In the biopharmaceutical industry, essentially, there are three components that play the main role in producing biopharmaceutical products, the host cell, the expression vector and the bioreactor and/or production environment. To produce the highly valued and desired products, the choice of a suitable host is one of the most important aspects. The host required is not only required to produce the desired product, but also needs to demonstrate robustness in a bioreactor system. Constantly facing challenges in a bioreactor, cells often undergo apoptosis, a well-known limiting factor in biopharmaceutical production, which ultimately leads to low yield of valuable protein(s). We have genetically engineered a CHO-K1 cell line to constitutively express human insulin-like growth factor-1 (IGF-1) and murine polyoma large T-antigen (PyLT-Ag) to generate Super-CHO and CHO-T respectively, two cell lines that can potentially serve different niches in the biopharmaceutical industry. In the first part of the project, we hypothesised that suspension-adapted Super-CHO and CHO-T cells are both resilient cell lines relative to the suspension-adapted CHO-K1 (designated as CHO-XL-99) when facing nutrient depletion, one of the most common problems in a bioreactor. Furthermore, in the second part of this project, the suspension-adapted CHO cell lines were also tested against a cytotoxic heavy metal, cadmium. Without the protection of the metal-resistance element, metallothionein, both Super-CHO and CHO-T cells were also challenged with cadmium to demonstrate their robustness over the parental cell line, CHO-XL-99. In the subsequent study, this project also focussed on the transfection efficiency of each parental and engineered CHO cell lines. Different strategies have been employed in the past in an attempt to improve productivity in the biopharmaceutical industry, from alterations in vector construction, improved culture condition, down to enhanced product recovery. However, the transfer and expression of the gene-of-interest (GOI) has still proven to be the limiting factor for achieving increased specific productivity. In an effort to improve transfection efficiency, strategies including cell cycle synchronisation and various transfection methods to deliver the GOI into the cells have been employed. Thus, the third part of this project has used synchronising agents in conjunction with commercially available lipid- and polymer-based reagents as delivery vehicle for the model protein, EGFP. The combination of cell synchronisation and transfection vehicle on transfection efficiency is studied here, in addition to their individual or collective effect on cell growth, apoptosis and viability. In summary, this project demonstrates the incidence of apoptosis in the cell culture induced by nutrient depletion and heavy metal, and that the use of transfection reagents solely, or in combination with synchronising agents also correlates with the increase of apoptotic indices in the cell culture. The use of the robust cell lines for transfection is an important aspect, and the balance between cell viability and the effort for augmenting transfection efficiency has to be met in order to achieve the maximum biopharmaceutical yields.

Poplar Bark Storage Proteins (BSP) are important in storing nitrogen (N) recovered from autumn-senescent leaves, and supply N for spring growth. Plants of Populus tremula x P. alba were transformed with a poplar BSP antisense cDNA fused to a double 35S promoter. Regenerated lines were screened for reduced BSP accumulation in short day photoperiod, and two lines were selected for further studies. Under long-day conditions, both BSP-antisense lines were characterized by larger leaves, longer internodes and slower growth rates, for a net shift in dry-matter partitioning from stem to leaf. Antisense lines also show reduced N concentration in leaf and stem tissue, and altered nitrate uptake. Grafting studies show that these effects on leaf and stem partitioning and N content are determined by the shoot genotype. These results indicate an important role of BSP in long day growth and partitioning. BSP-antisense plants did not show altered Nitrate Reductase activity, as determined by in vivo assay. Wild-type poplar plants were grown hydroponically on solutions of 0 to 30 mM nitrate, and NR activity determined on leaf, stem and root tissue. Leaf activity was >20x higher than root or stem, with the highest activity found in young expanding leaves. NR activity of both leaves and roots increased with N supply. During autumn, BSP-antisense leaves abscised earlier than the untransformed wt. Abscised wt leaves contained a higher proportion of pre-senescent N levels. Comparisons among ecotypes of P. deltoides and among clones of P. trichocarpa x P. deltoides demonstrated genetic variation in both time of BSP induction, and amount of BSP accumulation. In six P. deltoides ecotypes grown at a common site, time of maximum BSP mRNA was inversely correlated with latitude of origin. Eight to ten clones from each of six full-sib families of P. trichocarpa x P. deltoides were screened for SD BSP accumulation. Clonal differences in BSP accumulation were significant in 5 of 6 families, and clones with high BSP levels also had higher total stem N content. These results further confirm the importance of BSP in autumn N resorption. / Graduation date: 2000

Graduation date: 1997

Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2007. / Includes bibliographical references (leaves 97-105). Also available in electronic version.

