ALLERGEN SENSITIZATION AND IMMUNOMODULATION BY SYNTHETIC LIGANDS, PUL-042, IN AN ALLERGEN-INDUCED ASTHMA MURINE MODEL

Allergen-induced asthma is the leading form of asthma and a chronic condition worldwide. Common allergens are known to contribute to the pathogenesis of this disease. Murine models of allergic asthma have mostly used an intraperitoneal route of sensitization (not airway) to study this disease. Allergic asthma pathophysiology involves the activation of TH2-specific cells, which triggers production of IgE antibodies, the up-regulation of TH2-specific cytokines (i.e. IL-4, IL-5, IL-9 and IL-13), increased airway eosinophilia, and mucin hypersecretion. Although there are several therapeutics currently treating asthmatic patients, some of these treatments can result in drug tolerance and may be linked to increased mortality. CpG oligodeoxynucleotides (ODNs) is a synthetic ligand that targets Toll-like Receptor (TLR) 9. It has been evaluated as a therapeutic agent for the treatment of cancer, infectious diseases, and for treating allergy and asthma. PUL-042 is also a synthetic TLR ligand and is composed of two agonists against TLR2/6 heterodimer and TLR9. Previous studies have evaluated PUL-042 for its ability to confer resistance against bacterial and viral lung infection. These findings, combined with studies performed using CpG ODNs, led to speculation that PUL-042 dampens the immune response in allergen-induced asthma. My thesis research investigated airway route sensitization and airway delivery of PUL-042 to evaluate its effects in reducing an allergen-induced asthma phenotype in a murine model. The results of this study contribute to the foundation for future investigations to evaluate the efficacy of PUL-042 as a novel therapy in allergic-asthma disease.

DETERMINING THE GENOTYPE-PHENOTYPE CONNECTION IN SYNTHETIC INDUCIBLE GENE EXPRESSION SYSTEMS

Introduction Gene expression is an important process whereby the genotype controls an individual cell’s phenotype. However, even genetically identical cells display a variety of phenotypes, which may be attributed to differences in their environment. Yet, even after controlling for these two factors, individual phenotypes still diverge due to noisy gene expression. Synthetic gene expression systems allow investigators to isolate, control, and measure the effects of noise on cell phenotypes. I used mathematical and computational methods to design, study, and predict the behavior of synthetic gene expression systems in S. cerevisiae, which were affected by noise. Methods I created probabilistic biochemical reaction models from known behaviors of the tetR and rtTA genes, gene products, and their gene architectures. I then simplified these models to account for essential behaviors of gene expression systems. Finally, I used these models to predict behaviors of modified gene expression systems, which were experimentally verified. Results Cell growth, which is often ignored when formulating chemical kinetics models, was essential for understanding gene expression behavior. Models incorporating growth effects were used to explain unexpected reductions in gene expression noise, design a set of gene expression systems with “linear” dose-responses, and quantify the speed with which cells explored their fitness landscapes due to noisy gene expression. Conclusions Models incorporating noisy gene expression and cell division were necessary to design, understand, and predict the behaviors of synthetic gene expression systems. The methods and models developed here will allow investigators to more efficiently design new gene expression systems, and infer gene expression properties of TetR based systems.

Induction of synthetic lethality in mutant KRAS cells for non-small cell lung cancers chemoprevention and therapy

Lung cancer is the leading cause of cancer death in both men and women in the United States and worldwide. Despite improvement in treatment strategies, the 5-year survival rate of lung cancer patients remains low. Thus, effective chemoprevention and treatment approaches are sorely needed. Mutations and activation of KRAS occur frequently in tobacco users and the early stage of development of non-small cell lung cancers (NSCLC). So they are thought to be the primary driver for lung carcinogenesis. My work showed that KRAS mutations and activations modulated the expression of TNF-related apoptosis-inducing ligand (TRAIL) receptors by up-regulating death receptors and down-regulating decoy receptors. In addition, we showed that KRAS suppresses cellular FADD-like IL-1β-converting enzyme (FLICE)-like inhibitory protein (c-FLIP) expression through activation of ERK/MAPK-mediated activation of c-MYC which means the mutant KRAS cells could be specifically targeted via TRAIL induced apoptosis. The expression level of Inhibitors of Apoptosis Proteins (IAPs) in mutant KRAS cells is usually high which could be overcome by the second mitochondria-derived activator of caspases (Smac) mimetic. So the combination of TRAIL and Smac mimetic induced the synthetic lethal reaction specifically in the mutant-KRAS cells but not in normal lung cells and wild-type KRAS lung cancer cells. Therefore, a synthetic lethal interaction among TRAIL, Smac mimetic and KRAS mutations could be used as an approach for chemoprevention and treatment of NSCLC with KRAS mutations. Further data in animal experiments showed that short-term, intermittent treatment with TRAIL and Smac mimetic induced apoptosis in mutant KRAS cells and reduced tumor burden in a KRAS-induced pre-malignancy model and mutant KRAS NSCLC xenograft models. These results show the great potential benefit of a selective therapeutic approach for the chemoprevention and treatment of NSCLC with KRAS mutations.

