Litopenaeus vannamei or Pacific white shrimp is the most widely farmed crustacean in the world. Shrimp are commonly fed feed containing 30-40% soybean meal or other plant-based feeds that are more economically and environmentally sustainable than animal-based feed. However, plant-based pellets are less palatable and less chemically attractive compared to animal material. Based on that, current research and practice includes the addition of specific marine animal meals in order to enhance palatability and attractability of plant-based shrimp feed. Yet, it is not sustainable or economically achievable to continue relying on marine animal meal. In the herein study, the effect of proprietary chemical mixtures designed by our research group as feed additives was examined based on their attractability and palatability in comparison to krill meal, a highly attractive and palatable supplement for shrimp feed. In palatability assays, total amount of pellets was measured before and after one-hour and three-hour periods of feeding in group-housed animals. In attractability assays, responses of shrimp were measured based on the number of probes and grabs on the source (airstone) of the stimulus being released. Each diet-set used contained different concentrations of krill meal and synthetic chemical mixtures. Results demonstrated these chemical mixtures enhance attractability and palatability of soybean based feed in L. vannamei when compared to krill meal. Furthermore, the addition of a proprietary mixture (= “premix”) improved responses in the attractability assays when compared to stimuli that did not contain the premix. Overall, results support the hypothesis that synthetic chemical mixtures can improve palatability and attractability of soybean meal based shrimp feed. This work could provide a reference for the development of synthetic chemoattractants and chemopallatants for the aquaculture of shrimp.

Pyruvate kinase M2 (PKM2) is a glycolytic enzyme expressed in highly proliferating cells. Studies of PKM2 have been focused on its function of promoting cell proliferation in cancer cells. Our laboratory previously discovered that extracellular PKM2 released from cancer cells promoted angiogenesis by activating endothelial cell proliferation and migration. PKM2 activated endothelial cells through integrin αvβ3. Angiogenesis and myofibroblast differentiation are key processes during wound healing. In this dissertation, I demonstrate that extracellular PKM2 released from activated neutrophils promotes angiogenesis and myofibroblast differentiation during wound healing. PKM2 activates dermal fibroblasts through integrin αvβ3 and PI3K signaling pathway. I also claim that extracellular PKM2 plays a role during liver fibrosis. PKM2 protects hepatic stellate cells from apoptosis by activating the survival signaling pathway.

Rhodococcus rhodochrous DAP 96253, a well-known industrial bacterium, had various 1-hexene monooxygenase (1-HMO) activities when grown on YEMEA plates supplemented with eight different carbohydrates. Besides, 1-HMO exhibited different storage temperature preferences. Lactose could induce the highest 1-HMO activity in R. rhodochrous DAP 96253 while the cells showed the lowest 1-HMO activity when trehalose was the supplement. The 1-HMO activity of R. rhodochrous DAP 96253 was not maintained when stored at 37°C as well as at 4°C and 25°C. Trehalose-induced 1-HMO activity of R. rhodochrous DAP 96253 was more stable from Day 0 to Day 21 at all these three temperatures, compared with the other seven carbohydrates. Immobilization of enzymes can maintain enzyme activity longer, offer easier enzyme storage conditions and make some enzymes reusable, much research has been done in this area. In this study, R. rhodochrous DAP 96253, grown on YEMEA plates supplemented by glucose and urea, was investigated using whole bananas as the inducer of 1-HMO activity and different immobilization methods to maintain this enzyme activity. It was shown that calcium-alginate polyvinyl alcohol (PVA) beads could maintain 1-HMO activity of R. rhodochrous DAP 96253 more stable than calcium-alginate beads. Whole bananas exhibited very obvious effects of inducing 1-HMO activity of R. rhodochrous DAP 96253. A number of recent studies have clearly demonstrated that induced cells of R. rhodochrous DAP 96253 can prolong the shelf-life of post-harvested fruits. With USDA estimates of 40% of all harvested produce in the US not being consumed because of loss of quality, the ability to extend the period of ripeness of produce has great potential to improve the quality of nutrition. Modification or degradation of those signals (primary and secondary) associated with ripening in fruit or the perception of those signals represents a potential mode of action for delayed ripening by induced cells of R. rhodochrous DAP 96253. Ethylene and cyanide are the two primary signals in ripening. In this study, the role of 1-HMO from induced cells was investigated by time-course experiments focusing on 1-HMO activity and stability. In addition, fruit volatile organic compounds (VOCs) were detected and compared by GC-FID and GC/MS over the course of fruit ripening. The results show a correlation between 1-HMO activity and stability in delayed fruit ripening. It was further demonstrated that the presence of secondary signal fruit VOCs enhanced 1-HMO activity. Aromatic profiles of treated fruits, by GC-FID and GC/MS, show a consistent picture of VOCs associated with earlier fruit ripening stages.

