Thesis (M.S.)--Worcester Polytechnic Institute. / Keywords: NF-1 -- granule cell neuron. Includes bibliographical references (p. 38-39).

Thesis (Ph. D.)--University of Missouri--Columbia, 2003. / "August 2003." Typescript. Vita. Includes bibliographical references (leaves 158-174). Also issued on the Internet.

Thesis (Ph. D.)--University of Chicago, Pritzker School of Medicine, Department of Pathology, August 2001. / Includes bibliographical references. Also available on the Internet.

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy

NK-cell malignancies (NKLL) consist of two separate entities: Extranodal NK-cell lymphoma, nasal type (ENKL) and aggressive NK-cell leukemia (ANKL). ENKL is the second most common group of extranodal lymphomas in Hong Kong. Deletions in the 6q21 region in ENKL have been consistently reported in the literature and differential expression data indicated that the transcription factor PRDM1 (PR domain containing 1, with ZNF domain) located at 6q21-q22.1 is a candidate TSG in NK-cell neoplasms. PRDM1 exists as 2 isoforms generated from the same gene by alternative transcription promoter. PRDM1- differs from PRDM1-βin that it lacks the amino-terminal 101 amino acids with a disrupted PR domain. As the PRDM1- is functionally impaired, with a loss of repressive function on multiple target genes while maintaining normal DNA-binding activity, we hypothesize that the  -isoform, which is overexpressed in NKLLs, may act as a negative regulator of the tumor suppressive α-isoform in NKLLs. In this study, we investigated the possible role of PRDM1- as a negative regulator of tumor suppressor PRDM1-α in NK-cell lymphoma by using a gene silencing technique. Short hairpin-RNA (sh-RNA) construct with sequence targeting to PRDM1- purchasing from biotechnology company was used to knockdown of the gene expression. Series of functional assays were then performed to evaluate the effect of the PRDM1-  knockdown in two NK cell line, YT and NKYS, which xpress endogenous PRDM1-. Comparison was made between the 1) shRNA targeting to nt65-nt94 of PRDM1- sequence, sh-PRDM1 -pGFP-V-RS (shV2), and 2) scrambled-pGFPV-RS (scrambled shRNA), negative control with a non-effective shRNA cassette in pGFP-VRS plasmid. Western blot analysis was performed to examine the efficiency of shRNA in knockdown the expression of PRDM1-  in 293T cells (normal human embryonic kidney cells). The protein expression level for ectopic PRMD1- was reduced in cells expressing shV2 when compared with the negative control. NKYS cell line expressed with shV2 showed a significant reduction in the number of colonies. Percentage of dead cells was found higher in these cells. The proliferation rate of shV2 expressing cells started to retarded significantly on the third day of measurement in the MTS proliferation assay. The cell also underwent G1 cell cycle arrest and had lower proliferation rate, as indicated by cell cycle analysis. For YT cell line expressed with shV2, significant reduction in both colony number and size in methylcellulose colony formation assay was observed. Base on the results obtained from the two NK-cell lines, we suggest that the shV2 inhibit the tumor cell growth. The knockdown of the PRDM1-  lead to an increase level of PRDM1- α. PRDM1- α is a tumor suppressor gene with suppressive function by preventing damaged cells from proliferation or inhibiting the clonogenecity of the tumor cells. An imbalance expression of PRDM1- and PRDM1-αplay an important role in tumor growth and formation, and PRDM1 could possibly be the new tumor suppressor gene in NK-cells lymphoma. / published_or_final_version / Pathology / Master / Master of Medical Sciences

Breast cancer comprises of 22.9% of all cancers worldwide in females. In the year 2008, it has caused 458,503 deaths worldwide. De-regulation of transcription factors has been shown to play an important role in the progression of breast cancers. Snail and TWIST genes have been found to promote epithelial-mesenchymal transition (EMT). It has been suggested that the level of expression of each of these genes correlates with poor prognosis in different types of solid tumors. For breast cancer, the up-regulation of Snail was associated with recurrence and higher tumor grade, while the up-regulation and up-regulation of TWIST was associated with shorter survival and metastatic development. However, in recent studies conflicting results have been observed. Our collaborator had analyzed mRNA expression data obtained from the Gene Expression Omnibus (GEO) database together with patient survival data from the breast cancer cohort datasets, and found that expression of Snail when stratified against TWIST expression levels or vice versa, gave more significant association with survival than when expression levels of Snail or TWIST was considered on their own. To investigate whether these findings could be demonstrated at a protein level, we performed imrnuno-histochemisty analysis on breast cancer samples in tissue microarray blocks. Nuclear and cytoplasmic scores of TWIST were successfully assessed separately in 114 invasive breast cancer patients. The Snail scores were obtained from previous studies. As Snail and TWIST are both transcription factors, nuclear expression of each was examined for correlation of Snail and TWIST with pathological features and patient survival. Our results showed that nuclear Snail expression did not correlate with survival (p=0.498) but when stratified with nuclear TWIST, high levels of nuclear Snail expression associated with poorer survival in patients with low nuclear TWIST expression (p=O.2l2), though not statistically significant which agreed with the mRNA results of our collaborator. For nuclear TWIST expression, association with survival was in reverse from that of the mRNA findings. Low expression levels of TWIST mRNA was associated with shorter survival, however immuno-histochemistry showed that high levels of nuclear TWIST expression marginally correlated with poorer survival (p=O.079). Low levels of cytoplasmic TWIST expression on the other hand, correlated with poorer survival in patients (p=O.024), and when stratified against high nuclear Snail, expression was associated with shorter survival (p=O.022), which is in keeping with mRNA findings. The results show that Snail and TWIST expression gave more prognostic value when considered together than when considered individually, which suggests that Snail and TWIST might be functionally similar in the promoting of EMT mediated breast. It also highlights the importance of nuclear and cytoplasmic localization by immuno-histochemistry in evaluating results and in assessing its role in promoting breast cancer progression. In conclusion Snail and TWIST should be considered together for prognostication of breast cancer as they may complement each other in predicting the progression of the disease. / published_or_final_version / Pathology / Master / Master of Medical Sciences