Examination of synthetic retinoid -induced apoptosis in cutaneous squamous cell carcinomas: Mechanisms and implications for chemoprevention and chemotherapy with retinoids

Non-melanoma skin cancers, including basal cell carcinoma and squamous cell carcinoma (SCC), are the most common neoplasms in the United States with a lifetime risk nearly equal to all other types of cancer combined. Retinoids are naturally occurring and synthetic analogues of vitamin A that bind to nuclear retinoid receptors and modulate gene expression as a means of regulating cell proliferation and differentiation. Retinoids have been employed for many years in the treatment of various cutaneous lesions and for cancer chemoprevention and therapy. The primary drawback limiting the use of retinoids is their toxicity, which is also associated with receptor-gene interactions. In this study, the effects of the synthetic retinoids N-(4-hydroxyphenyl)retinamide (4HPR) and 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid (CD437) were examined in cutaneous keratinocytes. Four human cutaneous SCC cell lines were examined along with normal human epidermal keratinocyte (NHEK) cells from two donors. Sensitivity to 4HPR or CD437 alone or in combination with other agents was determined via growth inhibition, cell cycle distributions, or apoptosis induction. Both synthetic retinoids were able to promote apoptosis in SCC cells more effectively than the natural retinoid all-trans retinoic acid. Apoptosis could not be inhibited by nuclear retinoic acid receptor antagonists. In NHEK cells, 4HPR induced apoptosis while CD437 promoted G1 arrest. 4HPR acted as a prooxidant by generating reactive oxygen species (ROS) in SCC and NHEK cells. 4HPR-induced apoptosis in SCC cells could be inhibited or potentiated by manipulating cellular defenses against oxidative stress, indicating an essential role for ROS in 4HPR-induced apoptosis. CD437 promoted apoptosis in SCC cells in S and G2/M phases of the cell cycle within two hours of treatment, and this rapid induction could not be blocked with cycloheximide. This study shows: (1) 4HPR- and CD437-induced apoptosis do not directly involve a traditional retinoid pathway; (2) 4HPR can act as a prooxidant as a means of promoting apoptosis; (3) CD437 induces apoptosis in SCC cells independent of protein synthesis and is potentially less toxic to NHEK cells; and (4) 4HPR and CD437 operate under different mechanisms with respect to apoptosis induction and this may potentially enhance their therapeutic index in vivo. ^

(Table 2) Actual and synthetic mass accumulation rate data and their absolute differences for ODP Site 115-707

Synthetic mass accumulation rates have been calculated for ODP Site 707 using depth-density and depth-porosity functions to estimate values for these parameters with increasing sediment thickness, at 1 Ma time intervals determined on the basis of published microfossil datums. These datums were the basis of the age model used by Peterson and Backman (1990, doi:10.2973/odp.proc.sr.115.163.1990) to calculate actual mass accumulation rate data using density and porosity measurements. A comparison is made between the synthetic and actual mass accumulation rate values for the time interval 37 Ma to the Recent for 1 Myr time intervals. There is a correlation coefficient of 0.993 between the two data sets, with an absolute difference generally less than 0.1 g/cm**2/kyr. We have used the method to extend the mass accumulation rate analysis back to the Late Paleocene (60 Ma) for Site 707. Providing age datums (e.g. fossil or magnetic anomaly data) are available the generation of synthetic mass accumulation rates can be calculated for any sediment sequence.