Recent evaluations have demonstrated the ability of the bacteria Rhodococcus rhodochrous DAP 96253 to inhibit the growth of molds associated with plant and animal diseases as well as post-harvest loss of fruits, vegetables and grains. Pre-pilot-scale fermentations (20-30L) of Rhodococcus rhodochrous DAP 96253 were employed as a research tool with the goal of producing a practical biological agent for field-scale application for the management of white-nose syndrome (WNS) in bats and post-harvest fungal losses in several fruit varieties. Several key parameters within the bioreactor were evaluated for the potential to increase production efficiency as well as activity of the biocatalyst. These parameters included elapsed fermentation time, dissolved Oxygen, and carbohydrate concentration of which increased carbohydrate concentration at the time of harvest was shown to have a negative impact on the catalyst activity. In addition, process improvements including utilization of a liquid inoculum, an autoinduction feed strategy, and increased glucose concentration in the feed medium increased fermentation yields to 100-150g/L, while the biocatalyst efficiency was increased from previous work. To increase production efficiency, a multi-bioreactor scheme was developed that used a seed bioreactor and subsequent production tank, which doubled run yields per production cycle. Amidase, cyanidase, urease, and alkene-monoxygenase activity were monitored throughout the study as potential indicators for the multi-faceted mechanism of fungal antagonism. Of these amidase, cyanidase, and urease were demonstrated to be more elevated in cells that showed antifungal activity than those that did not. This study represents the first example of a reproducible pre-pilot plant-scale biomanufacturing process for a contact-independent biological control agent for established and emerging fungal pathogens of plants and animals, and facilitates large-scale production for broad application.

Heme is vital to a variety of cellular functions in bacteria ranging from energy generation to iron reserve. Group A streptococcus (GAS) is a prevalent bacterial pathogen that is responsible for an array of human diseases ranging from simple, self-limiting, mucosal and skin infections to invasive and systemic manifestations. GAS needs iron for growth and can satisfy this nutritional requirement by scavenging the metal from heme. The pathogen produces powerful hemolysins that facilitate heme release during infection. Heme is captured and relayed through the GAS cell wall and cytoplasmic membrane by dedicated receptors and transporters. To-date, the fate of the acquired heme is unknown in Streptococci. Although heme is nutritionally beneficial for GAS growth, its pro-oxidant and lipophilic nature makes it a liability with damaging effects on cellular components. The conundrum associated with heme use is particularly pertinent to GAS pathophysiology since invasive GAS infections involve massive hemolysis and the generation of unescorted heme in excess. In this dissertation, I aimed to describe the mechanisms that GAS uses for heme catabolism while managing its toxicity. I conducted a biochemical characterization of a new enzyme, HupZ in GAS that degrades heme in vitro. Similar to the heme oxygenase-1 (HO-1), HupZ activity leads to the formation of iron, CO, and a biliverdin-like product. I also investigated the impact of heme on GAS physiology and identified key mediators in the repair and detoxification process. This study demonstrated that heme exposure leads to a general stress response that involves the activation of antioxidant defense pathways to restore redox balance. Further, I studied a 3-gene cluster, pefRCD (porphyrin-regulated efflux RCD), which was activated by environmental heme, and provided support to my hypothesis that the pefRCD gene encodes a heme-sensing regulator (PefR) and heme efflux system (PefCD). I showed that the pef system protects GAS cells from heme-induced damage to the membrane and DNA by preventing cellular accumulation of heme. In conclusion, this dissertation addresses key knowledge gaps in GAS physiology and provides new insights into heme metabolism of GAS.

