Life Sciences Commons^™

Psf Sampling In Fluorescence Image Deconvolution, Eric A. Inman

Master's Theses

All microscope imaging is largely affected by inherent resolution limitations because of out-of-focus light and diffraction effects. The traditional approach to restoring the image resolution is to use a deconvolution algorithm to “invert” the effect of convolving the volume with the point spread function. However, these algorithms fall short in several areas such as noise amplification and stopping criterion. In this paper, we try to reconstruct an explicit volumetric representation of the fluorescence density in the sample and fit a neural network to the target z-stack to properly minimize a reconstruction cost function for an optimal result. Additionally, we do …

Development Of A Portable Low-Moisture Food Pasteurization Device Using Rf Heating, Eric Jason Ohata

Master's Theses

Bacterial presence in low-moisture foods such as flour, cereals, baby formula, and spices, have become a concern due to sanitizing challenges. The food industry currently focuses on wet food sanitation as opposed to low-moisture foods because of bacteria’s inability to reproduce in low water activity media. Traditionally, food processing RF heating pasteurizes in mass quantities while an equivalent consumer device does not exist the market today. A consumer product would help eliminate food waste by providing an easy way to sanitize food and extend shelf life. The Portable Food Pasteurization (PFP) project is an interdisciplinary project involving the Electrical Engineering, …

The Response Of Marine Synechococcus To A Landscape Of Environmental Stressors: A Proteomic Exploration, Dana E. Michels

Master's Theses

In the field of marine microbial ecology, many questions remain unanswered with regards to the physiological trade-offs made by phytoplankton to maximize growth (e.g., nutrient acquisition) and minimize loss (e.g., predation defenses). These tradeoffs, which occur at the cellular level, have wide reaching impacts on food web dynamics and global biogeochemical cycles. In the first chapter, we explored the use of a non-canonical amino acid (NCAA) technique, bioorthogonal non-canonical amino-acid tagging (BONCAT), in phytoplankton model systems. This technique has potential to work well in natural systems by enabling isolation of only newly synthesized proteins during an incubation period with the …

Study Of Plants Used Against Infections By California Native American Tribes, Maria J. Rojas

Master's Theses

The objectives of this research were to evaluate the antibacterial activity and to determine the chemical composition of a list of medicinal plants used by Native Americans in California. Artemisia californica, Mimulus aurantiacus, Equisetum telmateia, Equisetum hyemale, and Marah fabacea were selected from a list of plants reported as having been used for ailments related to infections by tribes located in California. The extracts obtained through steam distillation from E. telmateia, E. hyemale and M. fabacea were assayed for in vitro antibacterial activity against 16 Gram-negative and 6 Gram-positive bacteria using disk diffusion assays and measuring the diameters of inhibition …

Analysis Of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (Osa), A Bioactive Food Starch Modifier Compound, Matthew R. Borglin

Master's Theses

Matthew R. Borglin

This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection …

Analysis And Optimization Of Colorimetric Nanosensors For Rapid Detection Of Microbes In Water, Ruby A. Lang

Master's Theses

Access to safe water is a basic human right recognized by the United Nations General Assembly in 2010 (WHO, 2020). However, a least 2.2 billion people globally still are without safely managed water services meaning they use a drinking water source that can be contaminated with faeces (WHO, 2020). With such a pressing global health issue, it is clear that improvement to water systems is important and required in the Agenda 2030 Sustainable Development Goals (SDGs). However, to improve water systems and prove they are safe water sources, water quality testing must occur. A solution to this issue is the …

Development Of A Prolyl Endopeptidase Expression System In Lactobacillus Reuteri To Reduce The Clinical Manifestation Of Celiac Disease, Kara Lynn Jew

Master's Theses

Celiac Disease (CD) is an autoimmune disorder that emerges due to the ingestion of gluten, a protein found in a variety of common grains such as wheat, rye, and barley. Approximately 1 in 100 individuals in the US suffer from CD, making it the most commonly diagnosed gastrointestinal disorder (Ciclitira et. al., 2005). These proline-rich gluten peptides are resistant to proteolysis and accumulate in the duodenum of the small intestine. Once in the duodenum, these peptides illicit an autoimmune response resulting in villous atrophy. Current treatment for CD requires a rigorous adherence to a gluten-free diet. Nevertheless, gluten-containing grains are …

Integrated Aeration For Enhanced Nitrogen Conversion And Removal And The Effect Of Sampling Frequency On Productivity Estimates In Algae-Based Wastewater Treatment Systems, Lauren Parker

