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- Creator:
- Overton, Michael
- Description:
- Viruses have played a central role in the evolution and ecology of cellular life since it first arose. The discovery of viral lineages that infect members of all three domain suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. As well, investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. These aspects of viruses have motivated the current investigation into a novel, lysogenic variant of the archaeal virus Sulfolobus Turreted Icosahedral Virus (STIV), STIV3. Following previous work for STIV, a genetic system was developed for STIV3. This involved producing clones for five partitions of the viral genome. As well, an infectious clone was constructed using PCR and the Gibson assembly. Electroporating the infectious clone into pH shocked host cells produced free virions. Subsequent isolation of these virions in cell-free supernatant were applied to a fresh host culture, which, again, produced free virions. Cultures similarly infected with the original virus stock did produce a higher viral titer, but the timing of viral burst was highly coupled between the two. Bioinformatic investigations were also completed on STIV3, its sister variants STIV and STIV2, and metagenomic sequences collected from Yellowstone hot springs. 33 open reading frames were predicted for the 17,106bp STIV3 genome, all of which with homologs in at least one of the two other variants. Overall, the STIV3 genome resembled STIV more than STIV2 according to genetic distance, gene homology, and evolutionary signatures. dN/dS analysis of the turret-forming genes, A224, C384, and A586, revealed positive selection signatures that may be attributed to virus-host coevolution or host range expansion. The putative integrase gene B510 appears to be highly conserved among the STIV variants, particularly at the catalytic residues in the C-terminal. All other homologs exhibited high sequence similarity, indicating strong negative selection across most of the genome. Analyses were also carried out on metagenomic sequences, which found much higher sequence diversity in the environment than among STIV variants, even between STIV3 and STIV2, the latter of which was isolated from a hot spring in Iceland. Even with the small sample sets available, some population structuring was observed with PCA analysis. The work performed in this project provides a strong foundation for future investigations with this virus. A genetic system has been successfully constructed and partially validated. Future work can exploit this system to further our knowledge of virus biology, especially when combined with host molecular tools. As well, the STIV3 genetic system has the potential to further progress in biotechnology and bioengineering, particularly with the confirmed presence of a functioning integrase gene.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Biological Sciences
- Creator:
- Nworji, Kanayochukwu
- Description:
- Greenhouse crop cultivation using hydroponic techniques permits production of high-quality crops under controlled conditions that require less space, water, labor and time to harvest. In Nigeria, use of hydroponic cultivation is hampered by the availability of both capital and male labor in rural areas. This exploratory study set-out to determine whether a hydroponics system could be developed that is suitable to conditions there. A suspended net pot non-circulating method was selected as a proven system that minimized capital and technical requirements. Since the standard size of growing tanks is too large and too heavy to be manipulated by the female labor force in Nigeria, small tank sizes and large tank sizes were used to evaluate the economic viability of small tanks. Lettuce was selected as the crop due to its suitability for hydroponics cultivation and its importance commercially. Two trials were conducted, one during spring and one during winter. Also, the amount of light falling in different locations within the greenhouse was studied. The specific objectives were to determine: whether tank size affects leaf formation, size and shape; how tank location within the greenhouse affected the formation of leaves in both small and large tanks; and the economic feasibility of small tanks, due to expected nutrient temperature differences compared to big tanks. It was found that small production tanks had a significantly greater average fresh weight than the large tanks, in both studies. With regard to tank location, it was found this did not significantly affect the average fresh weight during the winter study but did during the spring study. Finally, with regard to economic feasibility, there was no significant quality or cost detriment in using smaller tanks. Overall, the use of the non-circulating net pot system with small tanks did not negatively impact crop production.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Plant Science
- Creator:
- Kent, Sarah
- Description:
