The purpose of this study was to assess the utility of confocal microscopy to examine nuclear organization and chromosome pairing for intact Arabidopsis male meiocytes. The efficiency of the confocal technique was evaluated by analyzing wild-type nuclei throughout meiosis. Early-mid leptotene meiocytes demonstrated the presence of several propidium iodide stained signals within the nucleolus prior to the onset of chromosome pairing in zygotene. Pachytene chromosomes were completely paired and were traced to confirm the Arabidopsis karyotype. Additionally, the confocal technique was employed on meiotic mutants, ahp2 and spo11-2-2, to characterize their meiotic defects. Leptotene ahp2 meiocytes and zygotene meiocytes in both meiotic mutants appeared normal. In contrast, pachytene meiocytes in ahp2 and spo11-2-2 mutants demonstrated a wide-spread lack of paired chromosomes. Despite this general lack of pairing, a small amount of chromosome pairing was detected on the short arms of NOR-bearing chromosomes 2 and 4 in ahp2 and spo11-2-2 mutants.

The purpose of this study was to assess the utility of confocal microscopy to examine nuclear organization and chromosome pairing for intact Arabidopsis male meiocytes. The efficiency of the confocal technique was evaluated by analyzing wild-type nuclei throughout meiosis. Early-mid leptotene meiocytes demonstrated the presence of several propidium iodide stained signals within the nucleolus prior to the onset of chromosome pairing in zygotene. Pachytene chromosomes were completely paired and were traced to confirm the Arabidopsis karyotype. Additionally, the confocal technique was employed on meiotic mutants, ahp2 and spo11-2-2, to characterize their meiotic defects. Leptotene ahp2 meiocytes and zygotene meiocytes in both meiotic mutants appeared normal. In contrast, pachytene meiocytes in ahp2 and spo11-2-2 mutants demonstrated a wide-spread lack of paired chromosomes. Despite this general lack of pairing, a small amount of chromosome pairing was detected on the short arms of NOR-bearing chromosomes 2 and 4 in ahp2 and spo11-2-2 mutants.

The population dynamics of transposons in self- and cross-fertilizing plant populations are investigated both theoretically and empirically. Models were developed to evaluate the influence of host breeding system on transposon populations. Modeling results suggest that the selfing rate is likely to have important effects on the abundance and polymorphism patterns of transposable elements in plant genomes. A primary characterization of diversity and abundance of transposons in the self-pollinating species Arabidopsis thaliana was conducted using genomic sequencing data, providing strong evidence for recent element mobility. Utilizing this information, a PCR-based approach was implemented to examine transposon dynamics in populations of Arabidopsis thaliana and its outcrossing relative, Arabidopsis lyrata. The results provide evidence for the importance of purifying selection in controlling transposon abundance in outcrossing populations, but not in selfers. Differences observed between the species are consistent with the hypothesis that host breeding systems influence the selective pressure acting on transposons.

In sexually reproducing individuals, intraorganismal genetic heterogeneity (IGH) or mosaicism is thought to occur infrequently while genetic homogeneity is presumed the norm. In organisms that undergo modular development, such as long-lived plants, IGH has been substantially documented. In Arabidopsis thaliana we have shown that non-parental DNA that is inherited at low but detectable rates can also manifest on single plants as genotypically distinct somatic sectors suggesting that even short-lived annual plants show IGH. The underlying mechanism responsible for generating this type of IGH remains unknown. In order to better understand this phenomenon I have tested the hypothesis that among genome changes that occur in response to stress, these putative triggers also up-regulate IGH. Metabolic stress, cold stress, mechanical damage and ROS exposure were examined. To test for IGH, transgene markers and polymorphic molecular markers were used. Also, presented in this thesis is work investigating the effect of in vitro propagation through tissue culture on IGH frequencies. Regenerated plants as well as undifferentiated callus tissue were genotyped and assayed for sequence reversions. Molecular genotyping revealed an outcome contrary to that predicted by the initial hypothesis showing instead that a high frequency of restoration occurred in the progeny of un-treated control plants. With the exception of samples passed through tissue culture, molecular marker changes, including single and double reversions of alleles, were detected in every line at some low level Furthermore, many of the revertants were found to be genetic mosaics. DNA sequence analyses revealed that sequences flanking three molecular markers that had undergone reversion were near identical to the great-grandparent of the sequenced individual. These results suggest that stress is perhaps an inhibitor of restoration. Although there may be other explanations for the results described in this thesis, the evidence implicates genome restoration as a mechanism for generating IGH.

No description available.