Thesis (Ph. D.)--Oregon State University, 1981. / Typescript (photocopy). Includes bibliographical references (leaves 167-178). Also available on the World Wide Web.

Thesis (Ph.D.)--Ohio University, March, 2006. / Title from PDF t.p. Includes bibliographical references (p. 205-250)

Anaerobic ammonium oxidation (anammox) is a pathway that has been known for almost 2 decades, but few studies have investigated its importance in natural groundwaters. This thesis investigated the presence of anammox cells and the groundwater geochemistry of 2 sites (Elmira and Putnam) in southwestern Ontario where groundwaters are contaminated with high levels of nitrate and ammonium. Fluorescence in situ hybridization (FISH) was used to quantify the relative abundance of anammox cells in these waters. Our results showed that anammox cells could be detected in many wells at both sites and that their relative abundance varied between 0.45 and 4.81 % at the Putnam site, whereas it ranged between 0.8 to 8.4 % at the Elmira site. These values are within the same range as those obtained for marine and freshwater environments where anammox cells have been detected. In addition, indirect observations point to the fact that N cycling at the 2 sites might be linked to Fe and Mn reduction, but additional experiments are needed. In summary, our results corroborate the findings of N-labeled microcosm experiments which demonstrated that anammox was an important pathway of N cycling in those groundwaters and molecular analyses that detected important anammox organisms at the same sites.

Proper progression through the cell cycle is critical for cell growth and survival. Disruption of cell cycle progression can lead to cell cycle arrest and cell death. In addition, uncontrolled cell cycle progression can lead to cancer. Cells have evolved complex mechanisms to regulate each phase of the cell cycle to ensure proper cell cycle progression. In the presence of cellular stress, cells will respond promptly to arrest the cell cycle and allow repair. In order to study this complex process, it is important to identify the complete complement of proteins involved. I took two large-scale approaches to study the cell cycle. First, I down-regulated the majority of essential genes in Saccharomyces cerevisiae, and determined how depletion of individual gene product affected progression through the cell cycle. I determined that over 65% of essential genes I tested are most important at a specific cell cycle phase. In addition, I found that two genes, Smc4 and Cse1, have novel roles in S-phase of the cell cycle. In the second approach, I discovered two anti-proliferative compounds. Both compounds caused cell cycle delay in G1 phase of the cell cycle. Chemical genetic screens in yeast allowed me to determine the pathways most sensitive to each of these two compounds. By studying the response of cells to these compounds, I confirmed that compound 13 causes mitochondrial dysfunction in cells and compound 15 causes nuclear DNA damage. Furthermore, I found that both compounds are toxic in mammalian cells and that the responses that they elicit in mammalian cells are similar to those observed in yeast cells.