The autonomic nervous system (ANS) controls most involuntary functions of the body. Dysfunctions of the ANS can be life-threatening. However, several critical questions related to cardiovascular and breathing regulations remain unclear. One of the open questions is how the system lose control of the vascular tones under certain circumstances. Using the septic shock model induced by lipopolysaccharide (LPS) in isolated and perfused mesenteric arterial rings, we found the vascular hyporeactivity is attributed to the decreased vasoconstriction to α-adrenoceptor agonists. The endotoxin-induced vasodilation can be intervened with endothelin-1 (ET-1), serotonin (5-HT) or vasopressin, which have never been used in clinical treatment. It is unclear how the excitability of endothelium affects vascular tones. Using optogenetics and transgenic mice with channelrhodopsin expression in endothelial cells (ECs), we found selective activation of the ECs induces a fast, robust, reproducible and long-lasting vasoconstriction in isolated and perfused hearts and kidneys. Breathing control by the ANS within the brain becomes abnormal in certain genetic diseases, such as Rett syndrome with defected norepinephrine (NE) system in locus coeruleus (LC). The LC neurons are hyperexcitable while NE release is deficient. Using optogenetics and double transgenic mice with Mecp2 null and channelrhodopsin expression in LC neurons, we found the NE-ergic modulation of hypoglossal neurons was impaired in transgenic mice, which cannot be improved with optostimulation, suggesting that LC neuronal hyperexcitability may not benefit the NE modulation in Rett syndrome. Collectively, our results provide insight into the autonomic dysfunctions using experimental interventions that have barely been used before.

Plastics are highly useful economically because of their resistance to diverse types of environmental and chemical agents and their ability to be molded into many types of products. Globally, plastic production is greater than 20 million metric tons per year. However, their widespread use and often their disposable nature results in significant plastic accumulation in the environment. Plastics are made of hydrocarbons, materials that are biodegradable depending on their molecular structure and size. It is hypothesized that pre-treatment of plastic materials could enhance their bioavailability, facilitating their microbial biodegradation. In this dissertation, a process was developed to treat nylon 6,6 polymers by acid hydrolysis to produce a microbial growth medium. The chemical composition of the medium was determined by low pressure liquid chromatography-spectrophotometry and electrospray ionization mass spectrometry and found that the medium was a mixture of molecules with molecular weight > 800 m/z and with similar chemical characteristics to polyamines. There was steady growth of Pseudomonas putida KT2440 in the medium with concomitant substrate biodegradation. Notably, the yeast Yarowia lipolytica grew well in the medium when supplemented with yeast extract. A similar medium derived from nylon 6,6 containing nylon-derived particles supported the growth of Beijerinckia sp. and Streptomyces sp. BAS1. Confocal laser scanning microscopy and flame ionization gas chromatography were used to identify and quantify the production of polyhydroxybutyrate, a type of “bioplastic”. The aforementioned microorganisms were cultivated in a bench-scale bioreactor that was developed as part of this dissertation. The bioreactor had a novel impeller design resulting in enhanced mixing and rotation and also a modular format allowing for diverse configurations. The bioreactor was notable for its durability and low cost. A detailed description of its design is included in the appendices. In summary, plastic materials can potentially be processed into growth media for microorganisms and can be used for production of value-added products. The media described herein can be used in bioconversion processes using a bioreactor.

Chemotherapy, employing single-molecule or multidrug concoctions inspired by the diverse repository of plant chemicals, has been the mainstay of cancer treatment for years. However, isolating single molecules has proven to be expensive along with limited therapeutic window and toxicity. On the other hand, whole foods, while preserving the natural complex balance between their constituent phytochemicals and being non-toxic, have proven to impart better disease-fighting efficacies, thus leading to an increased focus on dietary interventions to both treat and prevent cancer. Owing to the complex interactions between their constituent phytochemicals, several dietary agents have been investigated for their therapeutic and preventive efficacies. However, due to lack of emphasis on confounding factors like bioavailability, absorption, metabolism, and excretion, essentially driven by phytocomplexity, incorporation of whole foods in therapeutic regimen has not been successful. This thesis exemplifies the need to investigate factors associated with the limitations in the current approach with respect to dietary agents. Bioactivity-guided fractionation of sweet potato greens extract (SPGE) led to the identification of ~100-fold more potent fraction in vitro. However, this efficacy could not be translated in vivo. We also studied whole ginger extract (GE) for its in vitro and in vivo prostate tumor growth-inhibitory and apoptosis-inducing effects. In addition, GE proved to be more efficacious as compared to its individual most-active constituents owing to the differences in their pharmacokinetic (PK) and bioavailability measurements. Hence, these studies emphasize the crucial role of synergistic/additive interactions among the constituents of whole foods in successful translation of their therapeutic benefits. Another factor that seeks further attention is the unique cellular mechanisms engaged by these phytochemicals to confer their remarkable effects. Phenolic compounds, the most-abundant of all phytochemicals, are well known for their antioxidant properties and act via reactive oxygen species (ROS)-mediated mechanisms. We however assert the underappreciated xenohormetic prooxidant role of phenolics, where cancer cell death is caused by induction of intolerable levels of ROS. We demonstrated that a Piper betel constituent, hydroxychavicol (HC), mediates cytotoxicity via ROS-induced DNA-damage. This thesis thus provides compelling grounds for future preclinical studies to validate their potential usefulness for cancer management.

