Thesis (Ph. D.)--Rutgers University, 2007. / "Graduate Program in Toxicology." Includes bibliographical references (p. 115-131).

Thesis (M.S.)--University of Alabama at Birmingham, 2009. / Title from PDF t.p. (viewed July 20, 2010). Includes bibliographical references.

Thesis (M.Phil.) - University of Queensland, 2004. / Includes bibliographical references.

abstract: A novel small metal-binding protein (SmbP), with only 93 residues and no similarity to other known proteins, has been isolated from the periplasm of Nitrosomonas europaea. It is characterized by its high percentage (17%) of histidines, a motif of ten repeats of seven residues, a four α-helix bundle structure, and a high binding affinity to about six equivalents of Cu2+. The goal of this study is to investigate the Cu2+ binding sites in SmbP and to understand how Cu2+ stabilizes the protein. Preliminary folding experiments indicated that Cu2+ greatly stabilizes SmbP. In this study, protein folding data from circular dichroism (CD) spectroscopy was used to elucidate the role of Cu2+ in stabilizing SmbP structure against unfolding induced by decreased pH, increased temperature, and chemical denaturants. The significant stabilization effects of Cu2+ were demonstrated by the observation that Cu2+-SmbP remained fully folded under extreme environmental conditions, such as acidic pH, 96 °C, and 8 M urea. Also, it was shown that Cu2+ is able to induce the refolding of unfolded SmbP in acidic solutions. These findings imply that the coordination of Cu2+ to histidine residues is responsible for the stabilization effects. The crystal structure of SmbP without Cu2+ has been determined. However, attempts to crystallize Cu2+-SmbP have not been successful. In this study, multidimensional NMR experiments were conducted in order to gain additional information regarding the Cu2+-SmbP structure, in particular its metal binding sites. Unambiguous resonance assignments were successfully made. Cα secondary chemical shifts confirmed that SmbP has a four α-helical structure. A Cu2+-protein titration experiment monitored by NMR indicated a top-to-bottom, sequential metal binding pattern for SmbP. In addition, several bioinformatics tools were used to complement the experimental approach and identity of the ligands in Cu2+-binding sites in SmbP is proposed. / Dissertation/Thesis / Ph.D. Chemistry 2010

Protozoários do gênero Trypanosoma infectam milhões de pessoas todo ano e coletivamente contribuem muito para as misérias humanas, pois são causa de muitas das doenças negligenciadas tropicais. Várias vias metabólicas essenciais são encontradas nesses parasitas tornando-os particularmente atrativos para investigações moleculares. Mecanismos de controle pós-transcricional tem sido alvo de estudo por sua peculiaridade nesses organismos. Nesse cenário, proteínas da classe das poli-A-binding proteins (PABP) possuem função no início da tradução, turnover do mRNA e interação com o 5´-CAP. Nesse trabalho foi identificada a homóloga poli-A binding protein 1 (PABP1) de Trypanosoma brucei. O silenciamento do gene pabp1 revelou que a ausência da proteína é letal ao parasita, comprovando sua essencialidade nesse organismo. Da mesma maneira, na ausência da proteína observou-se erro no processamento do mRNA sugerindo possível função nos eventos de cis e trans splicing. Sua localização subcelular foi avaliada indicando localização citoplasmática, bem como o são suas homólogas. No citoplasma, a proteína apresenta-se em estrutura reticulada, co-localizada com proteínas de retículo endoplasmático. Porém, sob estresse induzido a proteína relocaliza para o compartimento nuclear, indicando ser uma proteína com trânsito núcleo-citoplasma ainda não demonstrada na literatura. As funções identificadas sugerem a existência de um sub-complexo a 3´ do mRNA que acopla poliadenilação e splicing. Além disso, a relocalização nuclear parece ocorrer em resposta a estímulo externo, sugerindo que a relocalização do mRNA para o núcleo pode ser uma estratégia da célula para modular sua resposta gênica frente a variações do ambiente. / Protozoa of the genus Trypanosoma infect millions of people every year and collectively contribute to the human misery by causing several neglected tropical diseases. Several intriguing molecular pathways are found in these parasites also, rendering them particularly attractive for biochemical investigation. This unique eukaryotic cells lack mechanisms to control gene expression at the transcriptional level, they mostly control protein synthesis by posttranscriptional regulation process. Several RNAs and proteins are involved in this process, including poly(A) binding proteins. The poly(A)- binding protein of eukaryotes plays a role in polyadenylation, translation initiation and metabolism of mRNA. In this work the poly(A) binding protein 1 (PABP1) was identified in Trypanosoma brucei. Depletion of TbPABP1 showed its essential role in the procyclic form of the parasite. Immunofluorescence assays showed localization in the cytosolic compartment despite of its functions in cis and trans splicing as shown by RNA analysis of cells free from PABP1. As it was shown in the homologs, PABP1 it´s not only a cytosolic protein but it shuttles between the nucleus and the cytoplasm. Together with the literature, these results suggest an active complex in the 3´ end of the mRNA which works in synchrony with the splicing and capping machinery implying PABP1 as possible link between these processes.

