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Understanding potential cross contamination pathways is essential to reducing the risk of food product contamination. The use of a fluorescing abiotic surrogate (GloGermTM) to visualize the potential spread of bacteria may be beneficial to researchers. To quantify cross contamination during experimental trials in a mock retail deli, a rating method for visualization of fluorescence levels using a trained sensory panel was developed. Panelists feedback led to a pre-defined strategy allowing for characterization of contamination seen in photographs and reduced variability within responses. Following validation, GloGermTM was used to visually represent how bacteria may spread through a deli environment. Six origination sites (slicer blade, meat chub, floor drain, preparation table, employee's glove, employee's hands) were evaluated separately and spread was photographed throughout the mock deli. The trained sensory panel then analyzed the photographs. Five of the six contamination origination sites transferred GloGermTM to surfaces throughout the mock deli. Contamination from the floor drain did not spread to any food contact surfaces. To determine the potential of using a GloGermTM/ bacteria mixture to simultaneously track and sample contamination spread; surfaces were co-inoculated with GloGermTM and bacteria to determine if co-inoculation would affect the recoverability of microorganisms from these surfaces. Three common foodborne bacteria (E. coli O157:H7,Salmonella enterica ser. Enteritidis, Listeria monocytogenes, Listeria innocua) were inoculated on 2 by 2 stainless steel coupons alone and with GloGermTM . There was no significant difference found (p > 0.05) between the recovery of bacteria alone and the mixture for all bacteria. Finally, the use of co-inoculation was further explored by inoculating two contamination origination sites with either bacteria alone (L. monocytogenes and L. innocua) or a GloGermTM/bacteria cocktail. Nine recipient sites were sampled after a series of deli procedures were performed. Generally, no significant differences (p>0.05) were seen between the transfer of bacteria inoculated alone and the transfer of bacteria inoculated with GloGermTM to the selected recipient sites, regardless of contamination source or bacteria. These results suggest there may be potential in using L. innocua in combination with GloGermTM to visually track and sample contamination from a known source throughout a retail deli environment. / Ph. D.

Lipid transfer proteins (LTPs) constitute a pervasive class of small proteins implicated in many biological and physiological processes, including seed development, germination, cuticle formation, and abiotic stress responses. In this study, we explored the role of Arabidopsis LTP12 protein in mitigating environmental stresses. To address this, we analyzed the T-DNA knockout mutant ltp12, focusing on its responses to salinity and osmotic stress. Utilizing antioxidant enzyme assays, phenotypic analyses (including water loss, chlorophyll content, seed germination rates, root length, and relative water content), and lipid profile analysis via Thin Layer Chromatography (TLC), we found that ltp12 mutants showed reduced catalase and peroxidase activities and poorer hydration, chlorophyll content, germination, and growth under stress, compared to wild-type Col-0 plants. Mutants delayed vegetative-to-floral phase transition compared to wild-type. Additionally, lipid analysis indicated that the wild-type plants had increased phospholipids under high osmotic stress, suggesting LTP12's involvement in lipid reorganization during stress responses.

As climate change exacerbates heat stress during the summer season, it becomes increasingly critical to develop effective strategies to safeguard the productivity of tomato plants (Solanum Lycopersicon L.). This research delves into the tools and techniques aimed at enhancing the cultivation of summer tomatoes in the coastal region of Virginia. The study explores the optimization of transplant dates, the implementation of reflective mulches, and the application of kaolin clay particle films. Field trials spanning two seasons were carried out, comparing different planting dates in May, June, and July, as well as the use of reflective, black, and white plastic mulches, both with and without foliar kaolin sprays. The findings of this study underscore the impact of transplanting tomatoes in May, demonstrating a substantial increase in yields when compared to transplanting in June and July. Reflective mulches enhanced plant height and fruit production relative to the conventional black plastic mulch. The combination of kaolin clay sprays with standard black mulch, resulting in yield increases of over 35%, rivaling the outcomes achieved with reflective and white mulch treatments. The application of kaolin did not significantly affect leaf-level physiological processes. These results highlight the significant potential of strategic early planting and the adoption of emerging heat mitigation technologies, such as kaolin clay films, in sustaining and enhancing the productivity of summer tomatoes. This becomes particularly relevant as growing conditions continue to evolve due to rising temperatures and the increasing extremity of weather events resulting from climate change. / Master of Science in Life Sciences / With the challenge of hotter summers due to climate change, finding effective ways to grow tomatoes is more crucial than ever. In our two-season study in Virginia's coastal region, we experimented with various methods to improve tomato growth in these warmer conditions. What we discovered was quite promising. Planting tomatoes in early May resulted in significantly better yields than later planting times. Using reflective mulch was beneficial too; it helped the plants grow taller and produce more fruit compared to traditional black mulch. However, the most impressive result came from combining kaolin clay spray with black mulch. This approach led to a matching of the performance of black plastic plus the combination of kaolin clay against reflective and white mulches. It's interesting to note that the kaolin spray didn't alter the basic functioning of the plants at the leaf level. These findings are encouraging. They suggest that early planting and innovative approaches like kaolin clay sprays can effectively boost tomato production, even as we contend with rising temperatures and evolving climate patterns. Embracing these strategies could be key to successful tomato farming in an era of climate change

