Homeobox genes encode homeodomain (HD) proteins which function as transcription factors and play an important role in plant and animal development by controlling cell specification and pattern formation. (Knotted1 in Arabidopsis thaliana) KNAT1-like mRNAs referred to as PtKN1(HD+) and mRNA sequences which lack HD region referred as PtKN1(hd-) were cloned from embryos of loblolly pine (Pinus taeda L.). Production of PtKN1(hd-) mRNAs is developmentally regulated and their encoded protein is abundant in mature pine embryos. Both forms of PtKN1 are produced by the same gene which has 5 exons; the regulatory dynamic is between cleavage-polyadenylation or termination within intron 3 to produce PtKN1 mRNA lacking HD sequences and splicing of exon 3 to exon 4 which excludes the 3'UTR/exon3 sequence to create an mRNA which encodes a HD. KNAT1 mRNA in Arabidopsis which lacks HD sequences was identified and characterized. While KNAT1 has been studied for many years, this is the first report of a KNAT1 mRNA lacking HD. KNAT1 mRNA lacking HD sequences was identified for the RS1 gene of maize, a monocotyledon. This is the first report of splicing of KNAT1 genes to produce mRNAs lacking HD sequences. The phenomenon appears to be ubiquitous as it is observed in gymnosperms, and both dicotyledonous and monocotyledonous angiosperms.

Nuclear receptors play crucial roles in the transcriptional regulation of many biological processes such as development and cellular differentiation. ERRalpha is known, along with coactivator PGC-1alpha, to playa central role in the control of energy metabolism in cardiac and skeletal muscle. They activate the expression of many genes involved in mitochondrial oxidative metabolism. Here we identified PROX1, a factor that was previously shown to broadly influence metabolism, as a regulator of this pathway. Indeed, PROX1 interacts in vitro and in vivo with both ERRalpha and PGC-1alpha. To provide more insight on the hepatic functions of ERRalpha and PROX1, we performed ChIP-on-chip using mouse liver, identifying a large number of ERRalpha and PROX1 genomic targets and reinforcing their role in energy metabolism. Over 40% of the target genes were found to be common to both factors and we observed that PROX1 could be recruited to ERRalpha binding sites and act as a negative regulator o fthe ERRalpha/POC-1alpha pathway.

Visual system homeobox 1 (Vsx1) is a paired-like:CVC homeodomain transcription factor that is expressed in a subset of retinal bipolar cells. Vsx1-null mice have previously been shown to have defects in bipolar cell terminal differentiation characterized by the reduced expression of four OFF bipolar cell-specific markers and electrophysiological defects in the OFF visual signaling pathway. The availability of recently identified bipolar cell markers enables a further characterization of the Vsx1-null mutant. I determined that Vsx1 is expressed in Type 7 ON bipolar cells and observed the upregulation of three cell markers: Cabp5, Chx10, and alpha-gustducin:GFP in this cell type in Vsx1-null mice. These data reveal a trend in which Vsx1 functions as a transcriptional repressor in Type 7 ON bipolar cells and as an activator in Type 2 OFF bipolar cells. Lastly, my data indicate that Vsx1 is required for the expression of two Type 3a bipolar cell markers, however, the mechanism by which it does so appears to be complex, as I was unable to detect Vsx1 protein or reporter gene expression in this cell type. / Graduate

Self-renewal is central to the expansion of normal and cancerous stem cells. Its understanding is therefore critical for future advances in transplantation-based therapies and cancer treatment. Although the molecular machinery controlling stem cell self-renewal remains poorly defined, a number of genes important to this process have recently been identified. Two prominent genes in this group are Hoxb4 and Bmi1. Members of our group led the way to demonstrate important regulatory functions of these genes in hematopoietic stem cell (HSC) self-renewal and expansion. / The major goal of my thesis project is to dissect mechanisms that regulate self-renewal of HSCs. Our starting hypothesis was that HSC activity is regulated by complementary and independent self-renewal mechanisms: self-renewal of expansion and self-renewal of maintenance (Chapters 1-2). In order to further verify this theory, we have analyzed the genetic interaction between Hoxb4 and Bmi1. While Hoxb4 overexpression triggers HSC expansion, Bmi1 proper expression is essential to sustain long-term stem cell activity. We have also demonstrated that Hoxb4 and Bmi1 regulate distinct gene targets, likely suggesting a complementary and independent function for these two regulators in HSC activity (Chapter 3). / The second part of this thesis highlights efforts that were made in order to get a better understanding of self-renewal mechanisms. We have identified potential new regulators of stem cell activity by characterizing a stem cell leukemia population (Chapter 4) and by assessing the expression of asymmetrical distributed factors (Chapter 5) and selected nuclear factors of the Hematopoietic Stem Cell Nuclear Factor Database (Chapter 6) in stem cell-enriched sub-fractions. / This project will lead to a better understanding of the cellular basis regulating self-renewal of both normal and cancer stem cells and potentially to the future identification of new self-renewal determinants.

Diss. (sammanfattning Stockholm : Karol. inst. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Alabama at Birmingham, 2006. / Title from first page of PDF file (viewed Feb 18, 2009). Includes bibliographical references.

Thesis (Ph.D. in Molecular Biology) -- University of Colorado at Denver and Health Sciences Center, 2006. / Typescript. Includes bibliographical references (leaves 137-151). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

Thesis (Ph.D. in Cell & Developmental Biology) -- University of Colorado Denver, 2007. / Typescript. Includes bibliographical references (leaves 144-158). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;

Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (leaves 70-79).

Thesis (Ph.D. in Molecular Biology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 149-172). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;