Comparisons of observed ice properties and Envisat Advanced Synthetic Aperture Radar (ASAR) data during Nathanial B. Palmer cruise NBP09-01 and Oden cruise OSO08/09

Envisat Advanced Synthetic Aperture Radar (ASAR) Wide Swath Mode (WSM) images are used to derive C-band HH-polarization normalized radar cross sections (NRCS). These are compared with ice-core analysis and visual ship-based observations of snow and ice properties observed according to the Antarctic Sea Ice Processes and Climate (ASPeCt) protocol during two International Polar Year summer cruises (Oden 2008 and Palmer 2009) in West Antarctica. Thick first-year (TFY) and multi-year (MY) ice were the dominant ice types. The NRCS value ranges between -16.3 ± 1.1 and -7.6 ± 1.0 dB for TFY ice, and is -12.6 ± 1.3 dB for MY ice; for TFY ice, NRCS values increase from ~-15 dB to -9 dB from December/January to mid-February. In situ and ASPeCt observations are not, however, detailed enough to interpret the observed NRCS change over time. Co-located Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E) vertically polarized 37 GHz brightness temperatures (TB37V), 7 day and 1 day averages as well as the TB37V difference between ascending and descending AMSR-E overpasses suggest the low NRCS values (-15 dB) are associated with snowmelt being still in progress, while the change towards higher NRCS values (-9dB) is caused by commencement of melt-refreeze cycles after about mid-January.

Near-coastal circum-Antarctic iceberg size distributions determined from Synthetic Aperture Radar images

The Radarsat-1 Antarctic Mapping Project (RAMP) compiled a mosaic of Antarctica and the adjacent ocean zone from more than 3000 high-resolution Synthetic Aperture Radar (SAR) images acquired in September and October 1997. The mosaic with a pixel size of 100 m was used to determine iceberg size distributions around Antarctica, combining an automated detection with a visual control of all icebergs larger than 5 km**2 and correction of recognized false detections. For icebergs below 5 km**2 in size, the numbers of false detections and accuracies of size retrievals were analyzed for three test sites. Nearly 7000 icebergs with horizontal areas between 0.3 and 4717.7 km**2 were identified in a near-coastal zone of varying width between 20 and 300 km. The spatial distributions of icebergs around Antarctica were calculated for zonal segments of 20° angular width and related to the types of the calving fronts in the respective section. Results reveal that regional variations of the size distributions cannot be neglected. The highest ice mass accumulations were found at positions of giant icebergs (> 18.5 km) but also in front of ice shelves from which larger numbers of smaller icebergs calve almost continuously. Although the coastal oceanic zone covered by RAMP is too narrow compared to the spatial coverage needed for oceanographic research, this study nevertheless demonstrates the usefulness of SAR images for iceberg research and the need for repeated data acquisitions extending ocean-wards over distances of 500 km and more from the coast to monitor iceberg melt and disintegration and the related freshwater input into the ocean.

P-wave velocities and applied bed thickness and velocity changes for synthetic seismograms, ODP Leg 188 and Leg 119 sites

Synthetic seismograms provide a crucial link between lithologic variations within a drill hole and reflectors on seismic profiles crossing the site. In essence, they provide a ground-truth for the interpretation of seismic data. Using a combination of core and logging data, we created synthetic seismograms for Ocean Drilling Program Sites 1165 and 1166, drilled during Leg 188, and Site 742, drilled during Leg 119, all in Prydz Bay, Antarctica. Results from Site 1165 suggest that coring penetrated a target reflector initially thought to represent the onset of drift sedimentation, but the lithologic change across the boundary does not show a change from predrift to drift sediments. The origin of a shallow reflector packet in the seismic line across Site 1166 and a line connecting Sites 1166 and 742 was resolved into its constituent sources, as this reflector occurs in a region of large-scale, narrowly spaced impedance changes. Furthermore, Site 1166 was situated in a fluvio-deltaic system with widely variable geology, and bed thickness changes were estimated between the site and both seismic lines.

Residual effect of natural and synthetic zinc chelates on zinc in a soil solution of a waterlogged acidic soil. Evolution of the pH and redox potential.

