Browsing by Subject "Extraction"
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Item Concentration and extraction of Bacillus anthracis spores and ricin.(2009-06) Leishman, Oriana NicoleFood is an essential part of life for every human and animal. In order to feed the world, food production has become a global industry. This globalization brings efficiency of production, transportation, and year round availability of many ingredients. However, mass production of food also means that any mistake made during production is magnified in scale and distribution. Recent incidents of food contamination have involved not only traditional food pathogens, such as Salmonella and Escherichia coli O157, but also have included chemical contaminants such as melamine. These incidents serve to highlight the inherent vulnerability of food to contamination. Although the majority of foodborne illnesses are caused by a small group of pathogens, this does not preclude other bacteria or agents from being transmitted through food sources. Many potential bioterrorist agents have also the potential to be transmissible through food and water sources. Some of these agents, such as Bacillus anthracis spores and ricin toxin, are also resistant to the effects of existing food processing technologies such as pasteurization. Given the inherent vulnerability of the food production system, it seems a likely target for potential bioterrorism attack. Many rapid and sensitive tests have been developed to detect biological agents in a variety of settings. However, the complex nature of food matrices often limits the application of these tests to food sources. In addition, the distribution of a select agent in a food source may not be homogeneous, and testing of small samples may not represent the whole batch. The goal of this project was to design and test pre-analytical extraction techniques for two potential bioterrorism agents, B. anthracis spores and ricin toxin, from liquid foods. The outcome of this project was the development of a rapid concentration and extraction protocol for milk and fruit juice potentially contaminated with B. anthracis spores. The resulting sample was compatible with detection via real-time PCR for both milk and fruit juice samples and juice samples were compatible with detection with a commercially available lateral flow immunoassay. This concentration and extraction procedure enhanced the limit of detection by 2 log CFU/ml spores, such that real-time PCR can consistently detect B. anthracis at a level of 10 spores/mL in the initial sample. This project also examined the application of immunomagnetic separation for extraction of ricin toxin from liquids. Results from this portion of the project suggested that immunomagnetic beads can specifically bind ricin in traditional immunomagnetic separation. However, recirculating immunomagnetic separation using the Pathatrix® system was not demonstrated to specifically bind ricin.Item On the geometric and statistical signature of landscape forming processes.(2009-12) Passalacqua, PaolaThe physical processes that shape landscapes are complex and involve the interaction of water, soil, vegetation and biota over a range of scales. Yet, as complex as these interactions may seem to be, the landscapes we see around us often exhibit striking hierarchical order and geometric/statistical properties that are subject to scale renormalization. The overall goal of this research is to contribute to the theoretical foundation of extracting geomorphic features of interest from high resolution topography and use the extracted features for process understanding and for advancing landscape evolution modeling. Specifically, an advanced methodology for geomorphic feature extraction is developed and implemented on several high resolution data sets of different characteristics, from a steep and landslide-dissected basin, to a mountainous region, to a flat and partly artificially drained area. This new methodology incorporates nonlinear diffusion for the pre-processing of the data, both to focus the analysis on the scales of interest and to enhance features that are critical to the network extraction. Following this pre-processing, channels are defined as curves of minimal effort, or geodesics, where the effort is measured based on fundamental geomorphological characteristics such as flow accumulation and iso-height contours curvature. The developed channel network extraction methodology is compared in terms of performance to a previously proposed channel extraction methodology based on wavelets. The results show that the geometric nonlinear framework is more computationally efficient and achieves better localization and robust extraction of features, especially in areas where gentle slopes prevail. The automatic extraction of channel morphology, such as cross-section, banks location, water surface elevation, is also addressed, as well as the possibility of distinguishing the signature of natural features such as channels from the one of artificial features, such as drainage ditches. One motivation for extracting detailed geomorphic features from landscapes is the premise that this will lead to improved process understanding (e.g., by relating the observed form to physical processes that gave rise to that form) and improved modeling (e.g., incorporate important localized features in hydrologic or sediment transport models or develop sophisticated metrics for testing the performance of landscape evolution models). With this premise in mind, work herein presents preliminary results along a particular new direction related to geomorphic transport laws and landscape evolution modeling. Specifically, motivated by: (a) our experience that geomorphic attributes, such as slope and curvature, are scale-dependent and thus the resulting sediment flux computed from the typical transport laws would also be scale-dependent, and (b) that landscapes present heterogeneity over a large range of scales, we put forward the idea of a non-local sediment flux formulation to be explored in landscape evolution modeling. Along these lines, a simple landscape evolution model is proposed and its ability to reproduce some common statistical properties of real landscapes is examined.Item Patulin degradation by yeast protein extract(2014-05) Folger, Brian CharlesThe mycotoxin patulin, produced by a number of fungi, most prominently Penicillium expansum, has proven problematic for the apple industry due to contamination of apple juice and apple cider. Presently, techniques to control patulin accumulation have proven increasingly ineffective due to the presence of antifungal resistant strains of mold, stability of patulin during thermal processing, and conflicting data on the efficacy of other treatments. However, fermented apple products such as hard ciders and apple cider vinegars are devoid of patulin. Fermentation with yeast resulted in complete degradation of patulin, possibly due to enzymatic degradation by yeast enzymes. Patulin has also been shown to be susceptible to adduct formation with free thiol containing molecules such as glutathione, which is naturally present in yeast cells. Limited studies have also looked at patulin adsorptivity onto the call walls of yeast. Degradation of patulin is, therefore, hypothesized to be caused by multiple mechanisms mainly caused by yeast proteins/enzymes.To assess the loss of patulin by protein extracted from yeast (Rhodosporidium kratochvilovae strain 62-121), patulin extraction methods were compared to determine the optimal method for patulin extraction from protein rich environments. The effect of boiling to halt any possible enzymatic degradation on total patulin loss was assessed by comparing patulin recovery to that of samples placed on ice after the assay. Yeast growth was optimized for the production of patulin-degrading protein extracts by surveying days of growth and subsequent storage at 4°C. Additionally, free thiol group reactivity with patulin was assessed upon incubation with protein extract, cysteine, and glutathione. Liquid chromatography and mass spectrometry (LC/MS) was used to detect patulin degradation products. Potential enzymatic activity was assessed by comparing the degradation activity of different protein extracts from yeast. Finally, patulin loss due to adsorption to inactivated yeast cell walls was determined. The use of acid and salt to precipitate the protein before patulin extraction resulted in the best patulin recovery from protein rich media, and an additional extraction following a modified AOAC method allowed for removal of excess salt without sacrificing patulin recovery. The use of boiling to denature the protein after the assay resulted in 10% higher patulin loss than when the samples were placed on ice, presumably due to adduct formation with thiol groups. Growing yeast for 6 days at room temperature was deemed adequate to obtain optimal patulin degradation; and subsequent incubation of the yeast at 4°C did not impair the patulin degradation activity. Yeast protein extracts were found to be inconsistent with respect to patulin degradation activity, nevertheless patulin degradation activity (up to 100% patulin) was observed in several batches. Patulin incubated with cysteine showed signs of free thiol blockage in both samples of protein extract and pure cysteine. Patulin incubated with glutathione was degraded at both pH 7 and 3.7, and one patulin-glutathione adduct (462 m/z) was identified via LC/MS. Lyophilized yeast cells demonstrated patulin adsorption capabilities after incubation at 30°C for 20 min. Observed results confirm that patulin can be degraded by the protein extract from yeast. The exact mechanism of patulin degradation by protein extracts remains unclear, yet it appears to be either enzymatic or chemical through thiol adduct formation. Our results indicated that the mechanism is a combination of the two. This research offers insight into possible patulin degradation mechanisms, and can give direction in applying this new method of patulin control in an industrial setting.Item Rapid solid phase extraction of dissolved organic matter(2014-05) Swenson, Michael M.Dissolved organic matter (DOM) is a complex mixture of organic molecules found ubiquitously in freshwater and saltwater environments. Contained within the heterogeneous mixture of DOM lies valuable information content on the source of molecules as well as the biotic mechanisms at work within an aquatic ecosystem. Recent advancements in high resolution mass spectrometry and liquid chromatography have made inroads into determinations of the molecular structures within DOM, which have been largely unknown until recently. Liquid chromatography-mass spectrometry (LC-MS) analysis, however, generally requires a prior step to concentrate/isolate DOM, and this step often limits the number of samples that can be analyzed. This study has developed a fast (<20 min) method to concentrate dissolved organic matter on commercially available online solid phase extraction (SPE) cartridges which can be directly eluted onto an LC-MS system. This method is generally faster and requires far less sample (10-100 mL) than previous SPE methods for DOM isolation. Additionally, this study tested a suite of very different SPE phases to find a combination of phases that could improve DOM recovery as compared with commonly used approaches. When a styrene divinylbenzene phase (RP1) was coupled with activated carbon, recoveries were found to be significantly higher than in previous SPE studies relying upon single phases (either C18 or styrene divinylbenzene-based). The SPE method proposed here was tested for a diverse set of salty and fresh water samples and percent recoveries ranged from 46-78% of the total dissolved organic carbon (DOC).