Polycyclic aromatic hydrocarbons (PAHs) are a group of ubiquitous environmental contaminants with two or more aromatic rings and originating from different emission sources. They are extremely toxic, carcinogenic and mutagenic to human, animals and plants. Consequently, the need to expand economical and practical remediation technologies for PAH contaminated sites is evident. In this study, the effect of biotic and abiotic factors on degradation of PAH was studied. The degradation was studied on the key model PAH (phenanthrene, anthracene, fluoranthene and pyrene) in J. Arthur Bower’s top soil. The hypothesis for this study was that roadside soil would contain PAH degrading bacteria; pH would influence the microbial degradation of PAH, chemical oxidation of PAH would be as efficient as microbial breakdown of PAH and mobilising agents, would move PAH throughout soil, potentially making the PAH more available for biodegradation. The greatest degradations were found for the lowest molecular weight PAH, phenanthrene and anthracene; whilst lowest degradation was observed for higher molecular weight PAH, fluoranthene and pyrene. Twelve bacteria genera were isolated and identified by biochemical and molecular techniques from the roadside soil with the four PAHs as the sole carbon source. However, potentially new PAH biodegrader bacteria species and a novel were found in this study, which was not reported in the literature. The effect of pH between 5.0 and 8.0 at half pH intervals on biodegradation of the four PAHs and on bacterial populations in the soil over 32 days was monitored. The greatest population of bacteria and greatest biodegradation for the four PAHs was found at pH of 7.5. It is likely that the general increase in population was also linked with greater metabolic activities of bacteria at basic pHs which assists pollutant biodegradation. Although there is high pollutant mobility at low pHs, the biodegradation was limited due to reduced microbial activity. High pHs resulted in greater PAH biodegradation suggesting that pH manipulation by liming may be an effective way of stimulating biodegradation of PAH. The effect of potassium permanganate on oxidation of the four PAHs in the soil was examined. Studies in this thesis, indicated that potassium permanganate had a significant (p<0.05) effect on oxidation of the four PAHs at pH 7.5 over 35 days. However in comparison to biodegradation, chemical oxidation has significantly (p<0.05) less effect. Finally, the effect of Tween 20 only on translocation and biodegradation of the four PAHs at pH 7.5 over 35 days was examined. Studies indicated that Tween 20 had significantly (p<0.05) enhanced translocation of the four PAHs in the sterile soil. Moreover, the greatest biodegradation was found in the soil inoculated with only the roadside soil microorganisms but without Tween 20. This suggested that Tween 20 had a significant (p<0.05) inhibitory effect on the roadside soil microorganisms and therefore less microorganism were grown in the soil containing Tween 20. This indicated that Tween 20 was translocated PAH, but inhibited breakdown. This study indicated microbial biodegradation was the most effective technique for removing of the PAH from contaminated soil, which was cost effective and easier to perform in comparison to the other two techniques. Microbial biodegradation could be improved by adjusting pH through liming if soil was acid.

Systems biology methods can provide novel insight into the responses of an organism to a suboptimal environment, an infection or exposure to a xenobiotic. In the interaction of salmon and salmon lice, there are several areas requiring further research. These include the impacts of lice infection on wild salmon, response mechanisms of different salmon species or life stages to lice infections, effects of environmental conditions on lice stress, and mechanisms underlying the emergence of resistance to important parasiticidal chemicals. Here, I combine global gene expression analyses with phenotypic and physiological responses of salmon or salmon lice to further our understanding of these topics. In the first chapter, I introduce the work by discussing relevant background material on the current knowledge of salmon and salmon lice interactions, salmon immunity, the state of salmon and louse genomics and the emerging field of ecological genomics. I also discuss how these approaches are applied to the study of non-model organisms and sustainable aquaculture development and fisheries conservation. In the second chapter, I present the first large-scale transcriptome profiling of a Pacific salmon to a salmon lice infection, identifying transcript signatures associated with an infection in a sensitive life stage of pink salmon Oncorhynchus gorbuscha. In the third chapter, I present the results of multiple co-habitation infections of three species of Pacific and Atlantic salmon to compare physiological and transcriptomic responses at the local (skin) and systemic levels (anterior kidney). In the fourth chapter, I explore louse transcriptome functioning during temperature and salinity perturbations to characterize the molecular stress response and coping strategies of lice, as well as provide stressor context to response genes. In the fifth chapter, I evaluate sensitive Pacific and resistant and sensitive Atlantic lice responses to emamectin benzoate, an important compound for louse control which has recently been evaded by the louse through resistance development in multiple regions worldwide. In the sixth and final chapter, I conclude with a synthesis of what was learned about knowledge gaps discussed above and how to best apply this information by providing some approaches for future research to address remaining challenges. / Graduate / 0369 / 0792 / 0718 / bensutherland7@gmail.com

