<p>Bacteriophages are viruses that infect and kill bacteria. They are the most abundant organism on the planet and the largest source of untapped genetic information. Every year, more bacteriophages are isolated from the environment, purified, and sequenced. Once sequenced, their genomes are annotated to determine the location and putative function of each gene expressed by the phage. Phages have been used in the past for genetic engineering and new research is being done into how they can be used for the treatment of disease, water safety, agriculture, and food safety. </p> <p>Despite the influx of sequenced bacteriophages, a majority of the genes annotated are hypothetical proteins, also known as No Known Function (NKF) proteins. They are expressed by the phages, but research has not identified a possible function. Wet lab research into the functions of the hundreds of NKF phages genes would be costly and could take years. Bioinformatics methods could be used to determine putative functions and functional categories for these hypothetical proteins. A new bioinformatics method using algorithms such as Domain Assignments, Hidden Markov Models, Structure Prediction, Sub-Cellular Localization, and iterative algorithms is proposed here. This new method was tested on the bacteriophage genome PotatoSplit and dropped the number of NKF genes from 57 to 40. A total of 17 new functions were found. The functional class was identified for an additional six proteins, though no specific functions were named. Structure Prediction and Simulations were tested with a focus on two NKF proteins within lytic phages and both returned possible functional categories with high confidence.</p> <p>Additionally, this research focuses on the possibility of phage therapy and FDA regulation. A database of phage proteins was built and tested using R Statistical Analysis to determine proteins significant to phage infecting <i>M. tuberculosis</i> and to the lytic cycle of phages. The statistical methods were also tested on both pharmaceutical products recalled by the FDA between 2012 and 2018 to determine ingredients/manufacturing steps that could affect product quality and on the FDA Adverse Event Reporting System (FAERS) data to determine if AERs could be used to judge the quality of a product. Many significant excipients/manufacturing steps were identified and used to score products on their quality. The AERs were evaluated on two case studies with mixed results. </p>

The issue of food scandals originating from unsafe food has in recent years caught the attention of the public. Consequently, the number of food recalls has increased, and food retailers and food producers are getting questioned regarding their ability to provide consumers with safe food products. Thus, because the primary responsibility to deal with this problem is the food business operators who have real control over the products within the Food Supply Chain (FSC). Even though food safety has received more interest from academic researchers and practitioners in the latter years, we could identify that previous literature still lacks research on food recalls. In addition, prior research interprets food recalls as generalizable within the FSC and does not have its various product flows in mind. In order to fill the research gap, this study seeks to gain a deeper understanding of food recalls in the context of the different product flows within the FSC from a retailer perspective. Therefore, the purpose of this study was to investigate how the occurrence and the consequences of food recall differ across various product flows within the FSC by focusing on four elements. The elements include the challenges within the FSC to ensure food quality, the reasons behind food recall, the types of food recall, and the consequences they infer. The current study had finally answered the following research question: “How do the occurrence and the consequences of food recalls differ across various product flows within the FSC?” In order to answer the research question and address the purpose of the thesis, a qualitative study was conducted by focusing on Swedish food retailers and conducting interviews with responsible Purchasers within each of the product flows, and additionally, Quality Assurance Managers. The sample of the semi-structured interviews was selected based on the position and experience of food recalls within the retailers. This to assure that the interviewees possessed sufficient insights regarding the studied field to fulfill the purpose of the study and answer its research question. From the gathered data, several themes were derived through the thematic analysis, and the analysis and discussion regarding the elements led us to a conclusion. The result confirmed that the various product flows, and in some cases, even specific products within the flows, need to be taken into consideration when the occurrence and the consequences of food recalls are addressed within the FSC. This is because the different product flows include different products with different characteristics making them more or less complex to handle along the chain and when carrying out food recalls. Even though previous theories assume a general approach, the findings still confirmed the theories regarding the challenges within the FSC to ensure food quality, the reasons behind recalls, the types of recalls, and the consequences the recalls can infer. However, the main differences found between our study and prior research regarding the FSC were that supply chain-related reasons are more commonly related to food reclaims and that environmental consequences are considered an additional consequence of food recalls.

The safety of the food supply in the United States has become an issue of prominence in the minds of ordinary Americans. Several government agencies, including the United States Department of Agriculture and the Food and Drug Administration, are charged with the responsibility of preserving the safety of the food supply. Food is withdrawn from the market in a product recall when tainted or mislabeled and has the potential to harm the consumer in some manner. This research examines recall events issued by firms over the period of January, 2000 through October, 2009 in the United States. Utilizing economic and management theory to establish predictions, this study employs the Cox proportional hazard regression model to analyze the effects of firm size and branding on the risk of recall recurrence. The size of the firm was measured in both billions of dollars of sales and in thousands of employees. Branding by the firm was measured as a binary variable that expressed if a firm had a brand and as a count of the number of brands within a firm. This study also provides a descriptive statistical analysis and several findings based on the recall data specifically relating to annual occurrences, geographical locations of the firms involved, types of products recalled, and reasons for recall. We hypothesized that the increasing firm size would be associated with increased relative risk of a recall event while branding and an increasing portfolio of brands would be associated with decreased relative risk of a recall event. However, it was found that increased firm size and branding by the firm are associated with an increased risk of recall occurrence. The results of this research can have implications on food safety standards in both the public and private sectors.