by Tsui Hong Teng. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (leaves 174-181). / Abstracts in English and Chinese. / A CKNO WLED GMENTS --- p.7 / ABSTRACT --- p.8-10 / Chapter Chapter 1: --- Introduction: --- p.11-44 / Chapter 1.1) --- Glucose transporters / Chapter 1.2) --- Glucose transporters and cancers / Chapter 1.3) --- Antisense strategies / Chapter 1.4) --- Cellular uptake of oligonucleotides / Chapter 1.5) --- Hyperthermia and combined treatments / Chapter Chapter 2: --- Materials and methods --- p.45-60 / Chapter 2.1) --- Materials: / Chapter 2.1a) --- Cell lines and culture media / Chapter 2.1b) --- Oligonucleotides synthesis / Chapter 2.1c) --- Chemicals / Chapter 2.2) --- Methods: / Chapter 2.2a) --- Oligonucleotide design / Chapter 2.2b) --- Oligonucleotide treatment / Chapter 2.2c) --- Flow cytometry / Chapter 2.2d) --- Confocal microscopy / Chapter 2.2e) --- MTT assay for cytotoxicity or cell proliferation / Chapter Chapter 3: --- Cellular uptake of oligonucleotide spontaneously and Lipofectin-aided: --- p.61-85 / Chapter 3.1) --- Introduction / Chapter 3.2) --- Flow cytometric studies / Chapter 3.3) --- Confocal microscopic studies / Chapter 3.4) --- Cytotoxic effect of Lipofectin alone on MCF-7 cells / Chapter 3.5) --- Discussion / Chapter Chapter 4: --- Hyperthermia can enhance oligonucleotide uptake: --- p.86-118 / Chapter 4.1) --- Introduction / Chapter 4.2) --- Flow cytometric studies / Chapter 4.3) --- Confocal microscopic studies / Chapter 4.4) --- Cytotoxic effect of hyperthermia on MCF-7 cells / Chapter 4.5) --- FITC-ODN uptake in survival cells by propidium iodide (PI) exclusion method for hyperthermia / Chapter 4.6) --- Discussion / Chapter Chapter 5: --- The antiproliferative effects of antisense molecules against Glut-1 and 5 on MCF- 7 cells transfected by Lipofectin: --- p.119-146 / Chapter 5.1) --- Introduction / Chapter 5.2) --- The growth curve of MCF-7 cells / Chapter 5.3) --- The calibration of MTT assay / Chapter 5.4) --- The effect of antisense Glut-1 concentration without Lipofectin on MCF-7 cells / Chapter 5.5) --- The effect of antisense Glut-1 concentration with Lipofectin on MCF-7 cells / Chapter 5.6) --- The effect of antisense Glut-5 concentration without Lipofectin on MCF-7 cells / Chapter 5.7) --- The effect of antisense Glut-5 concentration with Lipofectin on MCF-7cells / Chapter 5.8) --- The effect of transfection time of antisense Glut-1 on MCF-7 cells / Chapter 5.9) --- The effect of transfection time of antisense Glut-5 on MCF-7 cells / Chapter 5.10) --- The effect of transfection time of antisense Glut-5 for higher concentration on MCF-7 cells / Chapter 5.11) --- The effect of antisense Glut-1 to Lipofectin (w/w) ratio on MCF-7 cells / Chapter 5.12) --- The effect of antisense Glut-1 to Lipofection (w/w) ratio for higher transfection time on MCF-7 cells / Chapter 5.13) --- The effect of antisense Glut-5 to Lipofectin (w/w) ratio on MCF-7 cells / Chapter 5.14) --- Discussion / Chapter Chapter 6: --- Combined treatments: --- p.147-162 / Chapter 6.1) --- Introduction / Chapter 6.2) --- The effect of combined treatment of antisense Glut-1 combined with antisense Glut-5 on MCF-7 cells / Chapter 6.3) --- The chronic effect of hyperthermia for 5 hours on MCF-7 cells / Chapter 6.4) --- The effect of combined treatment between antisense Glut-1 and hyperthermia on MCF-7 cells / Chapter 6.5) --- The net effect of antisense Glut-1 in combined treatment between hyperthermia and antisense Glut-1 on MCF-7 cells / Chapter 6.6) --- The effect of combined treatment between antisense Glut-5 and hyperthermia on MCF-7 cells / Chapter 6.7) --- The net effect of antisense Glut-5 in combined treatment between hyperthermia and antisense Glut-5 on MCF-7 cells / Chapter 6.8) --- Discussion / Chapter Chapter 7: --- Discussion: --- p.163-173 / Chapter Chapter 8: --- References: --- p.174-181