Salt marshes provide critical ecosystem services, such as shoreline stabilization, biogeochemical cycling and habitat for wildlife, to much of the world's population living on the coasts. Emergent vascular plants are a critical component of these ecosystems. This study was a comprehensive effort to gain a better understanding of the ecology of salt marsh plants in the Nueces River delta on the south Texas coast. This knowledge is essential to understand the potential anthropogenic impacts on salt marshes, including sea-level rise, global warming, reduced freshwater inflow and coastal erosion. A combination of remote sensing analysis, field studies and experiments were used to allow analysis across spatial scales ranging from landscape patterns of vegetation to leaf level measurements of the dominant species. A novel method of image classification was developed using high-resolution multi-spectral imagery integrated with ancillary data to map the major plant communities at a landscape scale. This included a high marsh assemblage composed primarily of Spartina spartinae and a low marsh community dominated by Borrichia frutescens and Salicornia virginica. Geospatial analysis determined that the location of these plant communities was related to the distance from the tidal creek network and elevation. The B. frutescens and S. virginica assemblage was more abundant at lower elevations along the waters edge, making it vulnerable to loss from shoreline erosion. At a finer spatial scale, gradient analysis was utilized to examine the relationship between elevation, which creates environmental gradients in salt marshes, and species distribution. I discovered that elevation differences of less than 5 cm can influence both individual species and plant community distribution. One interesting finding was that the two dominant species, B. frutescens and S. virginica, share similar responses along an elevation gradient yet are observed growing in monotypic adjacent zones. I constructed a large reciprocal transplant experiment, using 160 plants at 4 sites throughout the marsh, to determine what causes the zonation between these two species. The results of this study found that S. virginica fared well wherever it was transplanted but was a weak competitor. B. frutescens survival was significantly lower in the S. virginica zone than in its own zone suggesting that abiotic factors are important in determining the zonation of this species. However, high spatial and temporal variability existed in environmental parameters such as salinity. This variability may have been caused by the semi-arid climate and irregular flooding typical in the Nueces Marsh. Therefore, I utilized a greenhouse experiment to directly test the importance of the two dominant physical factors in salt marshes, flooding and salinity. The results found that for B. frutescens the effects of flooding were not significant, however salinity at 30% reduced growth. Salinity did not influence growth of S. virginica. The greater ability of S. virginica to tolerate salinity stress has important implications because reduced freshwater inflow or climate change can increase porewater salinity, thus favoring the expansion of S. virginica, and altering the plant community structure. / text

In recent decades, most countries of the world have experienced a shortage of water and increase its rate of consumption. Today, every country in the world are interested in this problem by trying to find alternatives to address this shortage. One solution is reuse greywater (GW) for irrigation after treatment. GW is all water generated from Household except toilet water. The risks associated with the reuse of these waters are the presence of pathogens that can infect humans, animals and plants. In this thesis focused on studying treatment by slow sand filtration and the survival of representatives of pathogens, such as E. Coli, P. aeruginosa , E. Faecalis and Bacteriophage MS2 which could be found in the greywater. The study factors was a physico-chemicals factors such as; temperature (6±2,23±2,42±2°c), salinity (1.75 and 3.5% Nacl), oxygen (aerobic and anaerobic condition), nutrient ( rich media , 50%: 50% salt and poor media ), light with photocatalysis ( UV and Visible lights) and slow sand filter (Egyptian desert sand and swimming pool sand). A combination of high temperature, sunlight and photocatlysis are mainly responsible for the rapid decline of bacteria and MS2 coliphage. Slow sand filter have clearly less influence on the survival of bacteria in the greywater, but it effective to decline turbidity and COD for short times.

Breeding for abiotic stress tolerance is one of main topics in plant breeding. Oilseed rape breeding programs were for a long time focused on morphological and physiological parameters. In this thesis few experiments focused on identification of genes involved in abiotic stress reaction were performed using RT-qPCR (quantitative reverse transcription PCR). Simultaneously SPR (surface plasmon resonance) method were used as modern optical method facilitating very low native protein concentration even in presence of other substances. This method facilitates quantification of concrete proteins by binding them to specific antigen and in oilseed rape research it was not used by now. ERD10 protein was identified by SPR as protein involved in cold stress reaction (or acclimation). The results show ERD10 accumulation in standard conditions affects dynamics of its accumulation change during cold stress. In case we are searching for genotypes great in acclimation ability even during short and warm autumn SPR method should be suitable method for fast, easy and relatively cheap screening of large number of genotypes in breeding collections. Also genes LTI78, RCI2A, NRP1 and two genes for hypothetical proteins were analysed. Their relative expression during cold stress was markedly increased too. Very little is known about these genes and proteins nowadays therefor it will be interesting topic of our oncoming experiment. Relative expression of genes picked according to MALDI-TOF/TOF analysis results was also tested in microspore embryo regenerants stressed by simulated drought. Genes for lactoylglutathione lyase I, phospholipase D 1 and peroxiredoxin antioxidase were tested. In tolerant cultivar was markedly decreased gene expression of peroxiredoxin antioxidase in standard conditions and early stress. These gene will be subject for next research as potential marker for more tolerant genotypes selection.