analytic investigations using Matlab codes, and measurements. / Graduate

The subject of this dissertation is the development of three-dimensional (3D) surface profilers for semiconductor back-end inspection. The value of this study is: 1) to provide a new phase-to-height relationship for Fourier Transform Profilometry (FTP) that is universal as it allows alternate FTP system architectures for a micrometer scale object measurement, and 2) to provide a new method for full field substrate warpage and ball grid array (BGA) coplanarity inspection using machine vision. The desire to increase electronic device performance has resulted in denser and smaller IC packaging. As the dimensions of the devices decrease, the requirements for substrate flatness and surface quality become critical in avoiding device failure. For a high yield production, there is an increasing demand in the requirement for the dimensional verification of height, which requires 3D inspection. Based on the current demands from the semiconductor industry, this dissertation addresses the development of fast in-line surface profilers for large volume IC package inspection. Specifically, this dissertation studies two noncontact surface profilers. The first profiler is based on FTP for measuring the IC package front surface, the silicon die and the epoxy underfill profile. The second profiler is based on stereovision and it is intended for inspecting the BGA coplanarity and the substrate warpage. A geometrical shape based matching algorithm is also developed for finding point correspondences between IC package images. The FTP profiler provides a 1 σRMS error of about 4 μm for an IC package sample in an area of 14 mm x 6.5 mm with a 0.13 second data acquisition time. For evaluating the performance of the stereovision system, the linearity between our system and a confocal microscope is studied by measuring a particular IC sample with an area of 38 mm x 28.5 mm. The correlation coefficient is 0.965 and the 2σdifference in the two methods is 26.9 μm for the warpage measurement. For BGA coplanarity inspection the correlation coefficient is 0.952 and the 2difference is 31.2 μm. Data acquisition takes about 0.2 seconds for full field measurements.