A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding these transcription factor binding sites (TFBS) have been developed. In vivo technologies analyze DNA binding regions known to have bound to a TF in a living cell. Most widely used in vivo methods at the moment are chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing. In vitro methods derive TFBS based on experiments with TFs and DNA usually in artificial settings or computationally. An example is the Protein Binding Microarray which uses artificially constructed DNA sequences to determine the short sequences that are most likely to bind to a TF. The major drawback of this approach is that binding of TFs in vivo is also dependent on other factors such as chromatin accessibility and the presence of cofactors. Therefore TFBS derived from the PBM technique might not resemble the true DNA binding sequences. In this work, we use PBM data from the UniPROBE motif database, ChIP-seq data and DNase I hypersensitive sites data. Using the Spearman’s rank correlation and area under receiver operating characteristic curve, we compare the enrichment scores which the PBM approach assigns to its identified sequences and the frequency of these sequences in likely binding regions and the human genome as a whole. We also use central motif enrichment analysis (CentriMo) to compare the enrichment of UniPROBE motifs with in vivo derived motifs (from the JASPAR CORE database) in their respective TF ChIP-seq peak region. CentriMo is applied to 14 TF ChIP-seq peak regions from different cell lines. We aim to establish if there is a relationship between the occurrences of UniPROBE 8-mer patterns in likely binding regions and their enrichment score and how well the in vitro derived motifs match in vivo binding specificity. We did not come out with a particular trend showing failure of the PBM approach to predict in vivo binding specificity. Our results show Ets1, Hnf4a and Tcf3 show prediction failure by the PBM technique in terms of our Spearman’s rank correlation for ChIP-seq data and central motif enrichment analysis. However, the PBM technique also matched the in vivo binding specificities of FoxA2, Pou2f2 and Mafk. Failure of the PBM approach was found to be a result of variability in the TF’s binding specificity, the presence of cofactors, narrow binding specificity and the presence ubiquitous binding patterns.

