The bacterial pathogen Vibrio cholerae is responsible for ongoing cholera outbreaks in Haiti and elsewhere. Association of V. cholerae with the human host is responsible for fatal disease, but the bacteria also reside as natural inhabitants of aquatic environments, commonly attaching as biofilms to chitinous surfaces of copepods and crabs. Prior studies in V. cholerae demonstrated that competence for genetic transformation, a mechanism of horizontal gene transfer (HGT), requires the TfoX regulator protein that is triggered by chitin, and the HapR transcription factor that is made in response to quorum sensing (QS) signals produced by V. cholerae and Vibrios. To define regulatory components connecting extracellular signals to natural competence, I first demonstrated that QS molecules produced by Vibrios within multi-species chitinous biofilms are required for DNA uptake by V. cholerae, confirming the critical role of QS signals in HGT. Second, I identified by transposon-mutagenesis a new positive regulator of competence, CytR (cytidine repressor), only studied prior in E. coli as a regulator of nucleoside scavenging. Specific mutations in V. cholerae CytR impaired expression of competence genes and halted DNA uptake; and the addition of exogenous cytidine had similar affects as predicted in E. coli. V. cholerae and other competent Vibrios encode TfoX, HapR, and CytR, although none of these regulators directly controls genes coding for the DNA uptake apparatus. Thus, these results have uncovered a regulatory network, likely used by many Vibrios, that contains additional factors linking several extracellular chemical molecules (cytidine, chitin, and QS signals) to DNA uptake. My study has begun to define a molecular mechanism by which both environment and genetics contribute to genome evolution for this important marine pathogen.

Organic solar cells have caught considerable attention in the past few years due to their potential for providing environmentally safe, flexible, lightweight, inexpensive, and roll-to-roll feasible production solar cells. However, the efficiency achieved in current organic solar cells is quite low, yet quick and successive improvements render it as a promising alternative. A hopeful approach to improve the efficiency is by exploiting the tandem concept which consists of stacking two or more organic solar cells in series. One important constituent in tandem solar cells is the middle electrode layer which is transparent and functions as a cathode for the first cell and an anode for the second cell. Most studies done so far have employed noble metals such as gold or silver as the middle electrode layer; however, they suffered from several shortcomings especially with respect to reproducibility. This thesis focuses on studying a new trend which employs an oxide material based on nano-particles as a transparent cathode (such as Zinc-oxide-nano-particles) along with a transparent anode so as to replace the middle electrode. Thus, this work presents a study on solution processable zinc oxide (ZnO) nanostructures, their proper handling techniques, and their potential as a middle electrode material in Tandem solar cells in many different configurations involving both polymer and small molecule materials. Moreover, the ZnO-np potential as a candidate for acceptor material is also investigated.

In silico ligand docking is a versatile and common technique when predicting ligands and inhibitors for protein binding sites. The various docking programmes aim to calculate binding energies and to predict interactions, thus identifying potential ligands.The currently available programmes lack satisfying means by which to account for structural water molecules which can either mediate protein-ligand contacts or be displaced upon ligand binding. The present project aims to generate data to facilitate the global work of developing scoring functions in docking programmes to account for structural water molecules contribution to ligand binding to fill the said void. This is done by validating the performance of docking using a simple model system (cytochrome C peroxidase (CCP) W191G) containing four well ordered, deeply buried structural water molecules which are known to either interact with a ligand or to be displaced upon ligand binding.Known ligands were docked into eight (crystallographically determined) receptor set-ups comprising the receptor and no, one or two of the water molecules. The performance was validated by comparison of the binding modes of the docked ligands and the crystal structures, comparison of docking scores of the ligands in the different set-ups, enrichment of the ligands from a database of decoys and finally by predicting new ligands from the decoy database. In addition a high resolution crystal structure of CCP W191G in complex with 3-aminopyridine (3AP) was determined in order to resolve ambiguities in the binding mode of this ligand.

