The purpose of this study was twofold. The first was to isolate, purify, and characterize the deoxyribonucleic acid (DNA) of Azotobacter vinelandii ATCO 12837. The second was to determine if there was irreversible binding of homologous 32P labeled DNA to recipient A. vinelandii cells.

No description available.

A thesis submitted to the Faculty of Science under the school of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Doctor of Philosophy. Gauteng, Johannesburg, 2016. / Overexpression of RBBP6 in cancers of the colon, lung and oesophagus makes it a potential target in anticancer therapy. This is especially important because it associates with the tumour suppressor gene p53, inactivation of which has been linked to over 50% of all cancer types. Cancer is an enormous burden of a disease globally. Today, more people die from cancer than HIV/AIDS, tuberculosis and malaria combined. And in females, breast and cervical malignancies remain the most common types. Currently, cervical cancer is the most diagnosed gynaecological cancer type, whose mortality rate is the highest in developing countries due to the asymptomatic nature of the disease coupled with inadequate cancer control tools and facilities. Breast cancer incidence rate has increased beyond that of lung cancer, making it the most common malignancy among women. / GR2016

A Dissertation submitted to the Faculty of Science, University of Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. 2015. / Prdm1/Blimp1 is a transcription factor whose mechanism of action is mainly repression; however it has been identified as an activator in some cases. As a transcriptional repressor, it plays multiple roles during embryonic development, including neural crest specification. Prdm1 acts by repressing large sets of genes via sequence specific recruitment of co-repressors, many of which are epigenetic modifiers. Neural crest is a transient, migrating cell population that gives rise to a number of diverse cell lineages that form important structures in the vertebrate embryo. Examples of these include peripheral nervous system, melanocytes and cranial cartilage. Prdm1 is expressed during neural crest specification in Xenopus, zebrafish and lamprey. The expression of Prdm1 had not yet been investigated in the neural crest during chick embryonic development. The mechanism of Prdm1 action or the nature of possible binding partners that mediate its effects in the neural crest had not yet been addressed. Prdm1 binding partners are known to play important roles during embryonic development, yet in many cases no spatiotemporal expression analysis during early vertebrate development has been performed. Single and double in situ hybridization for Prdm1 and all the binding partners was performed to determine localization of mRNA during early stages of chick embryonic development. We report the expression patterns of Prdm1 and seven of its known or putative binding partners (Hdac1, Hdac2, Tle1, Tle3, G9a, Prmt5 and Lsd1) during early stages (HH4-HH10) of chicken embryogenesis. Prdm1 expression was observed in the neural plate border and pre-migratory neural crest during chick development. Six Prdm1 binding partners (except Tle1) are co- expressed with Prdm1 in the prospective neural plate border at HH4-HH6, and all seven show strong and specific expression in the neural plate border at HH7-HH8, suggesting all of them co-operate with Prdm1 during neural crest development in chick embryos. Future work will focus on protein interaction studies in order to directly demonstrate the association between Prdm1 and the binding partners it co-localizes with.

Hydrogen Sulfide (H2S) is an important biologically produced gasotransmitter along with carbon monoxide (CO) and nitric oxide (NO). Unlike CO and NO, the bioinorganic chemistry of H2S reactivity with biologically relevant metal centers remains underinvestigated. To address this gap, several model bio(in)organic complexes were used to understand the ligation and reaction chemistry of H2S, including phthalocyanine, protoporphyrin IX, tetraphenyl porphyrin, and a pyridine diimine zinc complex. In addition to being a reactive gasotransmitter, the hydrosulfide anion (HS–) has been found to be an important biological anion. Studies with readily available cobalt and zinc phthalocyanines in organic solution illustrated the importance of protonation state in the ligation and redox chemistry of H2S and highlighted the need for an organic-soluble source of HS–. To address this need, we developed a simple method to prepare tetrabutylammonium hydrosulfide (NBu4SH). Using NBu4SH, we expanded the knowledge of H2S reaction chemistry to encompass a significantly larger set of biologically relevant metals beyond iron using the protoporphyrin IX scaffold, revealing three principle reaction pathways: binding, no response, or reduction and binding. Iron in biology is of particular importance given its role in oxygen transport in hemoglobin. The swamp-dwelling bivalve L. Pectinata hemoglobin 1 (Hb1) transports H2S, via ligation to heme, to symbiotic bacteria. The stabilization of H2S in Hb1 is believed to be from one of the following: a protected pocket, hydrogen bonding with a proximal glutamate residue, or a complex combination of these or other factors. By using Collman's "Picket-Fence" porphyrin to isolate the protected pocket model, we determined that a protected pocket alone as insufficient to account for H2S stabilization on Hb1. This realization led to an examination of hydrogen bonding in the secondary coordination sphere of a zinc complex. Finally, we explored the role of HS– as a biologically relevant anion using a bis(ethynylaniline) supramolecular receptor. We determined that rather than covalently modifying the receptor molecule, HS– was bound in the pocket, similar to bacterial anion transport channel. This dissertation includes previously published co-authored material.