The liver is the largest internal organ and performs a wide variety of functions to maintain organismal homeostasis. While some liver functions are carried out by all hepatocytes, other functions are restricted to certain populations of hepatocytes within the liver. This phenomenon, called zonal gene regulation or liver zonation, controls may metabolic processes within the liver including ammonia detoxification; glucose homeostasis; bile acid and glutamine synthesis; and metabolism of xenobiotics, lipids, and amino acids. The liver also expresses many genes in a developmental or sex-biased manner. Some genes are expressed at higher levels early or late in development, or alternatively, in male or female liver. Several years ago, our lab identified a transcription factor called Zinc finger and homeoboxes 2 (Zhx2) based on its ability to control the silencing of genes that are normally expressed in the fetal liver. Zhx2 belongs to a small gene family that also includes Zhx1 and Zhx3. These four exon genes have a rather unique structure in that their entire protein coding region is located on an unusually large third exon. Preliminary studies indicate that these proteins are found only in vertebrates. I have performed a comprehensive analysis of Zhx proteins across a number of chordate species to determine their relationship throughout chordate evolution. Using multiple sequence alignment and phylogenetic tree-building, my studies have found that the primordial Zhx gene is most related to Zhx3 and that this gene exists in lower chordates including lancelet, sea squirt, and sea lamprey. Additional studies from our lab showed that Zhx2 regulates numerous hepatic genes in the adult liver, including cytochrome p450 (Cyp) genes as well as other genes that exhibit sex-biased expression. Previous studies have demonstrated that female-biased expression of Cyp2a4, is controlled, in part, by Zhx2. I have extended these studies to perform a comprehensive analysis of Cyp2a4 and the highly related Cyp2a5 gene. Despite the high similarity of these two Cyp genes, my data indicate that these genes exhibit different zonal expression patterns and are differentially regulated in the regenerating liver. In the course of these studies, I discovered and characterized antisense transcripts for both Cyp2a4 and Cyp2a5. Both Cyp2a4as and Cyp2a5as have positively correlated expression patterns compared to their sense counterparts. In contrast to Cyp2a4 and Cyp2a5, Cyp2a4as and Cyp2a5as show sex-biased expression patterns earlier in development, suggesting that they might contribute to later sex-biased patterns established for Cyp2a4 and Cyp2a5.

Abstract not available

In recent years, the general public has recognized the dangers of a high fat diet and are demanding meat with lower fat content. This demand has stimulated research in the growth and regulation of adipocytes. However, despite much effort, no adipocyte-specific plasma membrane markers from any species are available as an aid to accurately distinguish adipocytes from non-adipocytes. One potential candidate for such a marker in porcine adipocytes has been identified by Killefer and Hu (1990b). Characterization of the cDNA for this protein, designated porcine adipocyte membrane protein (PAMP), is presented here. Sequence for the 910 by clone is 80% similar to an internal region of a rat prostaglandin F[subscript 2��] receptor regulator protein (FPRP) described by Orlickey (1996). Western blot analysis suggests that the pig protein is a homotetramer held together with disulfide bonds which form very close to the transmembrane region making the tetramer extremely difficult to reduce to monomeric units. Oligonucleotide primers were designed to amplify a genomic fragment by the polymerase chain reaction (PCR) and for a reverse transcriptase PCR (RT-PCR) assay to study the expression of the mRNA. A 2114 bp genomic clone revealed one intron in the coding region. A serum-free primary cell culture system was used to study the expression of the mRNA. Although message was detected every day over a ten day period, it appeared to peak between 6 to 8 days after plating. The PAMP protein is clearly of the same family as the rat FPRP but its size and conformation are quite different so it is not clear what function it performs in porcine adipocytes. Further experiments should focus on attaining full length cDNA's, confirming the molecular conformation of the protein, and assessing its function in a serum-free primary cell culture system. / Graduation date: 1997

Thesis (Ph. D.)--West Virginia University, 2002. / Title from document title page. Document formatted into pages; contains xii, 161 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 140-158).

