In the first part of this thesis, we study the kinetics of the complexation of a double-stranded DNA byNCp7 protein. To do this, we study the evolution of mechanical properties of DNA and its complexation by stretching the DNA/NCp7 complex with a optical trap. We observed that the persistence length of the complex decreases progressively during the complexation. Using astatistical model we describe the evolution of the flexibility of DNA complexed with NCp7. Our main result is that the fraction phi of base pairs that have reacted is not a linear function of time at low phi.We interpret our results assuming that the adsorption of NCp7 on DNA is highly cooperative. In the second chapter, we describe the dynamics of probe particles in a colloidal glassy suspension of Laponite. Laponite is a colloidal discoidal particle of 25 nm in diameter and 0.92 nm thick. We take advantage of evanescent wave microscopy, and follow the movement of fluorescent latex particles.Then we image these particles. We show that for a movement that has a single characteristic time scale, it is simply a linear function of time. We find that, what ever their size, the motion of probe particles can be described by a succession of two dynamic modes, where the fastest mode corresponds to the diffusion of particles in a viscoelastic fluid.

This thesis focuses on the manipulation of rubidium 87 atoms in a microscopic optical dipole trap. The experiments are performed in various regimes where the number of atoms in the microscopic trap ranges from exactly one atom to several thousands on average.The single atom regime allows us to calibrate the experimental setup. We use it a quantum bit, which state we can prepare and read out with efficiencies of 99.97% and 98.6%, respectively. When several atoms are loaded in the microscopic trap we observe a sub-Poissonian distribution of the number of atoms due to light-assisted collisions in the presence of near-resonant light. A study of these collisions in our particular case (microscopic trap) reveals extremely high loss rates approaching the theoretical Langevin limit. Finally, we demonstrate that the loading of the microscopic trap is more efficient when we superimpose on this trap a second macroscopic trap, which we use as an atom reservoir. This reservoir allows us to load the micro trap from the macro trap in the absence of any near-resonant light, thus avoiding light-assisted collisions.The loading of the micro trap from the macro trap leads to optimal initial conditions for forced evaporation towards Bose-Einstein condensation with about ten atoms only. After evaporation we reach phase-space densities approaching the degenerate regime.

This thesis describes experimental work towards developing a trapped ion quantum information processor. An existing ion trap apparatus was capable of trapping and laser-cooling single ions or small ion strings of 40 Ca+, and had been used for studies of quantum jumps and natural lifetime measurements in Ca. This thesis describes improvements in this apparatus, which have allowed the stability and the flexibility of experimental control of the ions to be greatly increased. This enabled experiments to read out the spin state of a single trapped ion, and to load ions with isotope selectivity through photoionization. The optical systems were improved by installation of new lasers, optical reference cavities, and a system of acousto-optic modulators for laser intensity switching and frequency control. The photon counting for fluorescence detection was improved, and a new photon time-of-arrival correlation circuit developed. This has permitted rapid and more sensitive detection of micromotion, and hence cancellation of stray fields in the trap. A study of resonant circuits in the low RF, high voltage (10 MHz, 1 kV) regime was carried out with a view to developing a new RF supply for the Paul trap with reduced noise and increased power. A new supply based on a helical resonator was built and used to trap ions. This technique has reduced noise and will permit higher secular frequencies to be attained in the future. A magnetic field B in the ion trap is used to define a quantization axis, and in one series of experiments was required to be of order 100 G to provide a substantial Zeeman splitting. A set of magnetic field coils to control the size and direction of B is described. The design of these posed some problems owing to an unforseen issue with the vacuum chamber. In short, it is magnetizable and acts to first approximation like a magnetic shield. The field coils had to be sufficiently substantial to produce the desired field at the ion even in the presence of this shielding effect, and dark resonance (and other) spectra with Zeeman splitting were obtained to calibrate the field using the ion as a probe. Finally, the thesis describes the successful loading of the ion trap by laser photoionization from a weak atomic beam. This involved two new lasers at 423 nm and 389 nm. Saturated absorption spectroscopy of neutral calcium is first described, then transverse excitation of an atomic beam in our vacuum chamber is used to identify all the main isotopes of calcium and confirm their abundances in our source (a heated sample of natural calcium). Finally, photoionization is used to load the trap. This has three advantages over electron-impact ionization. By avoiding an electron gun, we avoid charging of insulating patches and subsequent electric field drift as they discharge; the flux in the atomic beam and hence calcium (and other) deposits on the electrodes can be greatly reduced; and most importantly, the photoionization is isotope selective. Evidence is presented which suggests that even with an non-enriched source, the rare isotope 43 Ca can be loaded with reasonable efficiency. This isotope is advantageous for quantum information experiments for several reasons, but chiefly because its ground state hyperfine structure can act as a stable qubit.

