Biochemistry Commons^™

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

Cullin-3 Dependent Deregulation Of Actn1 Represents A New Pathogenic Mechanism In Nemaline Myopathy, Jordan Blondelle, Kavya Tallapaka, Jane T. Seto, Majid Ghassemian, Madison Clark, Jenni M. Laitila, Adam Bournazos, Jeffrey Singer, Stephan Lange

Biology Faculty Publications and Presentations

Nemaline myopathy is a congenital neuromuscular disorder characterized by muscle weakness, fiber atrophy, and presence of nemaline bodies within myofibers. However, understanding of the underlying pathomechanisms is lacking. Recently, mutations in KBTBD13, KLHL40, and KLHL41, three substrate adaptors for the E3 ubiquitin ligase Cullin-3, have been associated with early-onset nemaline myopathies. We hypothesized that deregulation of Cullin-3 and its muscle protein substrates may be responsible for disease development. Using Cullin-3–knockout mice, we identified accumulation of non-muscle α-actinins (ACTN1 and ACTN4) in muscles of these mice, which we also observed in patients with mutations in KBTBD13. Our …

Small Noncoding Rna Profiles Along Alternative Developmental Trajectories In An Annual Killifish, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of …

Ascorbic Acid, Lipid Peroxidation, And Aging, Brian Evan Leibovitz

Dissertations and Theses

The role of ascorbic acid with regard to lipid peroxidation and aging has been examined. A thorough literature analysis indicates that free radical-induced lipid peroxidation is a plausible biochemical explanation for aging. Lipid peroxidation causes cellular damage due to altered enzyme activities, error-prone nucleic acid metabolism, and membrane dysfunction, as well as the accumulation of aging pigments in the lysomes. Ascorbic acid, a water soluble free radical quencher, was examined with regard to carbon tetra-chloride-induced lipid peroxidation and in vivo aging. Carbon tetrachloride, a well-known free radical inducer, caused marked increases in the ration of oxidized/reduced vitamin C only …

The Role Of Zinc In Dihydroorotase, Pamela S. Gilchrist

Dissertations and Theses

Dihydroorotase (4,4—dihydroorotic acid amidolyase, EC 3.5.2.3.) which catalyzes the reversible cyclization of N-carbamyl-L-aspartate to L-dihydroorotate has been purified from orotate-grown Clostridium oroticum. The enzyme is stable in 0.3 M sodium chloride and 10 µ ZnSO₄. Sodium dodecyl sulfate gel electrophoresis indicates the enzyme to be composed of two identical subunits each with a molecular weight of 58,000 + 6000. Dihydroorotase is shown to be a zinc-containing metalloenzyme with 2 g atoms of zinc per 58,000 g of protein. The role of zinc in dihydroorotase is discussed.

A Study Of Rna Bacteriophage 7s Infection Of Pseudomonas Aeruginosa, Deanne Benson

Dissertations and Theses

A study was conducted to find the effect of magnesium, calcium, manganese and zinc ions on the infection of Psudomonas aeruginosa strain 1C by RNA bacteriophage 7s. When an 18 hour progeny experiment was performed, it was found that magnesium, calcium and manganese had different effects on bacteriophage production and was dependent on the bacterial growth conditions. RNA bacteriophage 7s progeny production was significantly enhanced by the addition of magnesium to cultures of Psudomonas aeruginosa 1C grown in a magnesium deficient medium. Under these environmental conditions there was a slight increase in progeny in the presence of calcium. When Psudomonas …

Enzyme Reactions Using Ureidosuccinate As A Substrate During Pyrimidine Biosynthesis And Degradation In Cl. Oroticum, Penny Amy

Dissertations and Theses

Cells of Clostridium oroticum, an anaerobic bacterium, were grown on orotate as a carbon and energy source. Ureidosuccinase, an inducible enzyme in the pathway for pyrimidine degradation has been shown to convert ureidosuccinate to aspartate, CO₂ and NH₃ as reported by Liebenmm and Kornberg (7). Aspartate and CO₂ were formed in approximately a 1:1 ratio from ureidosuccinase activity.

Ureidosuccinase was found to be a Mn+² requiring enzyme with a pH optimum of approximately pH 6.5. Enzyme activity is labile to O₂, temperature, pH, dilution and high ionic strength. The optimum conditions for storage …