- Gender plays a major role in an organism’s immune response to many pathogens. However, little is known about gender’s effect on Candida albicans (C. albicans) infections. C. albicans is a commensal organism that lives in the mucosa and skin of healthy individuals, however, C. ablicans can become an opportunistic pathogen in immunocompromised individuals. In our laboratory, it has been found that female mice are significantly more resistant to systemic C. albicans infections than male mice. Furthermore, castrated males are as resistant to the infection as female mice and that 5α-dihydroxytestosterone (the stable form of testosterone) supplementation of female mice decreases their ability to resist the yeast infection. Tumor necrosis factor-alpha (TNF-α), primarily secreted by macrophages, was one of the cytokines most affected by the sex hormone treatment. Thus, we suspect sex hormones play an important role in the immune response to C. albicans infection. It is possible that sex hormones (1) alter the growth rate of C. albicans and/or (2) that sex hormones alter immune responses to the yeast. To address (1), C. albicans was treated with different concentrations of β-estradiol (E2) or Testosterone (T), the yeast were plated on SAB agar, incubated at 37C and 24h later the yeast colonies were counted. To address (2), immortalized female (J774A.1) or male (RAW264.7) murine macrophages and Thiogylcollate-induced macrophages (TG-i M) derived from female and male c57BL/6 mice were treated with 1nM E2 or 10nM T for 24h and then challenged with C. albicans for various time points. Cytokines ((TNF-), interleukin-1 (IL-1), IL-6 and IL-10) and inducible nitric oxide synthase mRNA expression was determined via RT-qPCR. The concentration of TNF-, IL-2 and IL-6 protein secretion was quantified via Enzyme-linked Immunosorbent Assay. E2 inhibited TNF- protein secretion from J774A.1 after a 2h and 4h C. albicans challenge, however, E2 stimulated TNF- protein secretion from female derived TG-i M challenged for 24h with the yeast. Interestingly, while E2 had no effect on TNF- mRNA levels in yeast-challenged J774A.1 cells, this sex hormone suppressed TNF- mRNA levels in TG-i M cells. This results suggest that E2’s effects on TNF- mRNA produced from female derived macrophages is post-transcriptional and cell type dependent. E2 reduced IL-1 mRNA levels only in female derived TG-i M cells, but not in J77A.1 cells, supporting our hypothesis that E2’s effects are cell type dependent. E2 suppressed C. albicans-induced TNF- protein secretion from male derived TG-i M, but not from the immortalized male cell line RAW264.7. E2 had no effect on cytokine mRNA levels in male derived TG-i M, but E2 decreased TNF- mRNA levels while increasing IL-10 mRNA levels in RAW264.7 cells challenged with C. albicans for 2h. T did not affect the protein secretion of C. albicans-induced TNF- from female derived macrophages. However, T suppressed TNF- and IL-10 mRNA expression from J774A.1. T had no effect on cytokine mRNA levels in female derived TG-i M cells. T suppressed TNF- protein secretion from RAW264.7 cells, but stimulated the TNF- secretion from male derived TG-i M. These results suggest that E2, and to a lesser extent T, can alter C. albicans-induced cytokine production from macrophages derived from both sexes, and that these sex hormones act in a post-transcriptional manner.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Biological Sciences
- Creator:
- Overton, Michael
- Description:
- Viruses have played a central role in the evolution and ecology of cellular life since it first arose. The discovery of viral lineages that infect members of all three domain suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. As well, investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. These aspects of viruses have motivated the current investigation into a novel, lysogenic variant of the archaeal virus Sulfolobus Turreted Icosahedral Virus (STIV), STIV3. Following previous work for STIV, a genetic system was developed for STIV3. This involved producing clones for five partitions of the viral genome. As well, an infectious clone was constructed using PCR and the Gibson assembly. Electroporating the infectious clone into pH shocked host cells produced free virions. Subsequent isolation of these virions in cell-free supernatant were applied to a fresh host culture, which, again, produced free virions. Cultures similarly infected with the original virus stock did produce a higher viral titer, but the timing of viral burst was highly coupled between the two. Bioinformatic investigations were also completed on STIV3, its sister variants STIV and STIV2, and metagenomic sequences collected from Yellowstone hot springs. 33 open reading frames were predicted for the 17,106bp STIV3 genome, all of which with homologs in at least one of the two other variants. Overall, the STIV3 genome resembled STIV more than STIV2 according to genetic distance, gene homology, and evolutionary signatures. dN/dS analysis of the turret-forming genes, A224, C384, and A586, revealed positive selection signatures that may be attributed to virus-host coevolution or host range expansion. The putative integrase gene B510 appears to be highly conserved among the STIV variants, particularly at the catalytic residues in the C-terminal. All other homologs exhibited high sequence similarity, indicating strong negative selection across most of the genome. Analyses were also carried out on metagenomic sequences, which found much higher sequence diversity in the environment than among STIV variants, even between STIV3 and STIV2, the latter of which was isolated from a hot spring in Iceland. Even with the small sample sets available, some population structuring was observed with PCA analysis. The work performed in this project provides a strong foundation for future investigations with this virus. A genetic system has been successfully constructed and partially validated. Future work can exploit this system to further our knowledge of virus biology, especially when combined with host molecular tools. As well, the STIV3 genetic system has the potential to further progress in biotechnology and bioengineering, particularly with the confirmed presence of a functioning integrase gene.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Biological Sciences
- Creator:
- Hernandez, Jorge