One purpose of this study was to determine whether the ras protein from Dictyostelium discoideum (p23) binds guanine nucleotides like the ras proteins from mammals (p21) and yeast. The other purpose of this investigation was to purify or enrich for p23ras from D. discoideum by immunoaffinity chromatography. A number of different approaches were used to determine guanine nucleotide binding by p23RAS . A simple filter binding assay, binding to Western blots, and photoaffinity labeling all failed to demonstrate specific binding with lysates of D. discoideum cells. In contrast p21RAS from transformed NIH-3T3 cell lysate was successfully photoaffinity labeled in the presence of ³²P-α-guanosine 5¹-triphosphate (GTP) suggesting that the technique had been performed correctly. It was concluded that either p23RAS has a very low affinity for guanine nucleotides such that GTP binding was not detectable in these experiments or that the ras protein from D. discoideum simply does not bind guanine nucleotides. The purification of p23RAS from D. discoideum cells was attempted in order to provide a purified protein preparation for guanine nucleotide binding and for reconstitution studies. An anti-ras monoclonal antibody (Y13-259) was used as the ligand for the immunoaffinity chromatography. This approach was not successful in that the ras protein could not be enriched relative to other proteins because the immunoaffinity columns did not bind p23RAS. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Binding sites for prolactin have been identified and characterized in a plasma membrane enriched fraction isolated from livers of mature female rats. By chemical and enzymatic analysis the membrane preparation was shown to have slight contamination with nuclei and endoplasmic reticulum, while mitochondria were not detected. Sidedness analysis indicated that the membrane preparation was largely composed of inside-out vesicles. ¹²⁵I-oPRL prepared by the lactoperoxidase method had a specific activity of 40-60 μCi/μg. Competition studies using iodoprolactin indicated that iodination of the hormone did not affect its affinity for the receptor as compared to the native hormone. Binding of ¹²⁵I-oPRL was inhibited by prolactin from various species including ovine, bovine and rat prolactin while bGH, pACTH and AVP had no effect on binding. The binding of 125 I-oPRL was activated by both bivalent and monovalent cations - bivalent cations exerting a greater effect than monovalent cations. In the presence of 10 mM CaCl₂, binding of ¹²⁵I-oPRL was equal to the binding in the presence of the physiological concentration of NaCI. The association of ¹²⁵I-oPRL with the membrane was a time and temperature dependent process, being maximal at 37°. The dissociation of ¹²⁵I-oPRL was time and temperature dependent only with 150 mM NaCl at 37° while at all other temperatures and in the presence of 10 mM CaCl₂ dissociation was not.observed. The binding of ¹²⁵I-oPRL was strongly influenced by pH with an optimum observed at pH 6.5. Receptor activity was destroyed by pronase and phospholipase C, while neuraminidase increased binding. Treatment of the membranes by RNase and DNase did not effect the binding. Binding of ¹²⁵I-oPRL was inhibited by p-chloromercuribenzoic acid, dithiothreitol, and by brief exposure to high temperatures. Scatchard analysis of the binding of ¹²⁵I-oPRL to receptors indicates that prolactin has a high affinity for its receptor / Medicine, Faculty of / Biochemistry and Molecular Biology, Department of / Graduate

Agency is the capacity of an entity to act independently in a world. Many previous studies have demonstrated that inanimate objects without human or animal traits are under some circumstances perceived as having features of animate objects and can elicit attribution of mental states like motivation, emotion or intention. There are three main types of cues that evoke attribution of agency: morphological cues (head, face, biomechanical movement), behavioral cues (self-propelled movement, goal-directedness, changes in speed or direction, unpredictability, principle of rational (efficient) action) and communicative cues (interaction). In the current study we focused on examinaton of behavioral irregularity and its role in eliciting agency attribution to simple geometric figures. The aim of this study was to verify whether behavioral irregularity can lead to attribution of agency to irregular object. Two studies were designed to test this possibility. In Study A participants (N=20) watched a sequence of priming videoclips displaying four moving geometric shapes. In every trial one object was automatically selected and participans were asked to evaluate its movement on a seven-point scale. Six attributes related to attribution of agency (animacy, goal-directedness, freedom, dynamism, rationality and...

In an attempt to elucidate the transcriptional mechanisms that regulate the expression of the human α2(I) procollagen gene, cis-acting DNA-elements within the proximal promoter were identified and their corresponding trans-acting factors characterised. The fibroblast cell lines used in this study had previously been transformed with either simian virus 40 (SVWI-38) or by γ-radiation (CT-1). The SVWI-38 fibroblasts do not produce any α2(I) collagen chains, whereas the CT-1 cell line produces normal type I collagen. Previous studies suggested that trans-acting factor(s) may be responsible for the inactivation of the α2(I) procollagen gene in SVWI-38 fibroblasts (Parker et. al. (1989) J. Biol. Chem 264, 7147-7152; Parker et. al. (1992) Nucleic Acids Res. 20, 5825-5830). In this study, the SVWI-38 proximal promoter (-350 to +54) was sequenced and shown to be normal, thereby ruling out any possibility that mutations within this region was responsible for inactivation of the gene.