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Probiotic bacteria are increasingly prevalent in food and nutritional products today. These remarkable microorganisms are capable of imparting exceptional health benefits on their host, including prevention of infection by pathogens and stimulation of immune system function. Their most common mode of delivery is through dairy products (e.g. yogurt), which are also one of their preferred habitats. The interactions between probiotic bacteria and dairy systems have been studied, but are still not well discerned. There is a need for better understanding of these associations, as well as those surrounding the mode of bacterial transfer from the food product to the human gastrointestinal tract. Discoveries into the optimal means of probiotic transport to the body may lead to great advancements in both the design of probiotic foods and their exploitation in the support of human health. Much of the previous research on probiotic bacteria has explored their possible means of adherence in the intestine, as well their strengths in the promotion of human health. Studies relating to their interaction with dairy products are lacking, however, thus this work aims to elucidate some of these aspects. The primary endeavor of this thesis was to develop a technique to quantify the binding affinity of probiotic lactic acid bacteria for milk phospholipids. An additional objective was to exploit these bacteria, as well as dairy ingredients rich in bioactive molecules, in the creation of a highly nutritious food product. In these experiments, a collection of methods were used in progression in order to arrive at a novel protocol to assess binding with excellent reproducibility and simplicity. These included various membrane blotting techniques, as well as thin-layer chromatography. Essentially, phospholipids from both animal-derived standards and milk extracts were applied to a surface (e.g. PVDF membrane), and bacteria were incubated with them to allow binding reactions. The lactic acid bacteria selected for the final assays consisted of four strains of Lactobacillus, including L. reuteri (SD2112 and T-1), L. acidophilus, and L. casei (LC-10). Their adhesion to phospholipids was detected by either colorimetric or fluorescent labeling systems. To illustrate this, the final method developed was a procedure in which bacteria fluorescently stained with acridine orange were allowed to bind to dots of PVDF membrane coated with phospholipids. The results of this study showed that lactic acid bacteria undeniably exhibit selective binding affinity for phospholipids as opposed to other lipids such as triglycerides. The bacteria demonstrated significantly greater binding for a phospholipid extract from milk as opposed to individual phospholipid standards from other sources (p<0.05). Nonetheless, adhesion to all phospholipids was substantially greater than that to triglycerides. These findings, as well as the development of this method, should prove valuable in future research regarding the associations of probiotics with dairy systems. An additional purpose of this thesis was to design a dairy-based food product containing ingredient sources rich in milk bioactives. A gel-type product was created using primarily colostrum, buttermilk powder, and whey protein isolate, as well as selected strains of Lactobacillus. With the inclusion of immunoglobulin-rich colostrum, the product was analyzed alongside fluid milk and colostrum in order to quantify and compare these bioactive molecules. An enzyme-linked immunosorbent assay (ELISA) was used to complete this, and the results revealed concentrations that would be expected by the literature. Specifically, immunoglobulin G (IgG) was quantified by interpolation from a bovine IgG standard regression curve. The results showed that the concentration of IgG in the gel was nearly twice that of colostrum, and almost eight-fold higher than that of milk. This indicates that use of bioactive-rich substances, such as colostrum, in a food product may serve as a means of delivering more concentrated doses of bioactives than their respective ingredients. The research completed in this thesis is significant in that it contributes a valuable method to the elucidation of bacterial binding interactions with milk components, and also demonstrates the successful application of dairy ingredients to an innovative food product high in beneficial compounds. The insight provided by these studies could encourage further work in improving the understanding of probiotic delivery and advancing the development of bioactive-rich food products.