Infrared multiple photon dissociation (IRMPD) spectroscopy has been coupled with electronic structure calculations in order to elucidate the structures of several small biological molecules including: uracil, 5-fluorouracil, 5-fluorocytosine, ferulic acid, and a number of their related analogs. IRMPD is a powerful technique, that when combined with electronic structure calculations can provide convincing evidence for the structural characterization of ions in the gas phase. Isomers of uracil and 5-fluorouracil (5-FU) have been characterized by calculations performed at the MP2(full)/aug-cc-pVTZ level of theory; however, infrared multiple photon dissociation spectroscopy experiments proved to be unsuccessful for these species. Geometry optimization and frequency calculations have isolated the dominant isomer(s) for neutral and deprotonated uracil and 5-fluorouracil, along with several cluster interactions involving water, methanol, ammonia, and methylamine. For both uracil and 5-FU, a single relevant neutral isomer was determined, with each isomer existing in the diketo, as opposed to the enol form. Following the deprotonation of this neutral isomer, both uracil and 5-FU were permitted to form anionic cluster ions with water, methanol, ammonia, or methylamine, and based on the relative Gibbs free energies (298 K) of the calculated isomers, relevant cluster interactions were determined. For each cluster, several sites of intramolecular interaction were found to exist; however, interaction at the site of deprotonation was the most favourable in every instance. Ionic hydrogen bond interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, in addition to the cationic and anionic dimers have been characterized by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD spectra in combination with calculated spectra and relative energetics have indicated, quite conclusively, that a single isomer for each 5-FC cluster that is likely being observed experimentally except in the case of the anionic dimer, in which a combination of isomers is probable. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest energy isomer matches the experimental spectrum remarkably well. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) in which a unique tridentate ionic hydrogen bond interaction is formed. The three sites of intramolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significantly large calculated enthalpy of binding of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, indicates that the tridentate-bound dimer is observed predominantly in experiment. Comparison of the calculated relative Gibbs free energies (298 K) for this species with several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV. Protonated ferulic acid has been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311+G(d,p) level of theory. Neutral ferulic acid has been determined to undergo protonation on the carbonyl oxygen of the acid group, forming an ion of m/z 195. Due to its extensively conjugated structure, protonated ferulic acid (m/z 195) is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. First, proton transfer occurs from the carbonyl oxygen to the hydroxyl oxygen within the acid group, resulting in the loss of water and subsequently carbon monoxide, forming ions of m/z 177 and 149, respectively. The second proposed fragmentation pathway undergoes proton transfer from the phenolic group to the methoxy group resulting in loss of methanol and rearrangement to a five-membered ring of m/z 163. IRMPD spectra have been obtained for the ions m/z 195 and m/z 177, and anharmonic calculations have been performed on these species at the B3LYP/6-311+G(d,p) level of theory. The calculated anharmonic spectra for these ions match the experimental spectrum exceptionally well and strongly support the proposed fragmentation mechanisms.

In this thesis, the properties of the Bose-Einstein condensation (BEC) in low dimensions are reviewed. Three dimensional weakly interacting Bose systems are examined by the variational method. The effects of both the attractive and the repulsive interatomic forces are studied. Thomas-Fermi approximation is applied to find the ground state energy and the chemical potential. The occurrence of the BEC in low dimensional systems, is studied for ideal gases confined by both harmonic and power-law potentials. The properties of BEC in highly anisotropic trap are investigated and the conditions for reduced dimensionality are derived.

