Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2003. / Vita. Includes bibliographical references (leaves 74-84).

Hybrids and polyploids are very common in plants and some animals. Although hybrid vigor or heterosis has been widely adopted in agricultural practices, the underlying mechanisms are poorly understood partly because of their multigenic nature and the lack of a good model system for the study. Allotetraploidy is an emerging model system for investigating molecular mechanisms of hybrid vigor. An allotetraploid is formed by interspecific hybridization followed by chromosome doubling or hybridization between two autotetraploid parents and is genetically stable. A previous study showed nonadditive expression (different from the mid-parent value) of over 5% of genes in the allotetraploids, suggesting altered transcriptional and post-transcriptional regulation. Here oligo-gene microarray analysis of mRNA stability in allotetraploids was carried out to investigate how nonadditive gene regulation upon allopolyploidization is achieved at the posttranscriptional level. Approximately 1% of annotated genes were identified as unstable transcripts, and their estimated half-life is less than 60 minutes. The unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression and with stress and environmental responses. The nonadditively expressed genes identified in the previous study include those encoding proteins involved in energy and metabolic pathways, which are putative targets of circadian clock regulators. To test how circadian clock genes affect downstream genes and pathways, expression of CIRCADIAN CLOCK ASSOCIATED1 (CCA1) was up- or down-regulated by overexpressing CCA1 or cca1(RNAi) driven by the promoter of TIMING OF CAB EXPRESSION 1 (TOC1). Upregulation of CCA1 was associated with repression of downstream genes in chlorophyll biosynthesis and starch metabolism, whereas down-regulation of CCA1 correlated with upregulation of these downstream genes. As a result, chlorophyll and starch content was ~10% higher in the TOC1::cca1(RNAi) transgenic plants than the controls, while the growth vigor is lower in the TOC1::CCA1 transgenic plants. To further test the effects of clock genes in growth vigor, CCA1 expression was examined in reciprocal hybrids of A. thaliana ecotypes. The maternal effect on starch content was observed in several combinations of hybrids, which was correlated with preferential expression of maternal CCA1 during early stages of seed development. Although the cause of parent-of-origin effects is still unclear, the data have clearly documented parent-of-origin effects on circadian clock gene expression and starch metabolism in hybrids. / text

Circadian rhythmsare biochemical, physiological, and behavioral processes display oscillations of oughly 24-hour, which existing in both prokaryotes and eukaryotes. Circadian rhythms improve fitness of organisms in both constant and changing environments. The cryptochrome (CRY)and PAS-containing proteins are light sensors and key elements of the circadian system in eukaryotic organisms. Photolyases and cryptochromes are evolutionarily related flavoproteins which perform distinct physiological functions. Photolyases are evolutionarily ancient enzymes that activated by light and repairing UV-induced DNA damage. Although cryptochromes share structural similarity with the DNA photolyases, they lack the DNA repair activity. CRYs are key elements of mammal circadian system, and play roles in light sensing in insects and plants to entrain circadian rhythms. The PAS domains are widely distributed in proteins across all kingdoms of life and act as signal modules. They are common in photoreceptors and transcriptional regulators of eukaryotic circadian clock components including bHLH-PAS proteins (BMAL, CYC,CLK and NPAS2) and PER in animals, PHY and ZTL in plants, WC-1, 2and VVD in fungi. They are mainly involved in protein-protein interaction and light sensing functions. The CRY/PHR superfamily consists of 7 major subfamilies: CPD class I and CPD class II PHRs, (6-4) PHR, CRY-DASH, plant PHR2, plant CRY and animal CRY. Although the superfamily evolved primarily under strong purifying selection (average ω = 0.0178), it experienced strong episodic positive selection at some periods of evolution. The level of variation is subfamily-and domain-specific. The homologs with apparent circadian functions (i.e., plant and animal CRY) are significantly more conserved than the other photolyases. Photolyases were lost in eukaryotic groups like placental mammals, suggesting that natural selection apparently became weaker in the late stage of evolutionary history. The phylogenetic trees of fish Cry features two major clusters, which correspond to Cry1and Cry2. Teleost species possess extra copies of Cry1 due to fish-specific genome duplication (FSGD), and formed 3 clades of Cry1. Clade1B of Cry1(π= 0.129 ±0.062) is more conserved than the other paralogs (πrange from 0.173to 0.195). Test of positive selection revealed that fish cryptochromes evolved under strong purifying selection (average ω= 0.0066).Different fishes preserved different Cry duplicates that associated with reciprocal gene loss, thus generated the diverse circadian molecular mechanisms. The level of DNA variation in the PAS-containing proteins appears to be subfamily-specific. The animal PAS-containing homologs are more polymorphic than the plant and fungal homologs. Although the whole superfamily evolved primarily under strong purifying selection (average ω range from 0.0030to 0.1164), it experienced strong positive selection at some periods of the evolution. Although the PAS domains from different proteins vary in sequence and length, they maintain a fairly conserved 3D structure. The 3D fold of PAS domains is determined by only 8 conserved residues which shared by all subfamilies. The evolutionary time estimates showed that plant and animal Cry, WC-1& 2, bHLH-PAS proteins and Per originated in the Neoproterozoic Era (~1000 –542 Mya), plant Phy and ZTL evolved in the Paleozoic (541 –252 Mya), which might be a result of adaptation to the global climate and light regime changes. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

