Novel CO2 Regulated Proteins in Synechocystis PCC 6803

The large biodiversity of cyanobacteria together with the increasing genomics and proteomics metadata provide novel information for finding new commercially valuable metabolites. With the advent of global warming, there is growing interest in the processes that results in efficient CO2 capture through the use of photosynthetic microorganisms such as cyanobacteria. This requires a detailed knowledge of how cyanobacteria respond to the ambient CO2. My study was aimed at understanding the changes in the protein profile of the model organism, Synechocystis PCC 6803 towards the varying CO₂ level. In order to achieve this goal I have employed modern proteomics tools such as iTRAQ and DIGE, recombinant DNA techniques to construct different mutants in cyanobacteria and biophysical methods to study the photosynthetic properties. The proteomics study revealed several novel proteins, apart from the well characterized proteins involved in carbon concentrating mechanisms (CCMs), that were upregulated upon shift of the cells from high CO₂ concentration (3%) to that in air level (0.039%). The unknown proteins, Slr0006 and flavodiiron proteins (FDPs) Sll0217-Flv4 and Sll0219-Flv2, were selected for further characterization. Although slr0006 was substantially upregulated under C_i limiting conditions, inactivation of the gene did not result in any visual phenotype under various environmental conditions indicating that this protein is not essential for cell survival. However, quantitative proteomics showed the induction of novel plasmid and chromosome encoded proteins in deltaslr0006 under air level CO₂ conditions. The expression of the slr0006 gene was found to be strictly dependent on active photosynthetic electron transfer. Slr0006 contains conserved dsRNA binding domain that belongs to the Sua5/YrdC/YciO protein family. Structural modelling of Slr0006 showed an alpha/beta twisted open-sheet structure and a positively charged cavity, indicating a possible binding site for RNA. The 3D model and the co-localization of Slr0006 with ribosomal subunits suggest that it might play a role in translation or ribosome biogenesis. On the other hand, deletions in the sll0217-sll218- sll0219 operon resulted in enhanced photodamage of PSII and distorted energy transfer from phycobilisome (PBS) to PSII, suggesting a dynamic photoprotection role of the operon. Constructed homology models also suggest efficient electron transfer in heterodimeric Flv2/Flv4, apparently involved in PSII photoprotection. Both Slr0006 and FDPs exhibited several common features, including negative regulation by NdhR and ambiguous cellular localization when subjected to different concentrations of divalent ions. This strong association with the membranes remained undisturbed even in the presence of detergent or high salt. My finding brings ample information on three novel proteins and their functions towards carbon limitation. Nevertheless, many pathways and related proteins remain unexplored. The comprehensive understanding of the acclimation processes in cyanobacteria towards varying environmental CO₂ levels will help to uncover adaptive mechanisms in other organisms, including higher plants.

Non-Markovian Dynamics and the Quantum-To-Classical Transition for Quantum Brownian Motion

In this Thesis I discuss the dynamics of the quantum Brownian motion model in harmonic potential. This paradigmatic model has an exact solution, making it possible to consider also analytically the non-Markovian dynamics. The issues covered in this Thesis are themed around decoherence. First, I consider decoherence as the mediator of quantum-to-classical transition. I examine five different definitions for nonclassicality of quantum states, and show how each definition gives qualitatively different times for the onset of classicality. In particular I have found that all characterizations of nonclassicality, apart from one based on the interference term in the Wigner function, result in a finite, rather than asymptotic, time for the emergence of classicality. Second, I examine the diverse effects which coupling to a non-Markovian, structured reservoir, has on our system. By comparing different types of Ohmic reservoirs, I derive some general conclusions on the role of the reservoir spectrum in both the short-time and the thermalization dynamics. Finally, I apply these results to two schemes for decoherence control. Both of the methods are based on the non-Markovian properties of the dynamics.

Comparison of Classical and Secondary Cytologic Criteria Relative to Hybrid Capture for Diagnosing Cervical-vaginal Infection by Human Papillomavirus

Objective To compare the diagnostic accuracy of the classic Meisels cytologic criteria and the Schneider secondary criteria relative to the hybrid capture method for diagnosing HPV infection. Methods This was a retrospective study performed at a public university hospital. A total of 41 patients with a cytologic diagnosis of HPV infection and 40 HPV-negative patients were selected for review of the cervical-vaginal smears seeking to classical and secondary criteria. A single pathologist reviewed the slides in search of the criteria. The classical and secondary cytologic criteria were compared with the hybrid capture for diagnosing HPV infection. Bartleti test was applied for the age analysis, and Fisher's exact test was used to compare proportions. The tests were considered significant when the probability of rejecting the null hypothesis was less than 5% (p < 0.05). Results The Meisels criteria were less sensitive (34.0%) than the secondary Schneider criteria (57.5%) when compared with the hybrid capture (p < 0.0001), although the specificity of the former criteria was non-significantly higher (91.2% and 67.7%, respectively). In cases of moderate or intense inflammation, the sensitivity and specificity of the Schneider criteria were decreased, 33.3% and 50.0% respectively (p = 0.0115). Conclusions Compared with hybrid capture for diagnosis of HPV infection, the sensitivity of the secondary Schneider criteria was higher than the classical Meisels criteria.Moderate or intense inflammation reduces the sensitivity and specificity of the secondary Schneider criteria for diagnosing HPV infection using the hybrid capture as the gold standard.