The Cerulean Warbler (Setophaga cerulea) is a mature forest obligate and one of the fastest declining songbird species in the United States. This decline may be related to a lack of disturbance within contemporary forests; however, the consequences of disturbance on the species have not been rigorously evaluated. Thus, we assessed multiple responses by Cerulean Warblers to a range of experimental forest disturbances across the core of their breeding range in the Appalachian Mountains. We quantified individual and population responses to these manipulations, and assessed the potential consequences of disturbance on the sexual signaling system. Male ceruleans were strongly attracted to intermediate and heavy disturbances at the stand scale. Despite attraction to disturbed habitats, nest success declined in these conditions, particularly in the highly productive Cumberland Mountains of northern Tennessee. Taken together, these opposing responses suggest that anthropogenically-disturbed forests may act as local ecological traps, but the impact of these local traps on the global population is dependent on several unestimated parameters. At a finer scale, selection for habitat features varied spatially. Males consistently selected for territories near canopy gaps and on productive slopes, but they displayed inconsistent territory selection in regards to tree diameter, basal area, overstory canopy cover, and canopy height. Females were more consistent in their selection of features within territories, selecting nest patches with large, well-spaced trees near disturbances. Floristically, female ceruleans consistently selected for sugar maples (Acer saccharum), white oaks (Quercus alba), and cucumber magnolias (Magnolia acuminata) as nest trees and they selected against red maples (A. rubrum) and red oaks (Q. rubra). Disturbances had little effect on male age structure, but males that occupied disturbed forest habitat were in better condition than those in undisturbed habitat. Parental behavior differed among disturbances, with birds in more highly disturbed habitats provisioning their young at greater rates, but bringing smaller food loads, potentially helping to explain the decrease in nest survival in disturbances. Finally, we found that male ceruleans displayed various plumage ornaments that signaled individual quality. However, the relationship between breast band width and body mass was contingent on habitat, and only existed in intermediate disturbances.

Two problems hampering efforts to produce salt-tolerant plants through constitutive expression of transgenes include: 1. Spatial control. Particular cell-types must respond specifically to salt stress to minimise the amount of Na⁺ delivered to the shoot; and, 2. Temporal control. Transgenes are typically expressed in plants at similar levels through time, irrespective of the stress encountered by the plant, which may exacerbate pleiotropic effects and means that, particularly in low-stress conditions, costly and/or detrimental metabolic processes may be active, thus reducing yield. To address these issues, Gateway® destination vector constructs were developed combining the GAL4 UAS (upstream activating sequence) with the ethanol-inducible gene expression system to drive inducible cell-specific expression of Na⁺ transporter transgenes (or to silence salt transporter transgenes inducibly and cell-specifically). Rice (Oryza sativa L. cv. Nipponbare) GAL4-GFP enhancer trap lines (Johnson et al., 2005: Plant J. 41, 779-789) that express GAL4 and GFP specifically in either the root epidermis or xylem parenchyma (and therefore ‘trap’ cell-type specific enhancer elements) were transformed with this GAL4 UAS – ethanol switch construct, thereby allowing both spatial and temporal control of transgenes. In preliminary experiments, the expression system successfully limited the expression of RFP to specific cell-types after induction with ethanol. Other genes expressed using this system include PpENA1, a Na⁺-extruding ATPase from the moss, Physcomitrella patens, and AtHKT1;1, a Na ⁺ transporter from Arabidopsis thaliana. The two enhancer trap rice lines were also transformed with the GAL4 UAS driving stable expression of AtHKT1;1 and PpENA1 specifically in root epidermal or xylem parenchyma cells. Expression of AtHKT1;1 in root epidermal cells reduced Na⁺ accumulation in the shoots, while expression in the root xylem parenchyma appeared to have little effect on shoot Na⁺ accumulation. Using cryo-scanning electron microscopy (SEM) X-ray microanalysis, the outer cells of the roots of the line expressing AtHKT1;1 in the epidermal cells were found to accumulate higher levels of Na⁺ than the parental enhancer trap line. Additionally, this line had decreased unidirectional ²²Na⁺ influx. Similar results were observed for plants expressing AtHKT1;1 driven by the CaMV 35S / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1325289 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