by Chiu Sung Pui. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (leaves 99-100). / Abstract also in Chinese. / Chapter Chapter I --- Introduction --- p.6 / Chapter 1.1. --- An overview of Chomsky's Binding Theory --- p.7 / Chapter 1.2. --- Referential and Bound pronouns --- p.9 / Chapter 1.3. --- Definition of bound pronouns --- p.9 / Chapter Chapter II --- Literature on bound pronouns --- p.10 / Chapter 2.1. --- Higginbotham (1980) --- p.10 / Chapter 2.2. --- Reinhart (1983) --- p.17 / Chapter 2.3. --- Koopman & Sportiche (1982) --- p.20 / Chapter 2.4. --- lappin (1985) --- p.21 / Chapter 2.5. --- "aoun & hornstein (1991), aoun & li (1990)，aoun & li (1993)" --- p.23 / Chapter Chapter III --- Binding Facts in Chinese --- p.31 / Chapter 3.1. --- Patterns in which the antecedent c-commands the pronoun --- p.32 / Chapter 3.2. --- Patterns in which the antecedent does not c-command the pronoun --- p.53 / Chapter 3.3. --- Summary of the binding facts --- p.67 / Chapter Chapter IV --- A revisit of the proposals on Bound pronouns --- p.69 / Chapter 4.1. --- Review of Higginbotham (1980) --- p.69 / Chapter 4.2. --- Review of Reinhart (1983) --- p.70 / Chapter 4.3. --- Review of Koopman & Sportiche (1982) --- p.72 / Chapter 4.4. --- Review of Lappin (1985) --- p.73 / Chapter 4.5. --- "Review of Aoun & Hornstein (1991)，Aoun & Li (1990), Aoun & Li (1993)" --- p.74 / Chapter Chapter V --- Discussion & Conclusion --- p.78 / Chapter 5.1. --- Bound Pronoun Condition for Chinese --- p.78 / Chapter 5.2. --- Wh-phrases as A'-binders --- p.78 / Chapter 5.3. --- The Empty Reflexive Puzzle --- p.80 / Chapter 5.4. --- pro-drop & Montabeltii's Overt Pronoun Constraint --- p.81 / Chapter 5.5. --- Factors affecting pronominal binding --- p.82 / Chapter 5.5.1. --- Nature of Verbs --- p.82 / Chapter 5.5.2. --- Quantifier types and the size of the extension denoted by the QP --- p.90 / Chapter 5.5.3. --- Sentence types & the number feature of the quantified NPs --- p.94 / Conclusion --- p.98 / References --- p.99 / Appendix I --- p.101 / Appendix II --- p.102 / Appendix III --- p.105

Transcription factors (TFs) bind to specific DNA sequences near target genes to precisely coordinate their regulation. Despite the central role of transcription factors in development and homeostasis, the mechanisms by which TFs have evolved to bind and regulate distinct DNA sequences are poorly understood. This dissertation details the highly collaborative work to determine the genetic, biochemical and biophysical mechanisms by which distinct DNA-binding specificities evolved in the steroid receptor (SR) family of transcription factors. Using ancestral protein reconstruction, we resurrected and functionally characterized the historical transition in DNA-binding specificity between ancient SR proteins. We found that DNA-binding specificity evolved by changes in the energetic components of binding; interactions at the protein-DNA interface were weakened while inter-protein cooperativity was greatly improved. We identified a group of fourteen historical substitutions that were sufficient to recapitulate the derived protein's binding function. Three of these substitutions, which we defined as function-switching, were sufficient to change DNA specificity; however, their introduction greatly decreased binding affinity and was deleterious for protein function. A group of eleven permissive substitutions, which had no effect on DNA specificity, allowed for the protein to tolerate the deleterious effects of the function-switching substitutions. They non-specifically increased binding affinity by improving interactions at the protein-DNA interface and increasing inter-protein cooperativity. We then dissected the functional role of individual substitutions in both the function-switching and permissive groups. We first determined the binding affinity of all possible combinations of function-switching substitutions for a library of DNA sequences. This allowed for us to functionally characterize the sequence space that separated the ancestral and derived DNA-binding specificities as well as identify the genetic determinants for DNA specificity. Lastly, we dissected the effects of the permissive substitutions on the energetics of DNA binding to determine the mechanisms by which they exerted their permissive effect. Together, this work provides insight into the molecular determinants of DNA specificity and identifies the molecular mechanisms by which these interactions changed during the evolution of novel specificity in an important transcription factor family. This dissertation includes previously published and unpublished co-authored material. / 2016-01-14