Validation of a 3D model for oxygen combustion in a circulating fluidized bed

In this thesis, a model called CFB3D is validated for oxygen combustion in circulating fluidized bed boiler. The first part of the work consists of literature review in which circulating fluidized bed and oxygen combustion technologies are studied. In addition, the modeling of circulating fluidized bed furnaces is discussed and currently available industrial scale three-dimensional furnace models are presented. The main features of CFB3D model are presented along with the theories and equations related to the model parameters used in this work. The second part of this work consists of the actual research and modeling work including measurements, model setup, and modeling results. The objectives of this thesis is to study how well CFB3D model works with oxygen combustion compared to air combustion in circulating fluidized bed boiler and what model parameters need to be adjusted when changing from air to oxygen combustion. The study is performed by modeling two air combustion cases and two oxygen combustion cases with comparable boiler loads. The cases are measured at Ciuden 30 MWth Flexi-Burn demonstration plant in April 2012. The modeled furnace temperatures match with the measurements as well in oxygen combustion cases as in air combustion cases but the modeled gas concentrations differ from the measurements clearly more in oxygen combustion cases. However, the same model parameters are optimal for both air and oxygen combustion cases. When the boiler load is changed, some combustion and heat transfer related model parameters need to be adjusted. To improve the accuracy of modeling results, better flow dynamics model should be developed in the CFB3D model. Additionally, more measurements are needed from the lower furnace to find the best model parameters for each case. The validation work needs to be continued in order to improve the modeling results and model predictability.

Physiological response of American bullfrog tadpoles to stressor conditions of capture and hypoxia

The American bullfrog (Rana catesbeiana), recently named Lithobates catesbeianus is currently farmed for commercial purposes throughout various regions of Brazil. Stressful situations such as problems of management, inadequate facilities and environmental changes with consequent reduction of immunity are common in intensive production. The assessments of these situations of stress allow us detect these problems decreasing the injuries causes by confinement. The main objective of this study was to use the biological markers of plasma cortisol and glucose level and hematological parameters to evaluate the response of bullfrog tadpoles submitted to stressed mechanisms of capture and hypoxia. The animals were subjected to three treatments: stress due to individual capture with a hand net; stress due to batch capture with a hand net; and stress due to capture by emptying. The results obtained demonstrated that there were no statistically significant differences in the parameters tested when comparing the treatments with and without exposure to air (normoxia and hypoxia). Based on these results we can conclude that the stressful stimuli tested were not adequate to alter the biomarker tested. For the cortisol, probably this should have occurred due to the synergistic action between this hormone and thyroxin, which induces metamorphosis in these animals.

Prediction of 3D structure and ligand-binding properties : ABC transporters and flavodiiron proteins from Synechocystis sp. strain PCC 6803

Cyanobacteria are unicellular, non-nitrogen-fixing prokaryotes, which perform photosynthesis similarly as higher plants. The cyanobacterium Synechocystis sp. strain PCC 6803 is used as a model organism in photosynthesis research. My research described herein aims at understanding the function of the photosynthetic machinery and how it responds to changes in the environment. Detailed knowledge of the regulation of photosynthesis in cyanobacteria can be utilized for biotechnological purposes, for example in the harnessing of solar energy for biofuel production. In photosynthesis, iron participates in electron transfer. Here, we focused on iron transport in Synechocystis sp. strain PCC 6803 and particularly on the environmental regulation of the genes encoding the FutA2BC ferric iron transporter, which belongs to the ABC transporter family. A homology model built for the ATP-binding subunit FutC indicates that it has a functional ATPbinding site as well as conserved interactions with the channel-forming subunit FutB in the transporter complex. Polyamines are important for the cell proliferation, differentiation and apoptosis in prokaryotic and eukaryotic cells. In plants, polyamines have special roles in stress response and in plant survival. The polyamine metabolism in cyanobacteria in response to environmental stress is of interest in research on stress tolerance of higher plants. In this thesis, the potd gene encoding an polyamine transporter subunit from Synechocystis sp. strain PCC 6803 was characterized for the first time. A homology model built for PotD protein indicated that it has capability of binding polyamines, with the preference for spermidine. Furthermore, in order to investigate the structural features of the substrate specificity, polyamines were docked into the binding site. Spermidine was positioned very similarly in Synechocystis PotD as in the template structure and had most favorable interactions of the docked polyamines. Based on the homology model, experimental work was conducted, which confirmed the binding preference. Flavodiiron proteins (Flv) are enzymes, which protect the cell against toxicity of oxygen and/or nitric oxide by reduction. In this thesis, we present a novel type of photoprotection mechanism in cyanobacteria by the heterodimer of Flv2/Flv4. The constructed homology model of Flv2/Flv4 suggests a functional heterodimer capable of rapid electron transfer. The unknown protein sll0218, encoded by the flv2-flv4 operon, is assumed to facilitate the interaction of the Flv2/Flv4 heterodimer and energy transfer between the phycobilisome and PSII. Flv2/Flv4 provides an alternative electron transfer pathway and functions as an electron sink in PSII electron transfer.