Published information on the structure and regulation of H. pylori promoters is limited. The work presented in this thesis describes the cloning and characterisation of promoter regions from a clinical isolate of H. pylori, and the development of an alternative, non-radioactive method for verifying the location of transcriptional start sites of bacterial promoters. H. pylori 4187E promoters were randomly cloned into the promoter-trap vector pKK232-8 in Escherichia coli DH5α using two sets of restriction enzymes. Vector pKK232-8 contains a promoterless chloramphenicol acetyltransferase (CAT) gene. Seventy-four promoter-containing clones were isolated from selective media based on their resistance to chloramphenicol. The strength of each promoter was analysed qualitatively, using chloramphenicol minimum inhibitory concentrations, and quantitatively, using CAT assays following exposure of the clones to pH 4 and pH 7. Selected promoter fragments were subcloned into the GFP reporter vector pFPV25, containing a promoterless gfp gene. The subclones were exposed to buffered LB broth at pH 4, 5, 6, 7 and 8, for varying lengths of time, to study acid-induced regulation of gene expression. Subclones were examined qualitatively, using visual examination of GFP fluorescence and fluorescence microscopy, and quantitatively, using flow cytometry following acid shock. DNA sequences were determined for 61 of the 74 H. pylori promoters, and sequence alignments with the published H. pylori strains (26695 and J99) were performed. The transcriptional start site of 27 H. pylori promoter fragments was experimentally mapped using a fluorescence-based primer extension protocol developed by our group. Potential -35 and -10 sequences were identified for each promoter, and a new consensus sequence for H. pylori promoters was proposed based upon these results. This study has considerably expanded knowledge of H. pylori promoter sequences and transcriptional start sites based on those which also function in E. coli. It has also revealed several H. pylori promoters which appear to respond to acid stress

Thesis (M.S.)--Miami University, Dept. of Chemistry and Biochemistry, 2008. / Title from first page of PDF document. Includes bibliographical references.

Made available in DSpace on 2015-04-17T14:55:36Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 1145467 bytes, checksum: c728d8e2b9bf1205710f19f317acdccc (MD5) Previous issue date: 2009-02-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The use of trap nests supplies important biological information about nesting bees and wasps. However, the knowledge about the factors influencing on management of these groups is still scarce. This work aimed to analyze some community structure parameters (species abundance, richness, composition and predominance) in two agricultural areas in the Zona da Mata macro region of Paraiba State: Shading, block material (wood or vermiculite), and tubs opening diameter and cardinal orientation. It was verified the influence of these four factors in the community structure parameters. Both sites where similar in species richness and composition. Alhandra site had an accentuated abundance, due Trypoxylon aurifrons e Centris analis. In shaded area most species where more abundant than in sunny one. Otherwise, in Alhandra site the sunny area had higher species richness. Wood blocks where more expensive and difficult to manufacture. Meanwhile, they had more attractiveness than vermiculite blocks, especially for bees. Number of nests was smaller in predominant wind direction trap nests. The two most abundant species where diameter-generalists. The results and the Trypoxylon aurifrons behavior observed suggest that this species should compete by trap nests holes with bees. / A utilização de ninhos-armadilha provê informações importantes acerca da biologia das espécies abelhas e vespas nidificantes. Entretanto, o conhecimento sobre os fatores que influenciam o manejo dessas espécies ainda é escasso. O presente estudo analisou parâmetros da estrutura da comunidade (abundância, riqueza, composição e predominância de espécies) em duas áreas agrícolas dentro da Zona da Mata paraibana (Alhandra e EMEPA). Quatro variáveis foram avaliadas: grau de sombreamento dos ninhosarmadilha, tipo de bloco usado como substrato (madeira ou vermiculita), direção para a qual a entrada dos tubos encontrava-se voltada e diâmetro do tubo. Desse modo, foi verificado o grau de influência dessas quatro variáveis nos parâmetros da estrutura da comunidade estudados. As duas áreas se mostraram semelhantes quanto à riqueza e composição. Entretanto, em Alhandra foi observada uma abundância acentuada, ocasionada por Trypoxylon aurifrons e Centris analis. Apesar da maioria das espécies ter sido mais abundante na área sombreada, observou-se uma maior riqueza de espécies na área ensolarada em Alhandra. Quanto ao material, observou-se que os blocos de madeira, apesar de mais caros e de difícil manejo, foram mais atrativos que os de vermiculita, especialmente para as espécies de abelhas. O número de nidificações foi menor na direção voltada para os ventos predominantes nas áreas. As duas espécies mais abundantes foram mais generalistas quanto à utilização de diferentes diâmetros. Os resultados obtidos e o comportamento de Trypoxylon aurifrons sugerem que essa espécie pode competir com as espécies de abelhas pelos tubos de ninhos-armadilha agrupados.