Thesis (Ph. D.)--New York University, Graduate School of Arts and Science, 2003. / Typescript. Includes bibliographical references (leaves 231-284). Also available in electronic format on the World Wide Web. Access restricted to users affiliated with the licensed institutions.

Thesis (Ph. D.)--New York University, Graduate School of Arts and Science, 2005. / Typescript. Includes bibliographical references (leaves 239-258). Also available in electronic format on the World Wide Web. Access restricted to users affiliated with the licensed institutions.

Thesis (Ph. D.)--New York University, Graduate School of Arts and Science, 2005. / Typescript. Includes bibliographical references (leaves 177-189). Also available in electronic format on the World Wide Web. Access restricted to users affiliated with the licensed institutions.

Thesis (Ph. D.)--New York University, Graduate School of Arts and Science, 2005. / Typescript. On t.p., "[alpha]2A" is represented with "2A" in subscript. Includes bibliographical references (leaves 115-141). Also available in electronic format on the World Wide Web. Access restricted to users affiliated with the licensed institutions.

Thesis (Ph. D.)--New York University, Graduate School of Arts and Science, 2005. / Typescript. Includes bibliographical references (leaves 171-173). Also available in electronic format on the World Wide Web. Access restricted to users affiliated with the licensed institutions.

Thesis (M.S.)--University of Missouri-Columbia, 2004. / Typescript. Includes bibliographical references (leaves 60-66). Also available on the Internet.

<p>The typical flow of genetic information involves DNA being transcribed into RNA, which is then translated into protein. However, in some organisms this pathway requires an extra step where the RNA is post-transcriptionally modified before it can be translated. This process is referred to as RNA editing and can involve the substitution or the insertion and/or deletion of bases. Insertion/deletion RNA editing is rare, only occurring in the mitochondria of Physarum and trypanosomes, a group of parasitic protozoa. The RNA editing process in trypanosomes is called kinetoplastid RNA (kRNA) editing, after the kinetoplastid containing mitochondria, and creates translatable open reading frames by inserting and/or deleting uridine bases within the encoded mRNA sequence. The main proteins responsible for the kRNA editing process have been characterized and form a 20S editosome. Other accessory proteins have also been implicated in the editing process. Recently, the multiprotein mitochondrial RNA binding complex 1 (MRB1) has emerged as a key player in this process. One key component predicted to be involved in the MRB1 complex is MRB1590. In vivo experiments indicate a role for MRB1590 in editing mitochondrial mRNA transcripts, in particular the transcript encoding the ATP synthase subunit 6 (A6). The goals of this work were to structurally and biochemically characterize MRB1590 to characterize its role in the kRNA editing process, specifically in the editing of the A6 transcript.</p><p>The structure of MRB1590 was solved using X-ray crystallography under three different conditions. The overall structure shows the protein is dimeric and contains a central ABC-ATPase fold embedded between a novel N- and C-terminal domain, with a pore being created between the N-terminal domains. The structure of MRB1590 was solved in the presence of ADP and AMP-PNP, showing the nucleotide bound in a pocket located in the ABC-ATPase fold, similar to other ABC-ATPase proteins. The structure of MRB1590 solved in the presence of ADP and RNA revealed a distinct conformation compared to the other two structures in which it adopted an “open” state with a significantly expanded pore. These combined structures suggest that MRB1590 is in equilibrium between open and closed states with ADP binding favoring the open conformation allowing RNA to bind in the pore.</p><p>Fluorescence polarization (FP) experiments showed that MRB1590 binds with significantly enhanced affinity to a GC-rich RNA sequence from the A6 transcript compared to other RNA sequences that were tested. Because the MRB1590 structures predict the RNA binding pocket to be the pore created by N-terminal domains, basic residues present in this region were mutated and the effect on RNA binding was tested. The RNA binding of MRB1590 pore mutants was reduced, indicating that these residues are involved in RNA binding. Our findings support MRB1590 as a kRNA editing accessory protein and suggest it may act as an RNA chaperone that ensures the complete editing of the A6 transcript.</p> / Dissertation