Application of a Pid+fuzzy controller on the motion control system in machine tools

This work deals with an hybrid PID+fuzzy logic controller applied to control the machine tool biaxial table motions. The non-linear model includes backlash and the axis elasticity. Two PID controllers do the primary table control. A third PID+fuzzy controller has a cross coupled structure whose function is to minimise the trajectory contour errors. Once with the three PID controllers tuned, the system is simulated with and without the third controller. The responses results are plotted and compared to analyse the effectiveness of this hybrid controller over the system. They show that the proposed methodology reduces the contour error in a proportion of 70:1.

Be-Fe coupled method for the analysis of 3D elastodynamic problems in the time domain

By coupling the Boundary Element Method (BEM) and the Finite Element Method (FEM) an algorithm that combines the advantages of both numerical processes is developed. The main aim of the work concerns the time domain analysis of general three-dimensional wave propagation problems in elastic media. In addition, mathematical and numerical aspects of the related BE-, FE- and BE/FE-formulations are discussed. The coupling algorithm allows investigations of elastodynamic problems with a BE- and a FE-subdomain. In order to observe the performance of the coupling algorithm two problems are solved and their results compared to other numerical solutions.

Application of a non isotropic turbulence model to stable atmospheric flows and dispersion over 3D topography

A non isotropic turbulence model is extended and applied to three dimensional stably stratified flows and dispersion calculations. The model is derived from the algebraic stress model (including wall proximity effects), but it retains the simplicity of the "eddy viscosity" concept of first order models. The "modified k-epsilon" is implemented in a three dimensional numerical code. Once the flow is resolved, the predicted velocity and turbulence fields are interpolated into a second grid and used to solve the concentration equation. To evaluate the model, various steady state numerical solutions are compared with small scale dispersion experiments which were conducted at the wind tunnel of Mitsubishi Heavy Industries, in Japan. Stably stratified flows and plume dispersion over three distinct idealized complex topographies (flat and hilly terrain) are studied. Vertical profiles of velocity and pollutant concentration are shown and discussed. Also, comparisons are made against the results obtained with the standard k-epsilon model.

The Shadow Moiré method using the phase shifting technique and digital image processing: computational implementation and application to the 3D-reconstruction of a buckled plate

The Shadow Moiré fringe patterns are level lines of equal depth generated by interference between a master grid and its shadow projected on the surface. In simplistic approach, the minimum error is about the order of the master grid pitch, that is, always larger than 0,1 mm, resulting in an experimental technique of low precision. The use of a phase shift increases the accuracy of the Shadow Moiré technique. The current work uses the phase shifting method to determine the surfaces three-dimensional shape using isothamic fringe patterns and digital image processing. The current study presents the method and applies it to images obtained by simulation for error evaluation, as well as to a buckled plate, obtaining excellent results. The method hands itself particularly useful to decrease the errors in the interpretation of the Moiré fringes that can adversely affect the calculations of displacements in pieces containing many concave and convex regions in relatively small areas.

Seismic motion simulation based on Cassino Parallel Manipulator

In this paper we present a study of feasibility by using Cassino Parallel Manipulator (CaPaMan) as an earthquake simulator. We propose a suitable formulation to simulate the frequency, amplitude and acceleration magnitude of seismic motion by means of the movable platform motion by giving a suitable input motion. In this paper we have reported numerical simulations that simulate the three principal earthquake types for a seismic motion: one at the epicenter (having a vertical motion), another far from the epicenter (with the motion on a horizontal plane), and a combined general motion (with a vertical and horizontal motion).

Performance evaluation of 3D computer vision techniques

This work presents the implementation and comparison of three different techniques of three-dimensional computer vision as follows: • Stereo vision - correlation between two 2D images • Sensorial fusion - use of different sensors: camera 2D + ultrasound sensor (1D); • Structured light The computer vision techniques herein presented took into consideration the following characteristics: • Computational effort ( elapsed time for obtain the 3D information); • Influence of environmental conditions (noise due to a non uniform lighting, overlighting and shades); • The cost of the infrastructure for each technique; • Analysis of uncertainties, precision and accuracy. The option of using the Matlab software, version 5.1, for algorithm implementation of the three techniques was due to the simplicity of their commands, programming and debugging. Besides, this software is well known and used by the academic community, allowing the results of this work to be obtained and verified. Examples of three-dimensional vision applied to robotic assembling tasks ("pick-and-place") are presented.

Development of nano-meter motion control in Japan

Production machines for next generation LSIs such as 4G-DRAMs and for large liquid crystal displays such as 0.5mx0.5m size, and information equipment such as magnetic hard disks and DVDs must have the positioning accuracy of a nano-meter order. To realize such a high degree of the positioning accuracy, not only precision machine elements and mechanisms but also high precision sensors, actuators and controller design techniques becomes crucial. This paper introduces recent topics of precision positioning and motion control technology in Japan.