No description available.

Mitogen activated protein kinase (MAPK) pathways are conserved biochemical signal transduction pathways in eukaryotic organisms. These signaling pathways demonstrate great versatility in their ability to detect various environmental stimuli and direct an appropriate cellular response. The circadian clock is a timekeeping mechanism that temporally coordinates diverse biological functions in an organism with the environment. Thus, it is not surprising that MAPK pathways have been utilized by the circadian clock to regulate many essential functions. Due to the conserved nature of circadian clocks and MAPK signaling pathways in eukaryotes, it is possible to develop hypotheses in simple model organisms, such as the fungus Neurospora, that are relevant to more complex organisms. The OS-2 MAPK pathway in the filamentous fungus Neurospora is rhythmically activated by the circadian clock. In order to generate this rhythmic signal, the circadian oscillator directly regulates the rhythmic transcription of the os-4 MAPKKK and histidine phosphotransferase hpt-1, which are upstream regulators of the OS-2 MAPK. Also, the circadian rhythm in MAPK activation produces a more robust stress response during the time of the day that stress is most likely to be encountered. Based on these data, a model for the clock regulation of MAPK activation is presented, and a biological significance is assigned to the rhythms in this pathway. Informed by these findings in Neurospora, the related p38 MAPK pathway was studied in mammalian cell lines that represent functionally distinct tissues in regards to clock function. A rhythm in p38 MAPK activation was observed in cells derived from the suprachiasmatic nucleus and fibroblasts of a mouse, the master pacemaker and a peripheral tissue, respectively. In cells that lacked a functional circadian oscillator, the rhythm in p38 activation was absent, and overall levels of p38 protein were lower. These data demonstrate a circadian clock-dependent oscillation in p38 activity. These studies provide a basis to understand how the circadian clock generates endogenous rhythms in MAPK signal transduction pathways. Also, the characterization of clock-regulated stress response pathways provides an understanding of the adaptive advantage of the circadian clock.

No description available.

Thesis (Ph.D.) -- University of Adelaide, School of Paediatrics and Reproductive Health, Discipline of Obstetrics and Gynaecology, 2008. / Includes Errata sheet attached to inside back page (page numbered as 191). Bibliography: leaves 169-187. Also available in print form.

Thesis (M.S.)--West Virginia University, 1999. / Title from document title page. Document formatted into pages; contains vi, 62 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 35-42).

Thesis (M.S.)--West Virginia University, 1999. / Title from document title page. Document formatted into pages; contains v, 65 p. : ill. (some col.) Vita. Includes abstract. Includes bibliographical references (p. [36]-45).

Thesis (Ph. D.)--Florida State University, 2003. / Advisor: Dr. David Thistle, Florida State University, College of Arts and Sciences, Dept. of Oceanography. Title and description from dissertation home page (Aug. 27, 2004). Includes bibliographical references.