Browsing by Subject "Molecular biology"
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Item A Computational Approach To Rna Sequencing For Secondary Structure Prediction(2016) Bhattarai, Anup; Stojkovic, Vojislav; Computer Science and Bioinformatics Program; Master of ScienceRNA is not only a messenger of genetic codes from DNA to protein but also an active molecule in various biological functions. An RNA sequence and the structure formed determines the functions. Prediction of secondary structure of RNA is useful in determining its functions such as regulation of gene expressions, sensing of ligand, enzymatic features, translational control in mRNA, and replication in single-stranded RNA viruses. Also, RNA structures will provide insights into evolution, biology, and design of therapeutics. In this thesis research, I used hydrogen bond maximizing algorithm to predict RNA secondary structure, hydrogen bond maximizing program designed by Rex A. Dyer to create a Nussinov matrix, and a recursive or iterative algorithm to decode the Nussinov matrix, which gives RNA secondary structure. The Perl and Python programming languages have been used to solve the same problem in a recursive and iterative way. The comparison of execution time between an iterative and a recursive algorithm was done. The comparison between the programming languages Perl and Python gave an insight into speed, readability, and simplicity of these two programming languages, and comparison between recursive and iterative algorithms showed which one was faster in practice.Item Characterization of the DNA binding activity of NZF-1 zinc binding domains upon replacement of zinc with iron.(2011-05-18) Lue Sue, Niall D.; Cymet, Holly J.; Master of ScienceItem Computational methods for analysis of genomic databases for the identification of complex trait genes causing essential hypertension.(2006-09-28) Mukira, George Keru; Wachira, James; Master of ScienceItem Effects Of Neonatal Stress On Inflammatory Responses In The Brain Of Adult Balb/Cbyj Mice.(2015) Odebode, Gabi A.; Hohmann, Christine F.; Biology; Master of ScienceEarly childhood stress and trauma are risk factors for depression and other mental health disorders. Increased inflammatory cytokine levels are observed in the same mental health disorders. The hypothalamic-pituitary-adrenal (HPA) axis is known to regulate the inflammatory immune response. We hypothesized that early life stress may predispose the brain to neuroinflammation later in life. This thesis investigates the effects of neonatal stress on the production of pro-inflammatory cytokines, including interleukins (IL) 1Ī², 2, and 6 and tumor necrosis factor-a (TNF-Ī±), in mature Balb/CByJ mice. Half of the litter was removed for the maternal separation stress procedure (STR), while the other half remained with the dam as littermate controls (LMC). A separate group of age-matched, colony-reared pups (AMC) served as an additional control. First, male and female STR, LMC and AMC mice were analyzed for baseline IL-1Ī², 2, and 6 and TNF-Ī± levels in cerebral cortex and for corticosterone levels in sera, using commercially available ELISA kits. Second, mice received either saline or LPS injections two hours before being sacrificed for collection of brain tissues and blood for cytokine analysis. No significant differences in baseline levels of cytokines and corticosterone were found in the brains of uninjected STR, LMC and AMC mice. By contrast, LPS injections significantly increased production of IL-6 in brain tissue of STR and LMC mice, regardless of sex. In sera, significant increases of IL-6 and decreases of TNF-Ī± were measured, following LPS injections in the STR and LMC mice compared to AMC controls. These data suggest that neonatal experience in STR and LMC mice may have developmentally reprogrammed inflammatory responses in the brain, thus, producing altered cytokine release to an inflammatory agent in adulthood.Item Increased Expression Levels Of Igfbp-5 And Gpx1 In Bxpc-3 Pancreatic Cancer Cell Lines.(2017) Hazel, Kaisha An-Rae; Nyaga, Simon G; Denaro, Frank; Biology; Master of SciencePancreatic cancer is a highly fatal disease with death usually occurring within one year of diagnosis. American Cancer Society predicts that by the end of 2017, there will be 53,670 new cases and 43,090 fatalities of pancreatic cancer. Despite the aggressiveness of this disease, little is known about its mechanism of development. It has been speculated that reactive oxygen species (ROS) damages cellular DNA causing deleterious mutations which leads to altered proteins and cellular functions including transformation of normal to malignant phenotype. Insulin-like growth factor binding protein-5 (IGFBP-5) is associated with regulation of biological functions such as cell growth, differentiation, apoptosis, cell adhesion, and metastasis: processes that are known to be critical in the etiology of cancer. Additionally, Glutathione peroxidase 1 (GPx1) is an anti-oxidant enzyme that detoxifies hydrogen peroxide in cells thereby minimizing oxidative stress. We therefore, hypothesized that expression of IGFBP-5 and GPx1 may be altered in pancreatic cancer cells. To address our hypothesis, we analyzed the expression of IGFBP-5 and GPx1, in the pancreatic cancer cell line, BxPC-3 relative to the non-malignant pancreatic cell line, HPDE-6. Both cell lines were cultured in 5% CO2 incubators at 37oC and nuclear extracts were subsequently prepared. The protein concentrations were determined by BCA assay and the proteins resolved by SDS polyacrylamide gel electrophoresis (SDS-PAGE). The protein bands were stained with Coomassie Blue and de-stained with water. Antibodies against IGFBP-5, and GPx1 were used to assess protein expression via Western Blot Analysis. Interestingly, our results showed that multiple proteins with molecular weights ranging from 10 kDa to 300 kDa including IGFBP-5 and GPx1 were differentially expressed in BxPC-3 compared to the normal cell line. This expression was further verified by Western Blot Analysis. These findings are consistent with our hypothesis and implicate the involvement of IGFBP-5 and GPx1 in the etiology of pancreatic cancer. Further characterization of these proteins may yield useful insights essential in the understanding of the mechanisms underlying pancreatic cancer development. Furthermore, this research may be critical in identifying biomarkers useful in therapeutic intervention of pancreatic cancer.Item Large-scale analysis of gene expression in the developing cortex of 6-OHDA treated mice: Possible implications for behavioral deficits.(2005-08-29) Betts, Elizabeth S.; Hohmann, Christine F.; Cadet, Jean Lud; Master of ScienceItem The identification and characterization of novel basic helix-loop-helix proteins in Caenorhabditis elegans.(2004-09-23) McMiller, Tracee Lynn; Johnson, Casonya M.; Master of Science