The present Master thesis describes the development and optimization of a fed-batch process for production of recombinant proteins in Escherichia coli BL21(DE3) in a multi-fermentor system. The system consists of six 1-liter fermentors, capable of producing 500-1500 μg/mL with present protocol. Response surface methodology (RSM) was used for multivariable optimization regarding cultivation time, pH, temperature and feed rate. Optimal protein expression conditions were found out to be 17.8 h cultivation time, 36.7 ºC, pH 6.8 and a feed rate corresponding to specific growth of 0.23 h-1, on glucose substrate. The aggregation of expressed proteins to inclusion bodies, could not be affected by the various growth conditions employed during cultivations. A study was conducted regarding growth conditions effect on phosphogluconoylation of expressed proteins. In ten fed-batch cultivations on glucose, LC/MS analysis showed a gluconoylated fraction with additional 178 Da mass, but no correlation between growth conditions and gluconoylation could be found. In two fed-batch cultivations on glycerol-feed, a lower feed rate resulted in no gluconoylation, while a higher did. An explanation would be that the lower amount of available intra-cellular carbon limits formation of gluconoylation precursors.

STUDIES OF INTERACTION OF SMALL MOLECULES WITH WATER CONDENSED MEDIA<br /><br /> The present work reports experimental and theoretical studies of the intermolecular interactions in condensed water media. The chemical objects comprise pristine ice and polar organic substances: acetone, acetaldehyde, methanol and chloroform and bi-component water-organic deposits. The experimental part of the studies includes the Fourier Transform Infrared Reflection Absorption spectral (FTIR RAS) examination of the processes of film growth by vapor deposition on cold metal substrate and subsequent annealing. The theoretical studies include <em>ab initio</em> (<em>MP2</em>) and semi-empirical (<em>B3LYP</em>) calculations on the small water and water-organic clusters and classical molecular dynamics simulations of the adsorption of inert guests (Xe/Rn) on the ice surface. The FTIR RA spectral studies reveal that depending on the deposition conditions condensed water media exist in two principal structural forms: noncrystalline and polycrystalline. The former is characterized by porous structure while the latter exists as a non-porous medium with smooth external interface. On annealing, characteristic spectral changes indicate on a rapid crystallization occurring at a certain temperature range. The initial adsorption of organic molecules is accompanied by the hydrogen-bonded coordination between the functional group of organic species and non-coordinated hydroxyl group of the ice surface, the topology of which depends on the electronic properties of the functional group. The computational studies of small water-organic clusters reveal, in particular, two major coordination minima for carbonyl group: a single hydrogen-bonded in-plane complex and a double hydrogen-bonded in-plane complex. The classical molecular dynamics of Xe/Rn species on the ice interface is consistent with two distinctly different surface adsorption sites: one that delocalized over the entire surface and one that confined to small opening in the top ice layer, disrupted by the thermal molecular motion. The penetration barrier is associated with van der Walls repulsion of guest species from the ordered water hexagonal arrangement. A thermo-disruption of latter leads to a rapid diffusion of guest species inside ice medium.

Anisotropic molecules confined on a spherical or other curved surface can display coupled positional and orientational orderings, which make possible applications in physics, chemistry, biology, and material science. Therefore, controlling the order of such system has attracted much attention recently. Several distinct conformations of rod-like or chain-like molecules confined on a spherical surface have been predicted, including states such as tennis-ball, rectangle, and cut-and-rotate splay. These conformations have four +1/2 defects and are suggested to dominate over the splay conformation that has two +1 defects. For the purpose of investigating the conformations of 2-fold anisotropic molecules confined on the spherical surface, the author of this thesis utilizes the Onsager model to study the system of rigid rods and conducts Monte Carlo simulations on the bead-bond model to research the system of semiflexible polymer chains. At low surface coverage density, no particular pattern of the molecules would form. However, coupled positional and orientational ordering begins to emerge beyond a transition density. On the basis of the numerical solutions of the Onsager model of rigid rods, the splay conformation is shown to be the only stable state. On the other hand, Monte Carlo simulations on a polymer system indicate that the ordered state always accompanies the tennis-ball symmetry. With comparison to the continuous isotropic-nematic transition of a fluid of hard rods embedded in a flat two-dimensional space, the disorder-order transition for both the system of rigid rods and the system of polymer chains confined on the spherical surface has first-order phase-transition characteristics.

No description available.

No description available.