African monkey species are natural hosts of simian hemorrhagic fever virus (SHFV) and develop persistent, asymptomatic infections. SHFV was previously shown to also cause a rapid onset fatal hemorrhagic fever disease in macaques. Infection of macaques with a new isolate of SHFV from persistently infected baboon sera, that showed high nucleotide identity with the lab strain LVR, resulted in viremia, pro-inflammatory cytokine and tissue factor production, and symptoms of coagulation defects. Primary macrophages and myeloid dendritic cell cultures from disease-susceptible macaques efficiently replicated SHFV and produced pro-inflammatory cytokines, including IL-6 and TNF-α, as well as tissue factor. Cells from disease resistant baboons produced low virus yields and the immunomodulatory cytokine IL-10. IL-10 treatment of macaque cells decreased IL-6 levels but had no effect on TNF-α levels, tissue factor or virus production suggesting that IL-10 plays a role in modulating immunopathology in disease-resistant baboons but not in regulating the efficiency of virus replication. SHFV is a member of the family Arteriviridae. The SHFV genome encodes 8 minor structural proteins. Other arteriviruses encode 4 minor structural proteins. Amino acid sequence comparisons suggest that the four additional SHFV minor structural proteins resulted from gene duplication. A full-length infectious clone of SHFV was constructed and produced virus with replication kinetics comparable to the parental virus. Mutant infectious clones, each with the start codon of one of the minor structural proteins substituted, were analyzed. All eight SHFV proteins were required for infectious virus production. The SHFV nonstructural polyprotein is processed into the mature replicase proteins by several viral proteases including papain-like cysteine proteases (PLPs). Only one or two PLP domains are present in other arteriviruses but SHFV has three PLP domains. Analysis of in vitro proteolytic processing of C- and N-terminally tagged polyproteins indicated that the PLP in each of the three SHFV nsp1 proteins is active. However, the nsp1α protease is more similar to a cysteine protease than a PLP. Analysis of the subcellular localization of the three SHFV nsp1 proteins indicated they have divergent functions.

Assessing hormone receptors (the estrogen and progesterone receptors) and the human epidermal growth factor receptor 2 (HER2) to guide clinical decision making revolutionized treatment for breast cancer patients. However, in the years since these biomarkers were first incorporated into routine clinical care, only a few others have been validated as clinically useful in guiding adjuvant chemotherapy decisions and are recommended by the American Society of Clinical Oncology (ASCO) for patients with hormone-positive breast cancer. For patients with triple-negative breast cancer (TNBC), which lacks hormone and HER2 receptors, not any of these biomarkers are recommended by ASCO due to insufficient evidence that they meaningfully improve clinical outcomes. Breast cancer is the second-leading cause of cancer-related death among women in the US, indicating an unmet need to improve treatments, which can be accomplished in part by identifying and validating novel predictive and prognostic biomarkers that yield actionable information about the clinical course of breast cancers, especially TNBCs. A major obstacle to improving outcomes for breast cancer patients is intratumor heterogeneity (ITH), which can be extensive in breast cancer and drives treatment resistance and relapse. I envision that assaying drivers of ITH can inform clinicians about which breast tumors may be intrinsically more aggressive and carry a greater risk of breast cancer-related morbidity and mortality. My research, presented here, primarily focuses on testing the impact of drivers of ITH (namely, centrosome amplification [CA], the clustering protein KIFC1, and mitotic propensity and its drivers) on clinical outcomes in breast cancer in multivariable models as well as the correlates of in vitro efficacy of centrosome declustering drugs (which can selectively eliminate cancer cells with CA). Collectively, these studies reveal gene signatures and immunohistochemical biomarkers that are independent predictors of aggressive breast cancer course and rational strategies to optimize targeted therapy to combat cancer cells exhibiting CA, thereby contributing to the literature on the development of precision medicine for breast cancer patients, including TNBC patients.