Mollicutes (mycoplasmas) are pathogenic in a wide range of mammals (including humans), reptiles, fish, arthropods, and plants. Of the medically important mollicutes, Mycoplasma gallisepticum is of particular relevance to avian agriculture and veterinary science, causing chronic respiratory disease in poultry and turkey. Using two-dimensional electrophoresis based quantitative expression proteomics, the current study investigated the molecular mechanisms behind the phenotypic variability between a M. gallisepticum vaccine strain (6/85) and a competitive, virulent field strain (K5234), two strains which were indistinguishable using commonly accepted genetic methods of identification. Twenty-nine proteins showed a significant variation in abundance (fold change > 1.5, p-value < 0.01). Among others, the levels of putative virulence determinants were increased in the virulent K5234, while the levels of several proteins involved with pyruvate metabolism were decreased. It is hoped that the data generated will further the understanding of M. gallisepticum virulence determinants and mechanisms of infection, and that this may contribute to the optimization of diagnostic methodologies and control strategies.

This thesis documents the design and fabrication of an experimental facility that was built to produce a turbulent plane wall jet. The target flow was two-dimensional with a uniform profile of the mean streamwise velocity and a low turbulence level at the slot exit. The design requirements for a flow conditioning apparatus that could produce this flow were determined. The apparatus was then designed and constructed, and measurements of the fluid flow were obtained using particle image velocimetry (PIV). The first series of measurements was along the slot width, the second series was along the slot centerline and the third was at 46 slot heights off the centerline. The Reynolds number, based on the slot height and jet exit velocity, of the wall jet varied from 7594 to 8121. Data for the streamwise and transverse components of velocity and the three associated Reynolds stress components were analyzed and used to determine the characteristics of the wall jet.<p> This experimental facility was able to produce a profile of the mean streamwise velocity near the slot exit that was uniform over 71% of the slot height with a streamwise turbulence that was equal to 1.45% of the mean velocity. This initial velocity was maintained to 6 slot heights. The fully developed region for the centerline and the off-centerline measurements was determined to extend from 50 to 100 slot heights and 40 to 100 slot heights, respectively. This was based on self-similarity of the mean streamwise velocity profiles when scaled using the maximum streamwise velocity and the jet half-width. The off-centerline Reynolds stress profiles achieved a greater degree of collapse than did the centerline profiles.<p> The rate of spread of the wall jet along the centerline was 0.080 in the self-similar region from 50 to 100 slot heights, and the off-centerline growth rate was 0.077 in the self-similar region from 40 to 100 slot heights. The decay rate of the maximum streamwise velocity was -0.624 within the centerline self-similar region, and -0.562 within the off-centerline self-similar region. These results for the spread and decay of the wall jet compared well with recent similar studies.<p> The two-dimensionality was initially assessed by measuring the mean streamwise velocity at 1 slot height along the entire slot width. The two-dimensionality of this wall jet was further analyzed by comparing the centerline and off-centerline profiles of the mean streamwise velocity at 2/3, 4, 50, 80, and 100 slot heights, and by comparing the growth rates and decay rates. Although this facility was able to produce a wall jet that was initially two-dimensional, the two-dimensionality was compromised downstream of the slot, most likely due to the presence of return flow and spanwise spreading. Without further measurements, it is not yet clear exactly how the lack of complete two-dimensionality affects the flow characteristics noted above.

The aim of this work is to study the relation between two invariants of water flow in a channel of finite depth. The first invariant is the height of the water wave and the second one is the flow force. We restrict ourselves to water waves of small amplitude. Using asymptotic technique together with the method of separation of variables, we construct all water waves of small amplitude which are parameterized by a small parameter. Then we demonstrate numerically that the flow force depends monotonically on the height.