The human body is an intricate network of many highly regulated biochemical processes and cell adhesion is one of them. Cell adhesion is mediated by specific interactions between molecules on apposing cell surfaces and is critical to many physiological and pathological processes like inflammation and cancer metastasis. During inflammation, blood-borne circulating leukocytes regularly stick to and roll on the vessel walls, which consist in part, adhesive contacts mediated by the selectin family of adhesion receptors (P-, E- and L-selectin). This is the beginning of a multi-step cascade that ultimately leads to leukocyte recruitment in areas of injury or infection. In vivo, selectin-mediated interactions take place in a hydrodynamic milieu and hence, it becomes imperative to study these interactions under very similar conditions in vitro. The goal of this project was to characterize the kinetic and mechanical properties of selectin interactions with different physiologically relevant ligands and selectin-specific monoclonal antibodies (mAbs) under a mechanically stressful milieu, using atomic force microscopy (AFM). Elasticity studies revealed that bulk of the complex compliance came from the selectins, with the ligands or mAbs acting as relatively stiffer components in the stretch experiments. Furthermore, molecular elasticity was inversely related to selectin length with the Consensus Repeats (CRs) behaving as Hookean springs in series. Besides, monomeric vs. dimeric interactions could be clearly distinguished from the elasticity measurements. L-selectin dissociation studies with P-selectin Glycoprotein Ligand 1 (PSGL-1) and Endoglycan revealed that catch bonds operated at low forces while slip bonds were observed at higher forces. These results were consistent with previous P-selectin studies and suggested that catch bonds could contribute to the shear threshold for L-selectin-mediated rolling By contrast, only slip bonds were observed for L-selectin-antibody interactions, suggesting that catch bonds could be a common characteristic of selectin-ligand interactions. Force History studies revealed that off-rates of L-selectin-sPSGL-1 (or 2-GSP-6) interactions were not just dependent on applied force, as has been widely accepted but in fact, depended on the entire history of force application, thus providing a new paradigm for how force could regulate bio-molecular interactions. Characterizing selectin-ligand interactions at the molecular level, devoid of cellular contributions, is essential in understanding the role played by molecular properties in leukocyte adhesion kinetics. In this aspect, data obtained from this project will not only add to the existing body of knowledge but also provide new insights into mechanisms by which selectins initiate leukocyte adhesion in shear.

The work presented herein describes efforts to synthesize and characterize cyanide-bridged molecular compounds with high-spin ground states. This investigation focused primarily on the assembly of hexacyanometallate units with convergent cationic metal complexes that are coordinated to capping ligands. In this manner, a family of related compounds was developed that serve as models for understanding the role of magnetic exchange interactions and anisotropy in nanomagnetic materials. The work presented in Chapter II describes the successful incorporation of the [Fe(CN)6]3- building block into planar geometries with nuclearities ranging from three to ten metal centers. In Chapter III, this methodology was optimized to yield two pentanuclear FeIII/NiII clusters, namely, the trigonal bipyramidal unit, {[Ni(tmphen)2]3[Fe(CN)6]2}, and the extended square, {[Ni(bpy)2(H2O)][Ni(bpy)2]2-[Fe(CN)6]2}. Magnetic measurements on pure phases of these samples revealed that each system exhibits ferromagnetic coupling between the L.S. FeIII and NiII centers, but neither exhibits slow paramagnetic relaxation effects down to T=2K. In Chapter IV, this chemistry was extended to the [Mn(CN)6]3-building block in order to increase magnetic exchange coupling and anisotropy in this cluster type, efforts that resulted in the isolation of the molecule, {[Mn(tmphen)2]3[Mn(CN)6]2}. This cluster exhibits intramolecular antiferromagnetic exchange interactions between the Mn centers which lead to an S=11/2 ground state and a negative ZFS value (D=-0.348 cm-1), parameters that support the experimental observation of Single-Molecule Magnet (SMM) behavior at low temperatures. A detailed investigation of the physical and structural properties of {[Co(tmphen)2]3[Fe(CN)6]2} in Chapters V and VI led to the realization that the cluster exhibits sensitivity to temperature and humidity. The molecule exists in three different electronic isomeric forms in the solid state and undergoes a charge-transfer induced spin-transition (CTIST) under the influence of temperature. The results presented in Chapter VI describe the behavior of this same cluster in solution, the highlight of which is the discovery that water reacts with the cluster to form a fourth electronic isomer. Finally, it is described in Chapter VII that this Co/Fe trigonal bipyramidal unit can be used as a building block for systematically incorporating three metal types into a family of 1-D chain and cluster compounds.