- Description:
- While there are prior studies regarding teacher shortage solutions, compilations of study results regarding teacher shortages have been sparse. It is not known how, based on historical evidence, the public educational system has addressed the teacher shortage problem within the United States. The present study differed from prior studies because it considers secondary research, as opposed to primary research, where most prior studies focus on primary research. This will allow a greater breadth of understanding through utilizing multiple study results to obtain meaningful data. Prior studies are widespread regarding the teacher shortage being studied, meaning that some studies focus on bilingual education, others focus on special education and special needs, others focus on demographic details (such as teacher gender and/or ethnicity), and still others focus on STEM or the arts. However, the vast majority of these studies tend to only focus on one particular area. This study was unique because it considered multiple areas in order to develop a comprehensive viewpoint of the teacher shortage – regardless of other characteristics (demographic, subject, etc.) within the United States public school system. It was found that the teacher shortage issue is a widespread problem across the United States and that current strategies to alleviate the shortage are not sufficient or effective.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Education
- Creator:
- Nworji, Kanayochukwu
- Description:
- Greenhouse crop cultivation using hydroponic techniques permits production of high-quality crops under controlled conditions that require less space, water, labor and time to harvest. In Nigeria, use of hydroponic cultivation is hampered by the availability of both capital and male labor in rural areas. This exploratory study set-out to determine whether a hydroponics system could be developed that is suitable to conditions there. A suspended net pot non-circulating method was selected as a proven system that minimized capital and technical requirements. Since the standard size of growing tanks is too large and too heavy to be manipulated by the female labor force in Nigeria, small tank sizes and large tank sizes were used to evaluate the economic viability of small tanks. Lettuce was selected as the crop due to its suitability for hydroponics cultivation and its importance commercially. Two trials were conducted, one during spring and one during winter. Also, the amount of light falling in different locations within the greenhouse was studied. The specific objectives were to determine: whether tank size affects leaf formation, size and shape; how tank location within the greenhouse affected the formation of leaves in both small and large tanks; and the economic feasibility of small tanks, due to expected nutrient temperature differences compared to big tanks. It was found that small production tanks had a significantly greater average fresh weight than the large tanks, in both studies. With regard to tank location, it was found this did not significantly affect the average fresh weight during the winter study but did during the spring study. Finally, with regard to economic feasibility, there was no significant quality or cost detriment in using smaller tanks. Overall, the use of the non-circulating net pot system with small tanks did not negatively impact crop production.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Plant Science
- Creator:
- Manzatianu, Vlad
- Description:
- This paper will be focusing on estimating wind direction using sound source localization. This idea is being perused because of the rising popularity of micro drones being used in science filed for gas analysis. Knowing the direction and velocity of the wind in the micro drone frame is very important and can be used not only in the control system but also in better understanding the analyzed gases. I propose designing an ultra-small anemometer, weighing in at 50g or less, which will use an array of unidirectional electret microphones as the main sensor type. Although the movement of air particles is not enough to produce any type of sound that microphone can capture, obstacles in the way will create perturbations, which will cause the internal membrane of the microphones to vibrate. Once the air pressure is converted to electric energy by the microphone, the signal will be passed into an embedded system running a custom software in a Linux environment which will be using a sound source localization in order to estimate the direction from which the wind is blowing.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Electrical and Computer Engineering
- Creator:
- Kent, Sarah
- Description:
- Gender plays a major role in an organism’s immune response to many pathogens. However, little is known about gender’s effect on Candida albicans (C. albicans) infections. C. albicans is a commensal organism that lives in the mucosa and skin of healthy individuals, however, C. ablicans can become an opportunistic pathogen in immunocompromised individuals. In our laboratory, it has been found that female mice are significantly more resistant to systemic C. albicans infections than male mice. Furthermore, castrated males are as resistant to the infection as female mice and that 5α-dihydroxytestosterone (the stable form of testosterone) supplementation of female mice decreases their ability to resist the yeast infection. Tumor necrosis factor-alpha (TNF-α), primarily secreted by macrophages, was one of the cytokines most affected by the sex hormone treatment. Thus, we suspect sex hormones play an important role in the immune response to C. albicans