ABSTRACT The ability to detect and respond to environmental signals is fundamental in coordinating floral induction in plants to favourable conditions. An important flowering time cue is day length and it is proposed that light signals are perceived and measured by an interaction between photoreceptors and an internal pacemaker, the circadian clock. The control of flowering has been best characterised in the model plant Arabidopsis thaliana L. Heynh (Arabidopsis). The GIGANTEA (GI) gene has a complex role in both the promotion of flowering in response to photoperiod and the regulation of the circadian clock. The expression of GI is under circadian control and is affected by day length, light quality and temperature changes. The GI protein is also circadian regulated and is actively degraded in the dark. The biochemical function of GI is unknown and one method to elucidate the role of this protein is to identify protein interactors. The aim of this thesis project was to characterise proteins that interacted with GI. Previously, the BELL-LIKE HOMEODOMAIN 3 (BLH3) protein was identified as a putative GI protein interactor. As part of this thesis work, yeast 2-hybrid and in vitro pull down assays were utilised to confirm the interaction between GI and BLH3. Sequence and phylogenetic analyses were used to further examine the BELL family of proteins. The BELL-LIKE HOMEODOMAIN 10 (BLH10) protein was found to be closely related to BLH3 and also interacted with GI. Reverse 2-hybrid assays were used to determine the regions or domains within the GI, BLH3 and BLH10 proteins required to mediate protein interactions. Expression assays established that the BLH3 and BLH10 transcripts were present throughout plant tissues and times of development. Further analyses revealed that BLH3 and BLH10 are not directly regulated by the circadian clock. The results of GFP expression assays demonstrated that the BLH3 protein is localised to the nucleus in plant cells. Transgenic blh3 and blh10 mutant plants were identified and analysed for flowering and light response phenotypes. BLH3 and BLH10 do not function with GI in the photoperiodic pathway to control flowering, yet the blh3 and blh10 mutants do have a flowering phenotype in short day conditions. Like gi, the blh3 and blh10 mutants exhibited exaggerated hypocotyl elongation in response to red and low light conditions. These results are suggestive of a role for BLH3, BLH10 and GI in flowering and deetiolation responses to specific light conditions in plants. / This PhD research was sponsored by Dr George Mason

ABSTRACT The ability to detect and respond to environmental signals is fundamental in coordinating floral induction in plants to favourable conditions. An important flowering time cue is day length and it is proposed that light signals are perceived and measured by an interaction between photoreceptors and an internal pacemaker, the circadian clock. The control of flowering has been best characterised in the model plant Arabidopsis thaliana L. Heynh (Arabidopsis). The GIGANTEA (GI) gene has a complex role in both the promotion of flowering in response to photoperiod and the regulation of the circadian clock. The expression of GI is under circadian control and is affected by day length, light quality and temperature changes. The GI protein is also circadian regulated and is actively degraded in the dark. The biochemical function of GI is unknown and one method to elucidate the role of this protein is to identify protein interactors. The aim of this thesis project was to characterise proteins that interacted with GI. Previously, the BELL-LIKE HOMEODOMAIN 3 (BLH3) protein was identified as a putative GI protein interactor. As part of this thesis work, yeast 2-hybrid and in vitro pull down assays were utilised to confirm the interaction between GI and BLH3. Sequence and phylogenetic analyses were used to further examine the BELL family of proteins. The BELL-LIKE HOMEODOMAIN 10 (BLH10) protein was found to be closely related to BLH3 and also interacted with GI. Reverse 2-hybrid assays were used to determine the regions or domains within the GI, BLH3 and BLH10 proteins required to mediate protein interactions. Expression assays established that the BLH3 and BLH10 transcripts were present throughout plant tissues and times of development. Further analyses revealed that BLH3 and BLH10 are not directly regulated by the circadian clock. The results of GFP expression assays demonstrated that the BLH3 protein is localised to the nucleus in plant cells. Transgenic blh3 and blh10 mutant plants were identified and analysed for flowering and light response phenotypes. BLH3 and BLH10 do not function with GI in the photoperiodic pathway to control flowering, yet the blh3 and blh10 mutants do have a flowering phenotype in short day conditions. Like gi, the blh3 and blh10 mutants exhibited exaggerated hypocotyl elongation in response to red and low light conditions. These results are suggestive of a role for BLH3, BLH10 and GI in flowering and deetiolation responses to specific light conditions in plants. / This PhD research was sponsored by Dr George Mason