 As a neuropeptide, both secretin and secretin receptor are expressed in the central nervous system (CNS). It has been revealed that the activities of secretin on hypothalamic cells of rodents are important for osmoregulation and food intake. In the present study, embryonic mouse hypothalamic cell line N42 was used to study the promoter activity of mouse secretin receptor (mSR). By 5′ deletion analysis, a promoter element was identified within ?282 to ?443, relative to the ATG codon, and it contains a GC-box (-297 to -286), a ras responsive element (RRE) (-289 to -276) and an E-box (-416 to -411). Electrophoretic mobility shift assay (EMSA) and supershift analyses showed that Sp1 interacted with the GC-box, another zinc finger As a neuropeptide, both secretin and secretin receptor are expressed in the central nervous system (CNS). It has been revealed that the activities of secretin on hypothalamic cells of rodents are important for osmoregulation and food intake. In the present study, embryonic mouse hypothalamic cell line N42 was used to study the promoter activity of mouse secretin receptor (mSR). By 5′ deletion analysis, a promoter element was identified within ?282 to ?443, relative to the ATG codon, and it contains a GC-box (-297 to -286), a ras responsive element (RRE) (-289 to -276) and an E-box (-416 to -411). Electrophoretic mobility shift assay (EMSA) and supershift analyses showed that Sp1 interacted with the GC-box, another zinc finger / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

abstract / Surgery / Master / Master of Philosophy

The ability to sense and rapidly respond to oxygen availability is crucial to the survival and physiology of facultative anaerobes. In many gram negative bacteria such as Escherichia coli, this process is primarily controlled by the dimeric, [4Fe〖-4S]〗^(2+) containing global transcription factor FNR, which regulates transcription of genes necessary for the anaerobic metabolism. Activity of FNR is directly regulated by the presence of oxygen, which inactivates FNR by oxidizing the [4Fe〖-4S]〗^(2+) cluster and causing the dissociation of the FNR dimer. Although the biological function of FNR has been well established, structural and biochemical characterization of the FNR dimer has been limited due to its extreme lability to oxygen. In the current study, I conduct molecular engineering on FNR protein and obtain oxygen stable variants that are suitable for in vitro biochemical studies. By combining several approaches including covalently linking two FNR monomers using a flexible peptide linker, amino acid substitutions to promote dimerization, and removal of protease recognition sites to prevent proteolysis, a series of FNR variants which are potentially active in the presence of oxygen are constructed. Various in vivo and in vitro assays led to the identification of the construct (FNRD154A)2 which covalently links two copies of FNRD154A, an FNR variant that has greater dimerization capability, in tandem displays significantly improved transcription regulation and DNA binding to various FNR regulated promoters in the presence of O2. Circular Dichroism analysis showed that this variant maintains a similar secondary structure as that of native FNRD154A and in vivo transcription assay demonstrated that this protein retains other properties of the native FNR dimer including [4Fe〖-4S]〗^(2+) cluster binding, oxygen sensing, and capability to support the anaerobic growth of E. coli. All these together led the conclusion that an FNR variant that retains structural and functional properties of native FNR has been constructed, but with significantly improved O2 stability. Thus, it has the potential to be widely used in various biochemical and structural studies of FNR in the presence of oxygen. In addition to the major project of molecular engineering of FNR protein, in this thesis, I also initiated the study of using metabolomics approaches to identify the cellular substrates of the multidrug efflux pump MdtEF. MdtEF is an important efflux pump in E. coli and its expression has been shown to be induced under a number of stressed conditions. It is thus proposed to have a general detoxification function in E. coli, but the cellular substrates it expels have not been identified. In this study we established and applied metabolite profiling on the wild type and ΔmdtEF E. coli strains and confirmed that indole red, a metabolic by-product formed during anaerobic respiration of nitrate, is one of the cellular substrates of MdtEF under anaerobic conditions. This study provides a general methodology to identify endogenous substrates of efflux pumps and contributes to the understanding of the physiological roles of multidrug efflux pumps in bacteria. / published_or_final_version / Biological Sciences / Master / Master of Philosophy