Zinc chelates have been widely used to correct deficiencies in this micronutrient in different soil types and under different moisture conditions. The aging of the metal in soil could cause a change in its availability. Over time the most labile forms of Zn could decrease in activity and extractability and change to more stable forms. Various soil parameters, such as redox conditions, time, soil type and moisture conditions, affect the aging process and modify the solubility of the metal. In general, redox conditions influence pH and also the chemical forms dissolved in the soil solution. Soil pH also affects Zn solubility; at high pH values, most of the Zn is present in forms that are not bioavailable to plants. The objective of this study was to determine the changes in Zn over time in a soil solution in a waterlogged acidic soil to which synthetic and natural chelates were applied

Residual effect of synthetic Zn chelates on the availability of this metal in different soils under waterlogged conditions.

Adding Zn improves crop growth, increases seed yield and also positively affects nutritional quality. After Zn fertilization, there is normally a period of several years in which residual effects provide an adequate supply of Zn to successive crops. Immediately after the application of Zn sources water-soluble Zn slowly but continually decreases. Various factors, including time and moisture conditions, affect the aging process and modify the solubility of the metal in soil and therefore its availability. In previous experiments, we studied the residual effect of synthetic chelates, obtained that the amounts of potentially available Zn decreased in the second cropping year due to aging processes. The present study was undertaken to verify variations in the residual effects of applying four different synthetic Zn sources

Multipath Reflectivity Estimation in Urban Environments for Synthetic Aperture Radar Images

Synthetic Aperture Radar (SAR) images a target region reflectivity function in the multi-dimensional spatial domain of range and cross-range. SAR synthesizes a large aperture radar in order to achieve a finer azimuth resolution than the one provided by any on-board real antenna. Conventional SAR techniques assume a single reflection of transmitted waveforms from targets. Nevertheless, today¿s new scenes force SAR systems to work in urban environments. Consequently, multiple-bounce returns are added to directscatter echoes. We refer to these as ghost images, since they obscure true target image and lead to poor resolution. By analyzing the quadratic phase error (QPE), this paper demonstrates that Earth¿s curvature influences the defocusing degree of multipath returns. In addition to the QPE, other parameters such as integrated sidelobe ratio (ISLR), peak sidelobe ratio (PSLR), contrast (C) and entropy (E) provide us with the tools to identify direct-scatter echoes in images containing undesired returns coming from multipath.

Synthetic strategy of porous ZnO and CdS nanostructures doped ferroelectric liquid crystal and its optical behavior

A simple and scalable chemical approach has been proposed for the generation of 1-dimensional nanostructures of two most important inorganic materials such as zinc oxide and cadmium sulfide. By controlling the growth habit of the nanostructures with manipulated reaction conditions, the diameter and uniformity of the nanowires/nanorods were tailored. We studied extensively optical behavior and structural growth of CdS NWs and ZnO NRs doped ferroelectric liquid crystal Felix-017/100. Due to doping band gap has been changed and several blue shifts occurred in photoluminescence spectra because of nanoconfinement effect and mobility of charges.

Integrated studies for the evaluation of conservation treatments on stone material from archaeological sites. Application to the case of Mérida (Spain)

In recent decades archaeological sites have been subject of many interventions. The application of conservation treatments, such us consolidation and protection ones by means of using, for instance, synthetic resins or organosilicic compounds, has been demonstrated inadequate in many cases, and even harmful for the heritage materials [1]. Evaluation studies should be a mandatory task, ideally before and after the intervention, but both tasks are complex and unusual in the case of archaeological heritage. Moreover, there is a general lack of knowledge in the mid and long term effects of these treatments, and how to act when these have resulted in deterioration of the original material. Remains of Roman Augusta Emerita, located in Merida (Spain), have gone through many interventions since the first archaeological campaign, in 1910. Some of them have demonstrated already to be harmful [2], others, more recent, must be evaluated in order to determine its effectiveness and durability, considering that many of these treatments are currently still applied. For this purpose a range of parameters has been measured such as color, surface hardness and roughness, mechanical or hydric properties, porosity, etc. on the original material (granite, marble and mortars mainly), and then the transformations of those same parameters analyzed after treatment, both in situ, in places where a intervention is documented, and in the laboratory, in samples. The study is being conducted both in the laboratory (Petrophysics Laboratory within IGEO) and in situ, on selected archaeological sites of Mérida (Theater and House of Mitreo). The comparison of results in untreated and treated areas of the site, and in treated-untreated samples, allows the distinction of variables that affect the interaction between products and stone material, issues such us effectiveness and durability of treatment and its validation or dismissal.