ABSTRACT The ability to detect and respond to environmental signals is fundamental in coordinating floral induction in plants to favourable conditions. An important flowering time cue is day length and it is proposed that light signals are perceived and measured by an interaction between photoreceptors and an internal pacemaker, the circadian clock. The control of flowering has been best characterised in the model plant Arabidopsis thaliana L. Heynh (Arabidopsis). The GIGANTEA (GI) gene has a complex role in both the promotion of flowering in response to photoperiod and the regulation of the circadian clock. The expression of GI is under circadian control and is affected by day length, light quality and temperature changes. The GI protein is also circadian regulated and is actively degraded in the dark. The biochemical function of GI is unknown and one method to elucidate the role of this protein is to identify protein interactors. The aim of this thesis project was to characterise proteins that interacted with GI. Previously, the BELL-LIKE HOMEODOMAIN 3 (BLH3) protein was identified as a putative GI protein interactor. As part of this thesis work, yeast 2-hybrid and in vitro pull down assays were utilised to confirm the interaction between GI and BLH3. Sequence and phylogenetic analyses were used to further examine the BELL family of proteins. The BELL-LIKE HOMEODOMAIN 10 (BLH10) protein was found to be closely related to BLH3 and also interacted with GI. Reverse 2-hybrid assays were used to determine the regions or domains within the GI, BLH3 and BLH10 proteins required to mediate protein interactions. Expression assays established that the BLH3 and BLH10 transcripts were present throughout plant tissues and times of development. Further analyses revealed that BLH3 and BLH10 are not directly regulated by the circadian clock. The results of GFP expression assays demonstrated that the BLH3 protein is localised to the nucleus in plant cells. Transgenic blh3 and blh10 mutant plants were identified and analysed for flowering and light response phenotypes. BLH3 and BLH10 do not function with GI in the photoperiodic pathway to control flowering, yet the blh3 and blh10 mutants do have a flowering phenotype in short day conditions. Like gi, the blh3 and blh10 mutants exhibited exaggerated hypocotyl elongation in response to red and low light conditions. These results are suggestive of a role for BLH3, BLH10 and GI in flowering and deetiolation responses to specific light conditions in plants. / This PhD research was sponsored by Dr George Mason

ABSTRACT The ability to detect and respond to environmental signals is fundamental in coordinating floral induction in plants to favourable conditions. An important flowering time cue is day length and it is proposed that light signals are perceived and measured by an interaction between photoreceptors and an internal pacemaker, the circadian clock. The control of flowering has been best characterised in the model plant Arabidopsis thaliana L. Heynh (Arabidopsis). The GIGANTEA (GI) gene has a complex role in both the promotion of flowering in response to photoperiod and the regulation of the circadian clock. The expression of GI is under circadian control and is affected by day length, light quality and temperature changes. The GI protein is also circadian regulated and is actively degraded in the dark. The biochemical function of GI is unknown and one method to elucidate the role of this protein is to identify protein interactors. The aim of this thesis project was to characterise proteins that interacted with GI. Previously, the BELL-LIKE HOMEODOMAIN 3 (BLH3) protein was identified as a putative GI protein interactor. As part of this thesis work, yeast 2-hybrid and in vitro pull down assays were utilised to confirm the interaction between GI and BLH3. Sequence and phylogenetic analyses were used to further examine the BELL family of proteins. The BELL-LIKE HOMEODOMAIN 10 (BLH10) protein was found to be closely related to BLH3 and also interacted with GI. Reverse 2-hybrid assays were used to determine the regions or domains within the GI, BLH3 and BLH10 proteins required to mediate protein interactions. Expression assays established that the BLH3 and BLH10 transcripts were present throughout plant tissues and times of development. Further analyses revealed that BLH3 and BLH10 are not directly regulated by the circadian clock. The results of GFP expression assays demonstrated that the BLH3 protein is localised to the nucleus in plant cells. Transgenic blh3 and blh10 mutant plants were identified and analysed for flowering and light response phenotypes. BLH3 and BLH10 do not function with GI in the photoperiodic pathway to control flowering, yet the blh3 and blh10 mutants do have a flowering phenotype in short day conditions. Like gi, the blh3 and blh10 mutants exhibited exaggerated hypocotyl elongation in response to red and low light conditions. These results are suggestive of a role for BLH3, BLH10 and GI in flowering and deetiolation responses to specific light conditions in plants. / This PhD research was sponsored by Dr George Mason

Thesis (Ph. D.)--University of Nevada, Reno, 2006. / "December 2006." Includes bibliographical references. Online version available on the World Wide Web. Library also has microfilm. Ann Arbor, Mich. : ProQuest Information and Learning Company, [2006]. 1 microfilm reel ; 35 mm.