α-synuclein is an abundant and conserved presynaptic brain protein (Uversky 2007). It has received extensive attention since its aggregation was identified as the main component of Lewy bodies and Lewy neurites, which is the pathological hallmark of several neurodegenerative diseases, collectively known as synucleinopathies, including Parkinson's Disease (PD) (Uversky 2007). Considerable information has been collected about the structural properties and conformational behavior of α-synuclein, although the precise function is still under investigation. Metal ions such as copper and iron, can accelerate the aggregation and fibrillation of α-synuclein. Metal ions may exert their dual physiopathological properties through the interaction with α-synuclein, converting protein structure and/or inducing oxidative stress. In this study, isothermal titration calorimetry and electron paramagnetic resonance were used to determine the metal-binding property of the synuclein proteins, proving the presence of four Cu(II) binding sites per molecular of α-synuclein, with the coordination modes of 1N3O and 2N2O. Furthermore, α-synuclein has a catalytic action on the redox cycling of Cu(II), which was assessed by the application of cyclic voltammetry. However, this property is absent on β-synuclein and γ-synuclein, which belong to the synuclein family and have been suggested to be the physiological regulators of α-synuclein expression. In vivo, immunofluoresence studies revealed that Cu(II) increases the aggregates formation in mammalian doperminergic neuron cells overexpressing α-synuclein and the PD-associated mutants, while no aggregates have been found in cells overexpressing β-synuclein and γ-synuclein.

Ions play pivotal roles both biologically and environmentally. The effects felt from the impact of ions, much like their relative charge, can be positive or negative. Ions are responsible for catalyzing and executing precise control over many of the essential processes that occur in our bodies. Ions can also be major contributors as environmental pollutants having catastrophic effects. There is a great deal of interest in better understanding the role and effect of ions in the surrounding environments. The ability to study ions of interest relies on efficient recognition and sensing of these targets. The field of supramolecular chemistry is particularly well suited for this task as it utilizes non-covalent molecular interactions in much the same way natural system involving ions operate. Broadly, this body of research seeks to explore the subtle interactions of various targeted ions with supramolecular receptors. This research is an effort to further understand the nature of these interactions for potential recognition and sensing applications as well as better understanding the highly complex systems found in biology. Chapter I provides a brief overview of various mechanisms of ion coordination in supramolecular chemistry and emphasizes some key examples demonstrating the importance of the various types of coordination as it pertains to the research presented herein. Chapter II highlights a unique class of phosphine oxide-based tripodal ditopic receptors and presents studies on their interactions with alkali metals and halides. Chapter III covers the synthesis and study of anionic binding trends for a series of heteroaromatic-containing urea-based receptors and discusses the influence of anion binding on receptor conformation. Chapter IV provides preliminary results on the application of the bipyridal bisurea-based anion receptor, presented in Chapter III, as ligand for metal salts. Chapter V focuses on a series of pyridal bisurea-based receptors with regard to their ability to serve as chloride sensitive probes in cellular environments. This dissertation contains both previously published and unpublished co-authored material. / 10000-01-01

The AID/APOBEC protein family comprises a group of cytosine deaminases found in vertebrates that are capable of modifying cytosine to uracil in the context of RNA or singlestranded DNA. They exert diverse valuable physiological functions including antibody diversification and restriction of viral infection. However, off-target mutations have also been shown to contribute to cancer development, making it crucial to better understand the interactions and mechanisms that regulate AID/APOBEC activity and editing site fidelity. In this regard, a new focus on RNA as a putative regulator of AID/APOBECs has recently emerged. Regardless of whether it is used or not as a substrate for deamination, most members of the family have been shown to retain the ability to bind RNA, emphasizing a potential regulatory role for this interaction. However, little is known about AID/APOBECs RNA binding specificity. A promiscuous binding has been suggested in some cases while in vitro evidence for other members of the family indicate a certain level of specificity. Therefore, to thoroughly unravel the AID/APOBECs RNA binding specificity, in my doctoral research I applied cross-linking and immunoprecipitation (iCLIP), an unbiased technique that allows identification of protein-bound RNAs with nucleotide resolution in living cells. As a first approach, I adapted the technique for its use in yeast and probed the RNA binding of AID and APOBEC3G, revealing different degrees of preference for small structured RNAs and recognition of particular sites within them. I then expanded the analysis to mammalian cells (HEK293T) and evaluated an extended set of APOBECs finding that, even in the presence of a broader and more complex pool of RNAs, small RNAs were still significantly bound by some members of the family. Furthermore, the comparative analysis of AID, APOBEC1, APOBEC3G, APOBEC3A and APOBEC3B iCLIP data obtained in my research, revealed shared and individual preferences for certain RNAs, suggesting a degree of binding specificity among APOBECs. In summary, my thesis outlines for the first time a comprehensive analysis of the RNA binding specificity of different AID/APOBECs in vivo, including the description of novel interactions with nucleotide resolution. The results obtained are of great value and open the field for further investigation of the specific meaning and validation of each preferential binding, providing new insights into understanding the role of AID/APOBEC interaction with RNA.