infection. It is possible that sex hormones (1) alter the growth rate of C. albicans and/or (2) that sex hormones alter immune responses to the yeast. To address (1), C. albicans was treated with different concentrations of β-estradiol (E2) or Testosterone (T), the yeast were plated on SAB agar, incubated at 37C and 24h later the yeast colonies were counted. To address (2), immortalized female (J774A.1) or male (RAW264.7) murine macrophages and Thiogylcollate-induced macrophages (TG-i M) derived from female and male c57BL/6 mice were treated with 1nM E2 or 10nM T for 24h and then challenged with C. albicans for various time points. Cytokines ((TNF-), interleukin-1 (IL-1), IL-6 and IL-10) and inducible nitric oxide synthase mRNA expression was determined via RT-qPCR. The concentration of TNF-, IL-2 and IL-6 protein secretion was quantified via Enzyme-linked Immunosorbent Assay. E2 inhibited TNF- protein secretion from J774A.1 after a 2h and 4h C. albicans challenge, however, E2 stimulated TNF- protein secretion from female derived TG-i M challenged for 24h with the yeast. Interestingly, while E2 had no effect on TNF- mRNA levels in yeast-challenged J774A.1 cells, this sex hormone suppressed TNF- mRNA levels in TG-i M cells. This results suggest that E2’s effects on TNF- mRNA produced from female derived macrophages is post-transcriptional and cell type dependent. E2 reduced IL-1 mRNA levels only in female derived TG-i M cells, but not in J77A.1 cells, supporting our hypothesis that E2’s effects are cell type dependent. E2 suppressed C. albicans-induced TNF- protein secretion from male derived TG-i M, but not from the immortalized male cell line RAW264.7. E2 had no effect on cytokine mRNA levels in male derived TG-i M, but E2 decreased TNF- mRNA levels while increasing IL-10 mRNA levels in RAW264.7 cells challenged with C. albicans for 2h. T did not affect the protein secretion of C. albicans-induced TNF- from female derived macrophages. However, T suppressed TNF- and IL-10 mRNA expression from J774A.1. T had no effect on cytokine mRNA levels in female derived TG-i M cells. T suppressed TNF- protein secretion from RAW264.7 cells, but stimulated the TNF- secretion from male derived TG-i M. These results suggest that E2, and to a lesser extent T, can alter C. albicans-induced cytokine production from macrophages derived from both sexes, and that these sex hormones act in a post-transcriptional manner.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Biological Sciences
- Creator:
- Zabalza, Christina
- Description:
- Recycled water projects have been on the rise to secure reliable water supplies. Indirect and direct water reuse projects are vital in regions that are prone to drought. Currently regulations for implementing indirect and direct potable reuse in California, are at the beginning stages of development. The required monitoring for indirect and direct reuse have been continuously revised, as new technology and detection levels can expand upon the understanding if emerging contaminants and the need to protect public health. Many opportunities are available with reuse to increase dwindling water supplies; however, there are also challenges associated with implementation. The purpose of this research is to provide a recommendation for a priority list of contaminants of emerging concern (CECs) to be used for monitoring future water reuse projects. The priority list is founded upon an extensive literature review and parameters surrounding the following: molecular weight, solubility, membrane removal efficiencies, public health, occurrence in the environment, consumption, production, and regulatory framework. A recommended priority list of 38 CECs is presented in this paper for the monitoring of indirect and direct potable reuse projects. In the coming years levels are expected to further increase of CECs as of an ever increasing population density.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Department of Civil Engineering
- Creator:
- Meeks, Lauren
- Description:
- Physical activity reduces fat mass, but if not practiced, the risk of obesity-associated health problems and associated health care costs increase. The purpose of this study was to determine the effects of pedometer-metered walking in college-aged participants on body composition, waist-to-hip ratio (WHR), blood pressure (BP), fasting blood glucose (FBG), and diet choices within a four-week period. Following informed consent, participants (N=29; 18.5< BMI <25.0) wore a pedometer for four weeks and recorded the number of daily steps. Body composition, waist and hip measurements, BP, and FBG were performed at baseline, week 1, and week 4. Three randomized 3-day diet records were collected from participants. Daily motivational quotes were provided to a subset of participants (N=19) to determine if the number of steps changed. Significant decreases in waist (77.1cm ± 2.23cm to 74.5cm ± 2.03cm, p=0.002) and hip (99.8 ± 1.74cm to 99.0 ± 1.78, p=0.03) measurements were found. Results were not significant for BP, FBG, those receiving motivational quotes and body composition, but a decrease in fat free mass approached significance (p=0.06). Decreased fruit intake was observed in the second (p=0.007) and third (p=0.023) diet records. Waist and hip measurements decreased significantly at the end of the study, suggesting that monitored walking through the use of a pedometer may result in physical abdominal changes. More research is needed to determine the effects of pedometer-metered walking on diet choices as well as the effects of external motivation on physical activity.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Human Nutrition and Food Science Department