Master's Theses

Raceway ponds can be used to cultivate microalgae for purposes such as wastewater treatment and feedstock for animal feeds and biofuels. Besides nitrogen assimilation in biomass, nitrification can be a wastewater treatment mechanism but one that is hindered by the low nighttime dissolved oxygen concentrations (DO) common in wastewater treatment raceways. The large diel difference in pond conditions and changing influent wastewater quality also raises the question of the optimal frequency and timing of grab sample collection, to obtain representative water quality data. Three sets of triplicate pilot raceways (1,000-L, 0.30-m deep, fed primary clarifier effluent) were operated at an …

Study Of Paper Microbial Fuel Cells For Use In On-Site Wastewater Testing, William A. Tolmasoff

Master's Theses

This study demonstrated a technique for fabricating simple, low-cost Paper Microbial fuel cells (PMFC’s) in the model of a previous study to, for the first time, produce voltage from wastewater effluent. The PMFC’s were created by stacking and gluing the main components of an MFC together: reservoir layer; anode; cation exchange membrane (CEM); air cathode. A wax printer was used to create the hydrophobic borders of the PMFC’s on filter paper, and graphite paint was applied to the paper to create the anode. The CEM’s considered were filter paper, wax, and Nafion, with Nafion being the most efficient. Finally, the …

Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers

Master's Theses

In a large agricultural operation, such as the one at Cal Poly San Luis Obispo, disposal of deceased animals is an immense issue. The cost of transporting and rendering every dead animal is inhibitory to the general function of the agricultural operations and their thin budget. Therefore, we propose that composting mortalities could be an economical alternative. Composting is a recognized method for taking animal waste products along with carbon waste and turning it into a pathogen-free, nutrient-rich topsoil. Carcass composting is in fact performed in other countries and states to varying degrees of success. However, the California EPA limits …

Engineering Yeast To Evaluate Human Proteins Involved In Selective Rna Packaging During Hiv Particle Production, Ryan M. Bitter

Master's Theses

Despite recent advances in antiretroviral therapy, nearly 37 million people continue to live with human immunodeficiency virus (HIV). Basic and applied research on the assembly of HIV could be enhanced by using a genetically tractable organism, such as yeast, rather than mammalian cells. While previous studies showed that expression of the HIV Gag polyprotein in Saccharomyces cerevisiae spheroplasts resulted in the production of virus-like particles (VLPs), many questions regarding the utility of yeast in HIV assembly remain uninvestigated. Here, we report use of S. cerevisiae for both the production of VLPs with selectively packaged RNA and to evaluate the human …

Detecting A Probiotic Product Within The Gut Of Broiler Chickens, Anneka Pisula

Master's Theses

As of January 2017, the U.S. poultry industry banned the use of antibiotics and now relies on alternatives such as probiotics to help protect animal health. Although probiotic use is not a new concept in the poultry industry, identifying the best combination of bacterial strains to generate an effective probiotic formula requires further investigation. This study aimed to detect a probiotic product of four bacterial strains (Pedioccoccus acidilactici, Pediococcus pentosaceus, Lactobacillus plantarum, and Bacillus subtilis) in a feeding trial with broiler chickens. Birds given the probiotic were predicted to show an improved growth performance with …

An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon

Master's Theses

The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as …

The Effects Of Quorum Sensing And Temperature On The Soluble Proteome Of Vibrio Salmonicida, Christopher L. Massey

Master's Theses

Vibrio salmonicida causes cold-water vibriosis in salmon populations around the world and causes financial damage to fisheries designed to farm these salmon. Very little is known about the physiology of how V. salmonicida causes disease and measures to contain vibriosis are restricted to either vaccinating individual fish against disease or administering antibiotics when an outbreak is detected. These procedures are costly and increase the risk for selection of antibiotic-resistant V. salmonicida strains. A recent reoccurrence of outbreaks in Norwegian fisheries provided incentive to better understand the virulence mechanisms of V. salmonicida. In this thesis, a proteomic approach was used to …

Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, Alexander Colin Roberts

Master's Theses

Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.