This thesis documents the design and fabrication of an experimental facility that was built to produce a turbulent plane wall jet. The target flow was two-dimensional with a uniform profile of the mean streamwise velocity and a low turbulence level at the slot exit. The design requirements for a flow conditioning apparatus that could produce this flow were determined. The apparatus was then designed and constructed, and measurements of the fluid flow were obtained using particle image velocimetry (PIV). The first series of measurements was along the slot width, the second series was along the slot centerline and the third was at 46 slot heights off the centerline. The Reynolds number, based on the slot height and jet exit velocity, of the wall jet varied from 7594 to 8121. Data for the streamwise and transverse components of velocity and the three associated Reynolds stress components were analyzed and used to determine the characteristics of the wall jet.<p> This experimental facility was able to produce a profile of the mean streamwise velocity near the slot exit that was uniform over 71% of the slot height with a streamwise turbulence that was equal to 1.45% of the mean velocity. This initial velocity was maintained to 6 slot heights. The fully developed region for the centerline and the off-centerline measurements was determined to extend from 50 to 100 slot heights and 40 to 100 slot heights, respectively. This was based on self-similarity of the mean streamwise velocity profiles when scaled using the maximum streamwise velocity and the jet half-width. The off-centerline Reynolds stress profiles achieved a greater degree of collapse than did the centerline profiles.<p> The rate of spread of the wall jet along the centerline was 0.080 in the self-similar region from 50 to 100 slot heights, and the off-centerline growth rate was 0.077 in the self-similar region from 40 to 100 slot heights. The decay rate of the maximum streamwise velocity was -0.624 within the centerline self-similar region, and -0.562 within the off-centerline self-similar region. These results for the spread and decay of the wall jet compared well with recent similar studies.<p> The two-dimensionality was initially assessed by measuring the mean streamwise velocity at 1 slot height along the entire slot width. The two-dimensionality of this wall jet was further analyzed by comparing the centerline and off-centerline profiles of the mean streamwise velocity at 2/3, 4, 50, 80, and 100 slot heights, and by comparing the growth rates and decay rates. Although this facility was able to produce a wall jet that was initially two-dimensional, the two-dimensionality was compromised downstream of the slot, most likely due to the presence of return flow and spanwise spreading. Without further measurements, it is not yet clear exactly how the lack of complete two-dimensionality affects the flow characteristics noted above.

Cellular adhesion research has recently focused on the small scale at the level of individual receptor-ligand bonds. This trend in research is primarily due to experimental advances which allow such individual bond force measurements. Here, one of these techniques, micromanipulation, has been extended to not only determine the bond force of individual receptor-ligand pairs, but also the intrinsic kinetic rates of the interaction. Using transmembrane (TM ) Fc gamma receptor III (CD16a-TM) and human IgG (hIgG), the dependence of adhesion probability on receptor-ligand expression densities, contract duration and contact area was quantitated. A probabilistic based theoretical formulation was developed and validated that relates the intrinsic molecular kinetic rates of the receptorVligand interaction to the experimentally determined adhesion probability. This theoretical formulation describing individual receptor-ligand kinetics has also allowed direct evaluation of existing biophysical bond strength/kinetics paradigms at the extreme condition of single bonds. A force-displacement model was also developed to quantitate the force exerted on the RBC membrane transducer during the micropipette retraction process and found to be in agreement with previous work. In addition to CD16a-TM, the kinetic rates of CD16a anchored via a glycosyl phosphatidylinositol (GPI) moiety (CD16a-GPI) and the two alleles of CD16b (NA1 and NA2) were determined for human, rabbit, and mouse IgG species. The binding affinity of these CD16 interactions to soluble IgG was also measured by traditional bulk chemistry approaches and compared to those measured via the micromanipulation protocol in which the IgG ligand is membrane bound in the solid phase. These data suggest that the membrane anchor itself can alter CD16 binding properties. This represents the first reported effect of the anchor on an intrinsic receptor property, its kinetic rates and binding affinity. This thesis presents two specific aims or goals. These goals were achieved and reported in this thesis. During the course of this research, I also explored other directions and gathered initial data. These directions were further explored by other researchers but the initial data is also presented here.

The dual-writing process of holographic technique was applied to fabricate the two-dimensional surface relief gratings on azo-dye doped polymer film in this study. The structure of two-dimensional grooves was investigated under the various polarization state of writing beam, the various angle between two stages of writing, and the adoption of nematic liquid crystals as the interface. The results revealed that the depth of two-dimensional surface relief gratings produced by the writing beams with P-polarization and the interface of nematic liquid crystals in contact with azo-dye polymer film was about 2~3 times of that without nematic liquid crystals as the interface. As the angle between two stages of writing increases, the first order diffraction efficiency and the depth of surface relief structure in the second writing becomes smaller for the writing beam with S polarization; while the first order diffraction efficiency and the depth of surface relief structure becomes larger for the writing beam with P polarization.

