UMD Theses and Dissertations
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Item Genome-wide identification and analysis of imprinted genes in strawberry seed development(2022) Joldersma, Dirk; Liu, Zhongchi Anne; Taneyhill, Lisa Anne; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The activation of zygotic gene expression is of fundamental importance to reproductive biology, but its regulation remains poorly understood. Within Angiosperm plants, fertilization occurs simultaneously in two locations, the embryo and its genetic twin, the endosperm, a nutritive tissue that is a defining feature of Angiosperm reproduction. Auxin hormone synthesized in the endosperm is essential to seed and fruit development. In the diploid strawberry Fragaria vesca, that auxin synthesis is regulated by FveAGL62, which is expressed specifically after fertilization in endosperm. How fertilization activates FveAGL62 expression in the endosperm, however, is presently unknown. I investigated the hypothesis that epigenetically regulated maternally- and paternally expressed genes (MEGs and PEGs, and together, “imprinted genes”) regulate the expression of FveAGL62. I hybridized two F. vesca accessions, isolated the endosperm from the F1 seeds, and sequenced the transcriptome of the F1 endosperm—a result facilitated by strawberry’s uniquely accessible seed. To identify imprinted genes within the endosperm, I assembled and annotated the genome of the maternal parent, F. vesca accession “Yellow Wonder” (FvYW5AF7), a model for the commercial strawberry. The paternal parent genome was obtained from a collaborator. 809 PEGs and 825 MEGs were identified from RNA sequencing reads that align uniquely to the maternal or paternal genome. MEGs are enriched in genes catabolizing auxin and hence limit seed growth, while PEGs are enriched in genes involved in histone modification, thereby promoting cell differentiation and seed growth. The distinct roles of MEGs and PEGs supports and can be explained by parental conflict and kinship theories, which predict a maternal genome tends to restrict progeny consumption of maternal resources, while a paternal genome will encourage such consumption. In contrast to findings in other species, I find that the endosperm-specific auxin biosynthetic gene FveYUC10 is maternally expressed, but while its imprinting status has changed, it may still function as a fertilization sensor. The maternally expressed gene FveMYB98 contains a binding domain that targets motifs present in FveAGL62’s promoter and its homolog binds AtAGL62 promoter in Arabidopsis. With collaborators, I showed that overexpression and CRISPR knockout of FveMYB98 changes seed size. Transient expression, yeast one hybrid and quantitative PCR analyses suggest that FveMYB98 represses FveYUC10 expression directly and FveAGL62 expression indirectly. These results suggest that FveMYB98 expression is a vehicle for maternal regulation of the level of auxin in the endosperm and thereby endosperm proliferation and seed size. My dissertation research has produced a new genome assembly of a model strawberry, a transcriptome of strawberry endosperm, and identified imprinted genes at genomic scale. I find FveMYB98 regulates seed size—a function echoed broadly within MEG and PEG classes—providing supporting evidence for the parental conflict theory within the developing progeny. These results improve our understanding of zygotic expression in developing seeds, addressing a fundamental scientific gap and, more tangibly, may enable future production of fertilization-independent seeds and seedless fruits.Item Molecularly Imprinted Polymers for the Selective Recognition of Proteins(2009) Janiak, Daniel S.; Kofinas, Peter; Material Science and Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Molecular imprinting is a technique used to synthesize polymers that display selective recognition for a given template molecule of interest. In this study, the role of hydrogel electrostatic charge density on the recognition properties of protein-imprinted hydrogels was explored. Using 3-methacrylamidopropyl trimethylammonium chloride (MAPTAC) as a positively charged monomer and 2-acrylamido-2-methylpropane sulfonic acid (AMPS) as a negatively charged monomer, a number of acrylamide-based polyelectrolyte hydrogels with varying positive and negative charge densities were prepared. The imprinted hydrogels were synthesized in the presence of the target molecule bovine hemoglobin (Bhb). The ability of the hydrogels to selectively recognize Bhb was examined using a competitive template molecule, cytochrome c. The Bhb imprinted gels exhibited template recognition properties that were dependent on both the monomer charge density and on whether the chosen monomer carried a positive or negative charge. In addition to polyelectrolye hydrogels, polyampholyte hydrogels containing both positively and negatively charged monomers were also synthesized. The simultaneous presence of two oppositely charged monomers in the pre-polymerization mixture resulted in imprinted hydrogels with cavities that contain highly specific functional group orientation. The polyampholyte hydrogels exhibited decreased swelling when compared to their polyelectrolyte counterparts, due to the shielding of repulsive interactions between oppositely charge monomers. This decreased swelling resulted in greater template recognition, but lower selectivity, when compared to their polyelectrolyte counterparts. In addition, we found that common agents used in template extraction may be responsible for the specific and selective binding properties exhibited by molecularly imprinted polymers in many published studies, and the effect of variations of the template extraction protocol on the MIP recognition properties were also studied in depth.