A pilot facility was operated with nine CO₂-supplemented raceway ponds, each with a 33-m² surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed …

Demographics And Transfer Of Escherichia Coli Within Bos Taurus Populations, Joshua Ryan Dillard

Master's Theses

In the United States, symptoms caused by pathogenic strains of Escherichia coli are on the rise. A major source of these pathogenic strains is the E. coli in the digestive tract of cattle. The purpose of this project was to determine if E. coli are transferred between individuals of the same species and if interspecies transmission is possible. Proximity of cattle was also studied as a contributing factor to the transfer of E. coli. To accomplish this goal, E. coli isolates from cattle and cohabitating ground squirrels were compared through a new method of bacterial strain typing called pyroprinting. …

Virulence Gene Expression Of Vibrio Parahaemolyticus In The Viable But Nonculturable State, Tiffany Pui-Yun Tse

Master's Theses

Vibrio parahaemolyticus is a food-borne pathogen commonly associated with the consumption of raw or undercooked seafood resulting in primary infections of the human gastrointestinal tract. It is estimated to cause about 4500 illnesses each year in the United States. However, infection from this food-borne pathogen can be avoided if this organism is detected in the implicated food, prior to consumption. Current standard methods of detecting this organism are dependent on the culturability of the bacteria. Detection based on an organism’s culturability may be problematic as V. parahaemolyticus has been known to exist in a viable but nonculturable (VBNC) state. Bacteria …

Exploring The Physiological Role Of Vibrio Fischeri Pepn, Sally L. Cello

Master's Theses

The primary contributor to Vibrio fischeri aminopeptidase activity is aminopeptidase N, PepN. Colonization assays revealed the pepN mutant strain to be deficient at forming dense aggregates and populating the host’s light organ compared to wildtype within the first 12 hours of colonization; however the mutant competed normally at 24 hours. To address the role of PepN in colonization initiation and establish additional phenotypes for the pepN mutant strain, stress response and other physiological assays were employed. Marked differences were found between pepN mutant and wildtype strain in response to salinity, acidity, and antibiotic tolerance. This study has provided a foundation …

Methane Production By A Packed-Bed Anaerobic Digester Fed Dairy Barn Flush Water, Sean Richard Thomson

Master's Theses

Packed-bed digesters are an alternative to covered lagoon digesters for methane production and anaerobic treatment of dilute wastewaters such as dairy barn flush water. The physical media of packed-beds retain biofilms, often allowing increased treatment rates. Previous studies have evaluated several types of media for digestion of dilute wastewaters, but cost and media fouling have setback commercial development. A major operational cost has been effluent recirculation pumping.

In the present effort, a novel approach to anaerobic digestion of flush dairy water was developed at pilot-scale: broken walnut shells were used as a low-cost packed-bed medium and effluent recirculation was replaced …

The Influence Of Hydrogeomorphology, Soil Redox Conditions, And Salinity On The Spatial Zoning Of Saltgrass, Salt Rush, And Cattails In Scotts Creek Marsh, Swanton Pacific Ranch, Ca, Mark D. Gormley

Master's Theses

Scotts Creek Marsh (SCM) is a small coastal wetland ecosystem in Davenport, CA. The vegetation of SCM is dominated by three halophytic zones comprised of saltgrass, salt rush, cattails. The objectives of the study were (i) to investigate the variables that influence the zoning of the three dominant halophyte communities in SCM and (ii) to the test the effectiveness of Indicator of Reduction in Soil (IRIS) tubes to indicate the reduction of S. The study examined the following parameters from April 6 to July 21, 2013: (i) the HGM of Scotts Creek Marsh, (ii) soil oxidation and reduction (redox) conditions, …

Escherichia Coli Strain Diversity In Humans: Effects Of Sampling Effort And Methodology, Emily R. Neal

Master's Theses

Studies investigating Escherichia coli strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in E. coli strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. …

Enhanced Hydrocarbon Biodegradation Using Bioaugmentation With Biowish™-Aqua Fog, Michael Robert Lehrer

Master's Theses

This study was done to determine the effectiveness of a commercially available bioaugmentation product, BiOWiSH^TM-Aqua FOG, for remediating petroleum-contaminated sandy soil. Biodegradation enhancement by BiOWiSH^TM-Aqua FOG was evaluated in laboratory microcosms by directly measuring total petroleum hydrocarbon (TPH) and indirectly using respirometry. Attempts were made to enrich hydrocarbon-degrading bacteria in BiOWiSH^TM-Aqua FOG, and the resulting enrichment cultures were screened using respirometry as well. Potential hydrocarbon-degrading bacteria in BiOWiSH^TM-Aqua FOG were isolated. Experiments were performed at bench-scale using microcosm bottles containing sand contaminated with either motor oil or No. 2 diesel fuel. The …