Biological membranes form the structural boundaries and compartments of cells, owing to their robustness and impermeability facilitated by phospholipid bilayers. The strength of biological membranes is intricately linked to the behavior of membrane pores, whose formation and expansion can lead to membrane rupture. However, processes essential for drug delivery, gene editing via genetic material transfer, and antimicrobial peptide action necessitate controlled membrane disruption for efficient cellular entry. Likewise, fundamental phenomena such as exocytosis, including neurotransmitter release between neurons and hormone secretion for physiological responses, rely on membrane breach to release cargo beyond cell confines. Exocytosis involves the fusion of cargo-contained vesicle membranes with the cell's plasma membrane, resulting in the release of cargo into the extracellular milieu. Post-release, these fused vesicles may either integrate with the plasma membrane, remain stationary, enlarge, or depart the release site through fusion pore closure, which, in turn, can modulate exocytosis rate through site availability. However, the precise mechanism of membrane rupture remains elusive. Similarly, the pathway of membrane fusion facilitated by SNARE proteins, pivotal in cellular fusion machinery, remains a subject of debate. Additionally, the mechanisms governing exocytosis remain incompletely understood. To address these inquiries, we employ ultra-coarse-grained molecular dynamics simulations which can explore these phenomena in physiological timescale. These simulations explore membrane rupture mechanisms via pore formation and expansion under varying membrane tension. Furthermore, the research addresses how SNARE proteins drive membrane fusion. In addition, we also rigorously analyze confocal microscopy data from Ling-Gang Wu's research group and develop a quantitative model to elucidate exocytosis rate regulation. Furthermore, the research verifies the robustness of a mathematical model outlining Ca2+-mediated membrane fusion and establishes that hemifusion diaphragms (HDs), where only the outer leaflets of membranes fuse, act as hubs in the Ca2+-mediated fusion network. This finding casts new light on the role of membranes in SNARE-mediated fusion. In the extra study, we analyzed fission yeast contractile ring behavior based on z-stack confocal microscopy data from Mohan Balasubramanian's research group, offering insights into the mechanism behind a critical step in cytokinesis. Chapter one examines membrane pore energetics and bilayer rupture times through highly coarse-grained simulations operating at submillisecond time scales. No metastable states are detected during pore formation. At lower tensions, small hydrophobic pores mature into large hydrophilic pores that ultimately rupture from reversible hydrophilic pores, aligning with classical tension-dependent rupture times. At higher tensions, membranes rupture directly from small hydrophobic pores, with rupture times exhibiting exponential tension dependence. Upon reaching a minimum hydrophobic pore size, a critical tension threshold prompts immediate rupture. This analysis corroborates established experimental findings but reveals that the high-tension exponential regime is not related to long-lived pre-pore defects but rather to the instability of hydrophilic pores beyond a critical tension, leading to significant changes in pore dynamics and rupture kinetics. Chapter two describes utilizing ultra-coarse-grained simulations to dissect the core requirements of membrane fusion and unravel the intricacies of SNARE-mediated fusion. Remarkably, simulations conducted on a millisecond timescale expose the inefficiency of fusion through simple body forces pushing vesicles together. Successful inter-vesicle fusion hinges on the rod-like structure of fusogens, ensuring their sufficient length for effective fusion and subsequent clearance from the fusion site via entropic forces. Simulations featuring rod-shaped fusogens and SNARE proteins demonstrate the fusion of 50-nanometer vesicles in submilliseconds, propelled by entropic forces that direct a predictable fusion pathway. The entropic force hypothesis of SNARE-mediated membrane fusion garners strong support from these findings, emphasizing the necessity of the rod-like configuration of the SNARE complexes for entropic force generation and fusion. Chapter three focuses on the spatiotemporal dynamics of dense-core vesicle exocytosis events in chromaffin cells, deducing a novel mechanism for exocytosis regulation based on the availability of release sites. Repeated fusion supports membrane reservoir comprising incompletely merged or closed vesicles, occupying release sites and dampening exocytosis frequency. Mathematical modeling suggests reservoir formation relies on locally reduced membrane tension, eliminating the driving force for vesicle merging. Endocytosis facilitates the clearance of unmerged vesicles from the reservoir, ultimately restoring release site availability for subsequent exocytosis events. Chapter four introduces a mathematical model pinpointing the hemifusion diaphragm (HD) as the decision nexus dictating the outcomes of pathways and the fate of final products during multivalent cation-mediated membrane interactions. Transient formation of a high-tension hemifusion interface between membrane-enclosed compartments underscores the model's prediction of fusion, dead-end hemifusion, or vesicle lysis. This comprehensive framework offers predictive insights into interactions mediated by cationic fusogens within membrane-enclosed compartments. Chapter five offers a unique exploration of writhing contractile rings in fission yeast cell ghosts, resulting from controlled digestion of the cell wall and subsequent membrane permeabilization. This innovative approach unveils the intricate dynamics of contractile rings under exceptional circumstances. Writhing of rings is attributed to the detachment of sections from the weakened membrane, followed by their coiling due to apparent twisting torques at anchoring points. Iterative rotations give rise to multiple coils within the rings.

Ferroptosis is an iron-dependent form of cell death driven by peroxidation of phospholipids with polyunsaturated fatty acyl (PUFA) tails. Dietary factors, such as fatty acids and iron, regulate ferroptosis. Moreover, the incidence and progression of several cancers is correlated with diet; models of lymphoma have shown sensitivity to ferroptosis. We investigated the effects of altering dietary factors linked to ferroptosis on diffuse large B cell lymphomas (DLBCL). We found that DLBCL cells undergo ferroptosis in response to iron and PUFA treatments in vitro, and that their growth in xenograft models is substantially reduced. We observed that monounsaturated fatty acids (MUFAs), in contrast, suppress ferroptosis and promote growth in DLBCL cell and animal models. The inhibitory effect of the ferroptosis inducer imidazole ketone erastin (IKE) on DLBCL xenograft growth was lessened by dietary MUFA. Ferroptosis linked fatty acids and iron thus impact the growth and response to ferroptosis treatment of DLBCL tumors.

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