Browsing by Author "Liu, Fang"

This dissertation studies coordination mechanism design for sustainable supply networks in a globalized environment, with the goal of achieving long-term profitability, environmental friendliness and social responsibility. We examine three different types of supply networks in detail.

The first network consists of one supplier and multiple retailers. The main issue is how to efficiently share a scarce resource, such as capacities for green technology, among all members with private information under dynamically changing environment. We design a shared surplus supply agreement among the members which can lead to both efficient private investments and efficient capacity allocation under unpredictable and unverifiable market conditions.

The second network is a serial supply chain. The source node provides critical raw material (like coffee cherries) for the entire chain and is typically located in an underdeveloped economy, the end node is a retailer serving consumer at a developed economy (like Starbucks Co.). We construct a dynamic supply agreement that takes into account the changing market and production conditions to ensure fair compensations so that the partners have the right incentives to work together to develop sustainable quality supply.

The third network is a stylized global production network of a multinational company consisting of a home plant and a foreign branch. The branch serves the foreign market but receives a key component from the home plant. The distinctive feature is that both facilities belong to the same company, governed by the headquarters, yet they each also have their own autonomies. We analyze the role of the headquarters in designing coordination mechanism to improve efficiency. We show the headquarters can delegate the coordination effort to the home plant, as long as it keeps veto power.

Proteomic methods for disease state characterization and biomarker discovery have traditionally utilized quantitative mass spectrometry methods to identify proteins with altered expression levels in disease states. Unfortunately, these studies have not been as useful as expected at identifying disease-related proteins that can be exploited for diagnostic and therapeutic purposes, presumably due to the indirect link between a protein’s expression level and its function. Investigated here is the use of thermodynamic stability measurements to probe a more biologically relevant dimension of the proteome. It has the potential to become a new strategy for disease state characterization and to help elucidate the molecular basis of the disease. This thesis outlines the use of two discovery based techniques and one validation based technique to study protein folding and stability changes associated with breast cancer.

The first part of this dissertation describes the application of a mass spectrometry-based technique, stable isotope labeling with amino acids in cell culture and stability of proteins from rates of oxidation (SILAC-SPROX), in a comparison of the MCF-7 versus BT-474 breast cancer cell lines and a comparison of the MCF-7 versus MDA-MB-468 breast cancer cell lines. This work enabled ~1000 proteins to be assayed for breast cancer-related thermodynamic stability differences. The 242 and 445 protein hits identified with altered stabilities in these comparative analyses created distinct molecular markers to differentiate the three cell lines.

The second part of this dissertation describes the development of a SILAC-based limited proteolysis (SILAC-LiP) strategy. The applicability of the protocol was demonstrated in a proof-of-principle study using proteins from a yeast cell lysate and a ubiquitous ligand. The SILAC-LiP protocol was further applied in a comparison of the MCF-7 versus MCF-10A cell lines. This work identified ∼200 proteins with cell line dependent conformational changes, as determined by their differential susceptibility to proteolytic digestion using the nonspecific protease, proteinase K. The overlap between the SILAC-LiP hits reported here and the SILAC-SPROX hits previously identified in these same cell lines was relatively small (~20%). Thus, this work indicates that the SILAC-SPROX and SILAC-LiP techniques can be used together to provide complementary information on the disease states.

Furthermore, the protein hits identified in both the SILAC-SPROX and SILAC- LiP experiments included a large fraction (∼70%) with no significant expression level changes. This suggests protein folding and stability measurements can provide information about disease states that is orthogonal to that obtained in protein expression level analyses.

The last part of this dissertation focuses on the establishment of targeted mass spectrometry-based validation assays for the protein biomarker candidates with altered thermodynamic stabilities identified in the SILAC-SPROX experiments. Application of the PAB-SPROX protocol on the MCF-7 cell lysate enabled reproducible identification and quantitation of a subset of prioritized target peptides.