Investigation Of Bacillus Subtilis As A Biopesticide Against Botrytis Cinerea, Kenneth K. Ng

Master's Theses

The objective of this thesis was to investigate BiOWiSH^TM-Aqua, a commercial dry solid formulation containing a consortium of bacteria and yeast, as a biopesticide for treatment of Botrytis cinerea, a gray mold that affects strawberries. BiOWiSH^TM-Aqua was compared with another commercial product specifically used as a fungicide and bacteriocide, Serenade® Garden Disease Control Spray (concentrated Bacillus subtilis strain QST 713). Both laboratory tests as well as in vivo lab tests were conducted. BiOWiSH^TM-Aqua results varied widely from plate to plate, regardless of experimental conditions. In some of these plates, inhibition zones were observed …

Impact Of Collateral Enlargement On Smooth Muscle Phenotype, Alexander Jerome Bynum

Master's Theses

Peripheral Artery Disease is a very serious disease characterized by an arterial occlusion due to atherosclerotic plaques. In response to an arterial occlusion, arteriogenesis occurs, causing smooth muscle cells to transition from a contractile to synthetic state. Also following an arterial occlusion, functional impairment was seen in the collateral circuit. An immunofluorescence protocol was developed in order to assess the impact of collateral enlargement (arteriogenesis) on smooth muscle phenotype at various time points. Smooth muscle α-actin was used to mark all smooth muscle cells, Ki-67 was used to label proliferating smooth muscle cells, and a fluorescent nuclear stain was used …

Molecular Analysis Reveals Unique Microbiome In Ileal Pouch During Pouchitis Compared To Healthy Pouches In Ulcerative Colitis And Familial Adenomatous Polyposis, Tiffany Wallingford Glavan

Master's Theses

In severe cases of ulcerative colitis (UC) unresponsive to current treatment options, patients require a complete proctocolectomy, or surgical removal of the colon. Ileal pouch anal anastomosis (IPAA) has become the preferred surgical technique for patients who require surgery, as this method restores rectal function. This procedure is also used to treat colorectal cancers such as adenocarcinoma and familial adenomatous polyposis (FAP). The surgery involves an abdominal colectomy with the construction of an ileal pouch created from folded tissue recovered from the ileal portion of the small intestine. Up to 50% of patients who require IPAA surgery experience an episode …

Pcr Primers For The Detection Of Propane And Butane-Oxidizing Microorganisms, Brian Jeremy Chan

Master's Theses

In an increasingly energy-hungry world, our capacity to meet the heightened energy demands of the future has become a pressing matter. The most urgent of these concerns are tied to the accessibility of petroleum. Various experts have proselytized both the imminent arrival of peak oil production rates and the ensuing decline of those rates thereafter. And to that end, the development of novel and advanced oil exploration methodologies has become almost as important as finding the sources of oil themselves.

The soils above petroleum reservoirs play host to various communities of alkane- oxidizing bacteria that can utilize the natural gas …

Designing A Microbial Prolyl Peptidase Delivery System For The Treatment Of Celiac Disease, Matthew J. Shurtleff

Master's Theses

Celiac disease is an autoimmune enteropathy resulting from the ingestion of gluten and gluten-like proteins from wheat, barley and rye in afflicted individuals. Indigestible gluten-derived peptides rich in proline residues are known to be responsible for eliciting the inappropriate immune response characteristic of the disease. In this investigation, surface level expression of prolyl peptidase activity by genetically engineered probiotic lactobacilli was postulated to be a possible treatment for this disease. Plasmid-based reporter vectors were constructed utilizing a novel, homology-based cloning technique to assess the expression and localization signals from the S-layer protein gene of Lactobacillus acidophilus. These plasmids were mutated …

Temperature Influence And Heat Management Requirements Of Microalgae Cultivation In Photobioreactors, Thomas Hagen Mehlitz

Master's Theses

Microalgae are considered one of the most promising feedstocks for biofuel production for the future. The most efficient way to produce vast amounts of algal biomass is the use of closed tubular photobioreactors (PBR). The heat requirement for a given system is a major concern since the best algae growth rates are obtained between 25-30 °C, depending on the specific strain. A procedure to determine temperature influence on algal growth rates was developed for a lab-scale PBR system using the species Chlorella. A maximum growth rate of 1.44 doublings per day at 29 °C (optimal temperature) was determined. In addition, …