Hepatocyte growth factor (HGF) and its specific receptor MET play a role in many physiological functions including proliferation, migration and morphogenesis. Recently, research results in our laboratory showed that recombinant HGF variants (NK1, NK2, NK3 and NK4) became antagonists to HGF/MET pathway by suppressing proliferation, migration and invasion in human breast cancer cells (MDA-MB-435S, MDA). Similar results were achieved when HGF variants genes were introduced in MDA cells. To understand the molecular mechanism of breast cancer cells metastasis suppressed by HGF variants, MDA and five transfectants, including MDA-GFP, MDA-NK1, MDA-NK2, MDA-NK3 and MDA-NK4 cells were used for proteomic analysis using two-dimensional electrophoresis (2-DE). Differential analysis revealed that a total of 56 polypeptides were differentially expressed through five sets of comparison using wild-type MDA cells as a control. A total of 17 polypeptides were shown differential expression between MDA and MDA-GFP cells, with 11 down-regulated and 6 up-regulated. Eighteen polypeptides were differentially expressed between MDA and MDA-NK1 cells, with 15 down-regulated and 3 up-regulated. There were 22 differentially expressed polypeptides found between MDA and MDA-NK2 cells, in which 14 were down-regulated and 8 were up-regulated. Sixteen polypeptides were shown differentially expressed between MDA and MDA-NK3 cells, with 11 down-regulated and 5 up-regulated. A total of 18 polypeptides were shown differential expression between MDA and MDA-NK4 cells, with 15 down-regulated and 3 up-regulated. Proteomic analysis showed that a total of 43 polypeptides were differentially expressed through four sets of comparison (MDA-GFP and MDA-NK1, MDA-GFP and MDA-NK2, MDA-GFP and MDA-NK3, and MDA-GFP and MDA-NK4). To understand the differential expression among different HGF variants-transfected MDA cells, three sets of cross analysis were also carried out (MDA-NK1 and MDA-NK2, MDA-NK1 and MDA-NK3, and MDA-NK1 and MDA-NK4) and the results showed that a total of 37 differentially expressed polypeptides were found in the three sets of comparison. Similarly, when MDA-NK2 cells were used as a control to compare with MDA-NK3 and MDA-NK4 cells, 34 significantly differential expressed polypeptides were found. The last set of comparison between MDA-NK3 and MDA-NK4 cells, 19 polypeptides were found significantly differential expression. Therefore, our current results revealed that the differentially expressed polypeptides in MDA-MB-435S cells and HGF variants-transfected MDA cells could be related to the inhibition of proliferation and migration of human breast cancer cells by HGF variants.

Some fishes use sound to communicate. The majority of these soniferous fishes use superfast sonic muscles to set the vibration of the swim bladder which results in sound emission and sound amplification. Carapus, a benthic ophiidiform genus, use a slow contracting sonic muscle to pull the anteriormost part of the swim bladder, upon termination of the pulling action, the front part of the swim bladder is snap back setting the swimbladder fenestrum to vibrate. This vibration gives rise to the sound. Other ophiidiform fishes may also use a similar way to emit sounds. Among the soniferous percoids, an advanced perform suborder, glaucosomatid, pempherid, and terapontid share a fenestrum-like structure in the front part of their swim bladder. Previous molecular study suggested that the first two groups form a clade (monophyletic group). It is of great interest to compare the proteomic features of these groups with that of the ophiidiform representatives so that the effects of function and phylogeny to the proteomic characteristics of the sonic muscle can be compared. A species was selected for each of these four groups and their proteomics were analyzed. Results of this study, however, revealed the protein composition of the sonic muscles in the ophiidiform species was more similar to that of the pempherid species. The proteins contribute to the close relationship between these two groups was discussed. A total of 484 protein spots were found in these four species and only five were presented in the sonic muscles of all four species, but absent in the white muscles; and only three of them were successfully identified as: Flotillin-1 (spot 6), HBS1-like protein (spot 8), and Ras-related protein ralB-B (spot 10). Their functions which may be related to the specific role of the sonic muscle were discussed.

This study investigates the accuracy and efficiency of several flux splitting methods for the compressible, two-dimensional Euler equations. Steger-Warming flux vector splitting method, Van Leer flux vector splitting method, The Advection Upstream Splitting Method (AUSM), Artificially Upstream Flux Vector Splitting Scheme (AUFS) and Roe&rsquo / s flux difference splitting schemes were implemented using the first- and second-order reconstruction methods. Limiter functions were embedded to the second-order reconstruction methods. The flux splitting methods are applied to subsonic, transonic and supersonic flows over NACA0012 airfoil, as well as subsonic, transonic and supersonic flows in a channel. The comparison of the obtained results with each other and the ones in the literature is presented. The advantages and disadvantages of each scheme among others are identified.

In this thesis work, a detailed analysis of biometric technologies has been done and a new palmprint recognition algorithm has been implemented. The proposed algorithm is based on 2-D Gabor filters. The developed algorithm is first tested on The Hong Kong Polytechnic University Palmprint Database in terms of accuracy, speed and template size. Then a scanner is integrated into the developed algorithm in order to acquire palm images / in this way an online palmprint recognition system has been developed. Then a small palmprint database is formed via this system in Middle East Technical University. Results on this new database have also shown the success of the developed algorithm.