State-­‐owned Enterprises in China : An Analysis of Profitability, Science and Technology Development and Business Groups

After the end of the communist era in China in the late 1970’s, a key task for the government was to restructure the state-owned enterprises into separate autonomous units and make the transition towards a more market-­‐based economy. This report aims at developing an increased understanding of the SOE reorganization in China and policies related to these reforms. By extensive literature review and analysis of the most recent data, key elements of the reforms are identified and the implication and success of those are discussed. More specifically, the impact of SOE reforms on the profitability of SOEs, the development of internationally competitive domestic firms and the acquisition and development of technology and innovative capacity are evaluated. The evidence presented in this report show that the SOE reforms have been successful in increasing the profitability of SOEs, but SOEs are still lagging behind private firms in terms of profitability and efficiency and also use their R&D resources less efficiently

A Proteomic Dissection of Breast Cancer - Via Cells and Organelles to Pathways

Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death in females worldwide. Breast tumours are extremely heterogeneous, and each patient’s disease has different causes, prognosis and appropriate treatments associated with it. To enable a more individualised therapy, there is a substantial need for better characterisation of tumours and a deeper understanding of the molecular mechanisms of disease initiation, progression and treatment resistance. During the last decade, shotgun proteomics has evolved as a powerful tool, complementing the fields of genomics and transcriptomics, for the elucidation of pathway and network changes in cancer. The proteome is, however, with its large dynamic range and numerous post-translational modifications, tremendously more complex than the genome and an additional level of complexity is provided by the spatial arrangements of proteins in different organelles. In this thesis we have addressed technical challenges such as optimising proteomic coverage by evaluating different protein and peptide separation methods and mapping proteins to organelles with density gradient organelle fractionation followed by proteomic quantification of the fractions. Further, we applied both a discovery mode of proteomics and a focussed pathway centric method to evaluate the response of breast cancer cell lines to chemotherapeutic agents. Proteomic pathway analysis was also utilised to investigate and explain the differential response to therapy in different breast tumour subpopulations

State-­‐owned Enterprises in China : An Analysis of Profitability, Science and Technology Development and Business Groups

After the end of the communist era in China in the late 1970’s, a key task for the government was to restructure the state-owned enterprises into separate autonomous units and make the transition towards a more market-­‐based economy. This report aims at developing an increased understanding of the SOE reorganization in China and policies related to these reforms. By extensive literature review and analysis of the most recent data, key elements of the reforms are identified and the implication and success of those are discussed. More specifically, the impact of SOE reforms on the profitability of SOEs, the development of internationally competitive domestic firms and the acquisition and development of technology and innovative capacity are evaluated. The evidence presented in this report show that the SOE reforms have been successful in increasing the profitability of SOEs, but SOEs are still lagging behind private firms in terms of profitability and efficiency and also use their R&D resources less efficiently

A Breast Cell Atlas: Organelle analysis of the MDA-MB-231 cell line by density-gradient fractionation using isotopic marking and label-free analysis

Protein translocation between organelles in the cell is an important process that regulates many cellular functions. However, organelles can rarely be isolated to purity so several methods have been developed to analyse the fractions obtained by density gradient centrifugation. We present an analysis of the distribution of proteins amongst organelles in the human breast cell line, MDA-MB-231 using two approaches: an isotopic labelling and a label-free approach

Pathway-centric analysis of the DNA damage response to chemotherapeutic agents in two breast cell lines

The response to DNA damage by alkylation and DNA topoisomerase inhibition was studied in two breast cancer cells lines. We present data from both a shotgun and a targeted, pathway-centric approach to highlight the different DNA repair pathway modulation in the cell lines and the correlation with viability and DNA damage assays. This type of focussed profiling may be of utility in rapidly defining non-responders undergoing systemic neoadjuvant therapy

Critical Comparison of Multidimensional Separation Methods for Increasing Protein Expression Coverage

We present a comparison of two-dimensional separation methods and how they affect the degree of coverage of protein expression in complex mixtures. We investigated the relative merits of various protein and peptide separations prior to acidic reversed-phase chromatography directly coupled to an ion trap mass spectrometer. The first dimensions investigated were density gradient organelle fractionation of cell extracts, 1D SDS-PAGE protein separation followed by digestion by trypsin or GluC proteases, strong cation exchange chromatography, and off-gel isoelectric focusing of tryptic peptides. The number of fractions from each first dimension and the total data accumulation RP-HPLC-MS/MS time was kept constant and the experiments were run in triplicate. We find that the most critical parameters are the data accumulation time, which defines the level of under-sampling and the avoidance of peptides from high expression level proteins eluting over the entire gradient

Design of recombinant antibody microarrays for membrane protein profiling of cell lysates and tissue extracts.

Generating global protein expression profiles, including also membrane proteins, will be crucial for our understanding of biological processes in health and disease. In this study, we have expanded our antibody microarray technology platform and designed the first human recombinant antibody microarray for membrane proteins targeting crude cell lysates and tissue extracts. We have optimized all key technological parameters and successfully developed a setup for extracting, labeling and analyzing non-fractionated membrane proteomes under non-denaturing conditions. Finally, the platform was also extended and shown to be compatible with simultaneous profiling of both membrane proteins and water-soluble proteins

Critical Comparison of Multidimensional Separation Methods for Increasing Protein Expression Coverage

We present a comparison of two-dimensional separation methods and how they affect the degree of coverage of protein expression in complex mixtures. We investigated the relative merits of various protein and peptide separations prior to acidic reversed-phase chromatography directly coupled to an ion trap mass spectrometer. The first dimensions investigated were density gradient organelle fractionation of cell extracts, 1D SDS-PAGE protein separation followed by digestion by trypsin or GluC proteases, strong cation exchange chromatography, and off-gel isoelectric focusing of tryptic peptides. The number of fractions from each first dimension and the total data accumulation RP-HPLC–MS/MS time was kept constant and the experiments were run in triplicate. We find that the most critical parameters are the data accumulation time, which defines the level of under-sampling and the avoidance of peptides from high expression level proteins eluting over the entire gradient