The cyclin-dependent kinase (CDK) inhibitors have been demonstrated to be an important component in the regulation of plant cell cycle. Although they share a conserved CDK inhibitory region with a family of CDK inhibitors in mammals, the plant CDK inhibitors are very different from the animal and yeast CDK inhibitors. Thus studies of the plant CDK inhibitors could provide insight on the molecular mechanisms regulating the cell cycle in plants as well as the differences between plants and animals. The research described in this thesis investigated the seven Arabidopsis CDK inhibitors ICKs in terms of transgenic expression, phosphorylation, stability and interactions with other proteins. <p>ICKs were expressed in transgenic Arabidopsis plants as fusion proteins with the green fluorescent protein (GFP). Consistent with the previous studies on ICK1, ICK2 and ICK4, overexpression of all seven ICKs inhibited plant growth and resulted in plants with serrated leaves and flowers with altered morphology. A Survey based on large a number of independent transformants showed that GFP-ICK3 and GFP-ICK4 had weaker phenotypic effects compared to other GFP-ICKs. The Western blotting results showed that all GFP-ICKs were expressed at a low level in general. The levels of GFP-ICK3 and GFP-ICK4 were the lowest, suggesting that the weaker effects for ICK3 and ICK4 may partly be due to low protein levels. Treatments with MG132, an inhibitor of the proteasome, resulted in moderate but clear accumulation of fusion proteins for ICK1, ICK5, ICK6 and ICK7 in plants, suggesting that the proteasome is involved in the degradation of these proteins. <p>To study the state of protein phosphorylation, the proteins extracted from the plants were treated with calf intestinal phosphatase (CIP). The CIP treatment caused a faster migration of the GFP fusion protein for ICK1, ICK2, ICK5, ICK6 and ICK7, while the effect was not observed for control GFP and other non-specific proteins, indicating that these proteins can be phosphorylated in plants. The shift also differed among ICKs. Interestingly, dephosphorylation of ICK7 might have rendered it less stable. The protein pulldown experiments using p13Suc1-conjugated agarose beads showed that GFP-ICK4, GFP-ICK5 and GFP-ICK6 could associate with the CDK complex, similar to what has been shown for ICK1 and ICK2. CIP treatments of the p13Suc1 affinity-purified proteins also showed that ICK1, ICK2, ICK5 and ICK6 associated with the CDK complex were phosphorylated. <p>Attempts were also made to isolate peptide aptamers that are able to interact with ICKs for the purpose for expressing such an aptamer in plants. However, an aptamer that has a strong ability to interact with ICKs in two of yeast two-hybrid systems was not identified. In addition, the analysis of Arabidopsis CYCD3;1 for its interaction with ICK1 using a series of deletion mutants showed that the removal of both the N-terminal and C-terminal regions of CYCD3;1 greatly reduced or abolished the interaction with ICK1. <p> In summary, transgenic Arabidopsis plants have been obtained for expressing each of the seven Arabidopsis CDK inhibitors fused to GFP. The results confirmed and extended previous finding that overexpression of a CDK inhibitor inhibits plant growth as well as changes plant morphology. The observation that the ICK fusion proteins were generally at low and often undetectable levels, in comparison to much higher levels of the GFP protein, suggests that ICKs are unstable in the cell. Results from the MG132 experiments indicate that the 26S proteasome may play a role in the degradation of ICK1, ICK5, ICK6 and ICK7. Results from CIP treatments further show that most ICKs, particularly ICK1, ICK2, ICK5, ICK6 and ICK7, can be phosphorylated in vivo. Interestingly, ICK7 stability may depend on the status of protein phosphorylation. This study provides new understanding on how the family of proteins is regulated at the post-transcriptional level and the differences among Arabidopsis CDK inhibitors.

Proper progression through the cell cycle is critical for cell growth and survival. Disruption of cell cycle progression can lead to cell cycle arrest and cell death. In addition, uncontrolled cell cycle progression can lead to cancer. Cells have evolved complex mechanisms to regulate each phase of the cell cycle to ensure proper cell cycle progression. In the presence of cellular stress, cells will respond promptly to arrest the cell cycle and allow repair. In order to study this complex process, it is important to identify the complete complement of proteins involved. I took two large-scale approaches to study the cell cycle. First, I down-regulated the majority of essential genes in Saccharomyces cerevisiae, and determined how depletion of individual gene product affected progression through the cell cycle. I determined that over 65% of essential genes I tested are most important at a specific cell cycle phase. In addition, I found that two genes, Smc4 and Cse1, have novel roles in S-phase of the cell cycle. In the second approach, I discovered two anti-proliferative compounds. Both compounds caused cell cycle delay in G1 phase of the cell cycle. Chemical genetic screens in yeast allowed me to determine the pathways most sensitive to each of these two compounds. By studying the response of cells to these compounds, I confirmed that compound 13 causes mitochondrial dysfunction in cells and compound 15 causes nuclear DNA damage. Furthermore, I found that both compounds are toxic in mammalian cells and that the responses that they elicit in mammalian cells are similar to those observed in yeast cells.