<p> Biglycan is a small, leucine-rich repeat proteoglycan that has been shown to be elevated in the intervertebral discs (IVDs) of older adults (Cs-Szabo, 2002) and can interact with many different signaling molecules and structural proteins. TNF-alpha (TNF) is a general modulator of inflammation and may be a trigger in the chronic inflammatory response that leads to disc degeneration. Since biglycan has been shown to interact with TNFalpha (Tufvesson and Westergren-Thorsson, 2002), it may play a role in modulating its response in the IVD. Western (NFkB) and RT-PCR (MMP-1, -13, NGF and VEGF) assays were performed on both human and bovine cultured cells from IVD tissue. Treatment with biglycan alone was found to be almost indistinguishable from control groups; while biglycan in combination with TNF-alpha was able to significantly reduce transcription and expression response when compared with just TNF-alpha. Biglycan may help modulate the effects of TNF-alpha in the IVD.</p>

Diphtheria toxin-like human ADP-ribosyltransferase 3 (ARTD3) is a poorly characterized member of the ARTD superfamily of enzymes. ARTDs are enzymes that catalyze ADP-ribosylation, a reversible post-translational modification whereby growing chains of ADP-ribose is attached onto target proteins. ARTDs are involved in a wide variety of roles within the cell, including DNA damage repair and maintenance of genomic stability. ARTD3 is activated by damaged DNA and believed to play a role in double-strand break repair (DSBR) in the non-homologous end-joining (NHEJ) pathway, and has been implicated as a drug target in the treatment of cancer. In this study, an activity assay previously reported for other ARTDs was adopted for ARTD3 in order to screen the enzyme with two compound libraries consisting of 918 compounds in order to discover new potential chemical probes for the protein. The assay was validated through statistical criteria and its performance tested in a preliminary screen with 32 known ARTD inhibitors and their analogs. From all the compounds screened, 12 were ordered and 8 verified as hits in a counter-screen at 10 µM compound concentration. These 8 compounds were then further characterized with thermofluor to determine their ability to bind ARTD3 catalytic domain, fluorescence polarization (FP) to determine their effects on ARTD3’s binding affinity with DNA and the compounds had their IC50 values were measured. 6 compounds that exhibited interesting results in these experiments were classified according to their proposed mechanism of inhibition or compound class. These compounds consisted of two DNA chelating topoisomerase inhibitors, one insecticide, one heavy-metal containing polycyclic hydrocarbon (PHC) and two unclassified tumor suppressors. None of the compounds stabilized full-length ARTD3 or the catalytic fragment, but the DNA chelating agents lowered the binding affinity of ARTD3 to DNA. While no traditional ARTD inhibitor with potential for use as a chemical probe was discovered, the effects of DNA chelating agents on ARTD3’s binding affinity with DNA could be further investigated via binding affinity studies such as isothermal titration calorimetry (ITC). One of the unclassified tumor suppressors with decent potency (IC50: 2.7 µM) could also be tested against other ARTDs and if it was found to be selective against ARTD3, its binding to ARTD3 could be determined with co-crystallization and x-ray crystallography.

Mustikka (Vaccinium myrtillus L.) on Vaccinium-sukuun kuuluva kasvi, joka kasvaa Euroopan, Aasian ja Pohjois-Amerikan pohjoisosissa. Vaccinium-sukuun kuuluu mustikan lisäksi muun muassa karpalo ja kanadanmustikka. Mustikka sisältää paljon terveydelle hyödyllisiä hivenaineita, vitamiineja ja antioksidantteja, minkä vuoksi sitä voidaan pitää funktionaalisena elintarvikkeena. Iso osa mustikan terveyshyödyistä on liitetty fenoleihin kuuluviin antosyaaneihin, joilla on antioksidanttisten vaikutusten lisäksi muunlaisiakin vaikutusmekanismeja, kuten solusignalointiin, geeniekspressioon, DNA:n korjausmekanismeihin ja soluadheesioon liittyviä toimintoja. Antosyaaneilla on osoitettu olevan mm. soluja suojaavia, antimikrobisia, syöpää estäviä, hermostoa suojaavia sekä lihavuutta ehkäiseviä vaikutuksia. Tämän tutkielman tarkoituksena on koota yhteen tämänhetkistä tietämystä antosyaanin rakenteesta, toimintamekanismeista sekä terveysvaikutuksista.