Cell Biology & Molecular Genetics Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/2750

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Subject: search.filters.subject.Biology, Bioinformatics

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    BIOLOGY AND EVOLUTION OF CHROMALVEOLATE PROTISTS
    (2010) Miller, John James; Delwiche, Charles F; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Dinoflagellates and haptophytes are both prominent members of the marine phytoplankton and are considered chromalveolates. The interactions of the parasitic dinoflagellate Amoebophrya with its host dinoflagellate Akashiwo sanguinea were studied using cell biological techniques. The free-swimming dinospore stage of Amoebophrya has two flagella, trichocyts, striated strips, condensed chromatin resembling heterochromatin, and electron dense bodies. When entering the host cytoplasm and again when entering the host nucleus, the electron dense bodies appear in a tube of microtubules close to the surface of the host or its nucleus. Host entry is inhibited by cytochalasin D implying a role for microfilament polymerization in the entry process. While in the host cytoplasm, Amoebophrya appears to be separated from the host cytoplasm by two membranes. After entering the host nucleus, the parasite grows and undergoes mitosis forming a multinucleated trophont. The mastigocoel is an internal cavity that contains flagella and becomes the outside of the parasite after it leaves the host. This study indicates that the mastigocoel forms as a result of vesicle fusion. Eventually, Amoebophrya fills the host nucleus and takes on a beehive appearance. The beehive stage contains numerous trichocyts and striated strips. The level of chromatin condensation in intracellular trophonts is highly variable. It then exits its host as a multinucleated vermiform shaped creature, which then splits up into individual infective dinospores. A phylogenomic pipeline was designed to analyze the genome and evolutionary history of the haptophyte Emiliania huxleyi. It appears to have genes linking it to three lineages: heterokonts, green algae, and red algae. Genes with shared phylogenetic affinities appear to fit into limited functional categories and be physically localized in the genome. The phylogenetic affinities of E. huxleyi with the green algae may be an artifact of the much greater number of sequenced genomes from the Viridiplantae (=plants+ green algae) when compared to the rhodophytes. The evolutionary history of E. huxleyi is still unclear although they do seem to be similar in many ways to heterokonts and are generally believed to have red algae derived plastids.
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    IDENTIFICATION OF PUTATIVE O-REPEAT BIOSYNTHETIC GENES IN NEISSERIA SICCA 4320
    (2010) Miller, Clinton; Stein, Daniel C; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Lipopolysaccharide (LPS) and lipooligosaccharide (LOS) are important virulence determinants found in gram-negative bacteria. LOS differs from LPS in that it lacks the O-repeat characteristic of LPS. While the genetic basis of LOS production in the pathogenic Neisseria has been extensively studied, little research has focused on the genetics underlying LOS production and resulting diversity in commensal Neisseria. A commensal strain that caused a fatal case of bacterial endocarditis, Neisseria sicca 4320, was found to produce a unique polysaccharide similar to the O-repeat of LPS in addition to typical Neisseria LOS. N. sicca 4320 was analyzed by bioinformatic and molecular biological gene-finding screens to identify putative O-repeat biosynthesis genes. Twenty-one open reading frames (ORFs) with similarity to other polysaccharide biosynthesis genes were located in the screens of N. sicca 4320. Two open reading frames with similarity to glycosyltransferases were found to be unique to N. sicca 4320.
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    BIOINFORMATIC ANALYSIS OF THE FUNCTIONAL AND STRUCTURAL IMPLICATIONS OF ALTERNATIVE SPLICING.
    (2007-01-23) Melamud, Eugene; Moult, John; Molecular and Cell Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    In higher Eukaryotes, upon transcription of a gene, a complex set of reactions take place to remove fragments of a sequence (introns) from transcribed RNA. A large macro-molecular machine (the spliceosome) recognizes the ends of introns, brings ends into close proximity and catalyzes the splicing reaction. The selection of the location of the ends of introns (splice sites) determines the final message produced at the end of the process. In some cases, an alternative set of splice sites are chosen, and as a consequence different message is produced. This phenomenon is known as alternative splicing. It is now realized that nearly every Human gene undergoes alternative splicing, producing large variability in types and number of transcripts produced. In this thesis, we examine the functional and structural consequences of alternative splicing on proteins, we look into the mechanism of formation of complex splicing patterns, and examine the role of noise in the process.