The mechanisms underpinning gene regulation in P. falciparum malaria remain largely elusive, though mounting evidence suggests a major role for epigenetic feedback. Interestingly, long non-(protein)-coding RNAs (lncRNAs) have been found to play a dominant role in initiating and guiding the transcriptional, epigenetic, and post-transcriptional status of specific loci across a broad range of organisms. LncRNAs are uniquely poised to act co-transcriptionally on neighboring loci, and/or to remain physically tethered at their site of origin, and through sequence-specific binding activities can impart temporal and spatial specificity to ubiquitously expressed nuclear protein complexes. Proteins, on the other hand, must be translated in the cytoplasm, and hence lose memory of their transcriptional origins. Encouraged by these features of lncRNAs, we set out to investigate the regulatory capacity of P. falciparum lncRNAs on a genome-wide scale. First, we surveyed transcriptional activity across approximately one quarter of the P. falciparum genome using a custom high-density DNA tiling array. We predicted a set of 60 developmentally regulated intergenic lncRNAs, and found that many of these novel loci neighbored genes involved in parasite survival or virulence pathways. Remarkably, upon further analysis of intergenic lncRNA properties, we discovered a family of twenty-two telomere-associated lncRNAs encoded in the telomere-associated repetitive element (TARE) region of P. falciparum chromosome ends. We found that each lncRNA-TARE was encoded adjacent and divergent to a subtelomeric var virulence gene. Moreover, we found that lncRNA-TARE expression was sharply induced between the parasite DNA replication and cell division cycles, that lncRNA-TARE loci contained numerous transcription factor binding sites only otherwise found in subtelomeric var promoter regions, and that the GC content and evolutionary sequence conservation of lncRNA-TAREs was similar to that of P. falciparum ribosomal RNA. Next, we set out to assemble P. falciparum intergenic lncRNA and antisense RNA transcript structures using state-of-the-art deep sequencing and computational tools. Towards this end, we harvested an unprecedented sample set that finely maps temporal changes across 56 hours of P. falciparum blood stage development, and developed and validated strand-specific, non-polyA-selected RNA sequencing methods. This enabled the annotation of over one thousand high-confidence, bona fide lncRNA transcript models, and their comprehensive global analysis. We discovered an enrichment of negatively correlated, tail-to-tail overlapping sense-antisense transcript pairs, suggesting a conserved role for antisense-mediated transcriptional interference in P. falciparum gene regulation. We also discovered a highly correlated spliced antisense counterpart to a gene required for sexual commitment, that the expression of an intriguing subset of antisense transcripts significantly dropped during parasite invasion, and that lncRNA-TARE and 'sterile' var virulence gene transcription was markedly up-regulated during parasite invasion. Lastly, we predicted over one thousand circular RNAs (circRNAs), and validated six circRNA transcript structures. Importantly, this thesis work represents the first focused investigation of lncRNAs in P. falciparum malaria, with the characterization of a compelling family of telomere-associated lncRNAs and numerous antisense RNAs. The data, methods, and results herein offer exceptional technological advancements coupled with compelling insights into the biology of the devastating human pathogen P. falciparum malaria. It is my hope that this work will facilitate future P. falciparum lncRNA functional studies and the strand-specific profiling of additional P. falciparum samples.

The studies presented in this work were completed with the goal ofgaining greater insight into the roles of protein oxidation in brain aging and age-relatedcognitive impairment. Aging is associated with the impairment of physiological systemssuch as the central nervous system (CNS), homeostatic system, immune system, etc.Functional impairments of the CNS is associated with increased susceptibility to developmany neurodegenerative diseases such as Alzheimer's diseases (AD), Parkinson's disease(PD), and amyotrophic lateral sclerosis (ALS). One of the most noticeable functionalimpairments of the CNS is manifested by cognitive decline. In the past three decades, thefree radical theory of aging has gained relatively strong support in this area. Excessiveproduction reactive oxygen species (ROS) was demonstrated as a contributing factor inage-related memory and synaptic plasticity dysfunction. This dissertation use proteomicsto identify the proteins that are oxidatively modified and post-translationally altered inaged brain with cognitive impairment and normal aging brain.Ongoing research is being pursued for development of regime to preventoxidative damage by age-related oxidative stress. Among which are those that scavengefree radicals by antioxidants, i.e. ??-lipoic acid (LA), and protecting the brains byreducing production of neurotoxic substance, i.e. reducing production of amyloid ??(A??).Therefore, proteomics were also used to identify the alteration of specific proteins in agedbrain treated with LA and antisense oligonucleotides again amyloid protein precursor.This dissertation provides evidences that certain proteins are less oxidatively modifiedand post-translationally altered in cognitively impaired aged brain treated with LA andantisense oligonucleotides against the A?? region of amyloid precursor protein (APP)(AO).Together, the studies in this dissertation demonstrated that increased oxidativestress in brain play a significant role in age-related cognitive impairment. Moreover, suchincreased oxidative stress leads to specific protein oxidation in the brain of cognitiveimpaired subject, thereby leading to cognitive function impairment. Moreover, thefunctional alterations of the proteins identified by proteomics in this dissertation mayleads to impaired metabolism, decline antioxidant system, and damaged synapticcommunication. Ultimately, impairment of these processes lead to neuronal damages andcognitive decline. This dissertation also show that several of the up-regulated andoxidized proteins in the brains of normal aging mice identified are known to be oxidizedin neurodegenerative diseases as well, suggesting that the expression levels of certainproteins may increase as a compensatory response to oxidative stress. This compensationwould allow for the maintenance of proper molecular functions in normal aging brainsand protection against neurodegeneration.

Bibliography: leaves 175-186. / 186 leaves : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Aims to examine the AP in A. thaliana and to produce an inducible antisense plant to assist future studies of the role of AOX. / Thesis (Ph.D.)--University of Adelaide, Dept. of Botany, 1999?

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2005. / Härtill 6 uppsatser.

Thesis (Ph. D.)--University of New South Wales, 2000. / Also available online.