Exoribonucleases are indispensable for cellular RNA metabolism. RNA processing, end-turnover, and degradation all require the concerted action of exoribonucleases. In this thesis, two families of exoribonucleases that act in the final steps of RNA decay pathways are explored. The first of these is the RNR superfamily of processive 3’→5’ RNases with major roles in both mRNA and stable RNA degradation. The initial focus of this work is the structural and enzymatic characterization of an unusual RNR family enzyme from the radiation-resistant bacterium Deinococcus radiodurans. This enzyme is demonstrated biochemically to be an RNase II-type enzyme (DrII), based on its sensitivity to secondary structure. Analysis of the DrII X-ray structure reveals that a novel, winged-HTH domain has replaced the canonical RNA binding clamp typical of RNR family proteins. The exposed architecture of DrII’s RNA binding surface offers an explanation for the nuclease’s ability to approach within 3-5 nt of a duplex, an important mechanistic difference from the well-studied E. coli RNase II. The open, clamp architecture of DrII may have broader relevance to mechanisms of duplex RNA recognition in the RNR superfamily. RNA decay by processive exonucleases such as RNR family proteins leaves 2-5 nt nanoRNA limit products that are further degraded to mononucleotides by nanoRNases. In E. coli, the DEDD family enzyme Oligoribonuclease (ORN) executes nanoRNA decay and represents the first major family of nanoRNases, with homologs widely conserved in eubacteria and eukaryotes. The B. subtilis NanoRNase A (NrnA), a DHH family phosphoesterase, represents a second major class of nanoRNases, with broad phylogenetic distribution in organisms that lack orn homologs. The second major focus of this thesis is a structural and mechanistic study of this nanoRNase machinery. The atomic structure of the B. subtillis nanoRNase NrnA is described, and unveils a bi-lobal architecture similar to the 5’→3’ DNase RecJ, where the catalytic DHH domain is linked via a partially helical connector to the C-terminal RNA binding domain. NrnA is a highly dynamic molecule, adopting both open and closed conformations. Co-crystallization with several substrates shows that NrnA has a nanoRNA specific substrate-binding patch that offers a structural explanation for its 3’→5’ nanoRNase activity. This RNA binding site feeds substrate to the DHH active site in an orientation opposite to the 5’→3’ path proposed for RecJ. Surprisingly, NrnA also maintains a weak 5’→3’ activity on certain substrates, and thus possesses both 5’→3’ and 3’→5’ exonuclease activities. In conclusion, an overall model is presented for how DHH family exonucleaess can degrade nucleic acids from both the 5’→3’ and 3’→5’ directions. Thus, the studies described in this thesis offer both an atomic and a biochemical view of the macromolecular machinery critical to the degradation of RNA.

Like all phages, T4 requires a holin (T) to effect lysis. The lysis event depends on the temporally regulated action of T, which accumulates in the inner membrane (IM) until, at an allele-specific time, it triggers to form a large "hole" in the membrane. Hole formation then releases T4 lysozyme into the periplasm where it degrades the cell wall to elicit cell lysis. Unlike other phages, T4 is unique in exhibiting real-time regulation of lysis based on environmental conditions. Specifically, lysis can be delayed indefinitely in the lysis-inhibited state (LIN), where the normal temporal schedule for holin-triggering is over-ridden. Recently, it was shown that the imposition of LIN was correlated with the interaction of the periplasmic domains (PD) of RI and T. These studies have been extended in this dissertation using genetic, biochemical, and structural techniques to address the molecular mechanism of the RI-T LIN system. First, the PD of RI and an RI-T complex were purified, characterized biophysically, and crystallized to yield the first atomic resolution structures of either a holin or antiholin. The RI PD is mostly alpha-helical that undergoes a conformational change, as revealed by NMR spectroscopy studies, when bound to T. The PD of T is globular with alpha-helical, beta strand, and random coil secondary structures. Additionally, the holin was genetically characterized by mutagenesis techniques, yielding new information on its role in both lysis and LIN. Lysis defective mutants in all three topological domains: cytoplasmic, transmembrane, and periplasmic, were isolated. Analysis of these mutants revealed that both the cytoplasmic and periplasmic domains are important in the oligomerization of T. During LIN, the RI PD binds the PD of T, blocking a holin oligomerization interface. Finally, the signal for the imposition of lysis inhibition has been elucidated using NMR spectroscopy and other in vitro studies. These studies have shown that the RI PD binds DNA. From these studies, new models for lysis and LIN have been constructed. Lysis occurs with the accumulation and oligomerization of T via cytoplasmic and periplasmic domain interactions. LIN is imposed when the ectopically localized DNA of a superinfecting phage interacts with RI, stabilizing it in a conformation competent in inhibiting T oligomerization and leading to lysis inhibition.

Corrosion is the most important mechanical integrity issues the petrochemical industry has to deal with. While significant research has been dedicated to studying corrosion, it is still the leading cause of pipeline failure in the oil and gas industry. Not only is it the main contributor to maintenance costs, but also it accounts for about 15-20% of releases from the petrochemical industry and 80% of pipeline leaks. Enormous costs are directed towards fixing corrosion in facilities across the globe every year. Corrosion has caused some of the worst incidents in the history of the industry and is still causing more incidents every year. This shows that the problem is still not clearly understood, and that the methods that are being used to control it are not sufficient. A number of methods to detect corrosion exist; however, each one of them has shortcomings that make them inapplicable in some conditions, or generally, not accurate enough. This work focuses on studying a new method to detect corrosion under insulation. This method needs to overcome at least some of the shortcomings shown by the commercial methods currently used. The main method considered in this project is X-ray computed tomography. The results from this work show that X-ray computed tomography is a promising technique for corrosion under insulation detection. Not only does it detect corrosion with high resolution, but it also does not require the insulation to be removed. It also detects both internal and external corrosion simultaneously. The second part of this research is focused on studying the behavior of erosion/corrosion through CFD. This would allow for determining the erosion/corrosion rate and when it would take place before it starts happening. Here, the operating conditions that led to erosion/corrosion (from the literature) are used on FLUENT to predict the flow hydrodynamic factors. The relationship between these factors and the rate of erosion/corrosion is studied. The results from this work show that along with the turbulence and wall shear stress, the dynamic pressure imposed by the flow on the walls also has a great effect on the erosion/corrosion rate.

Nucleic acids are responsible for the storage of genetic information and directly participate in gene replication, transcription and expression, and thereby the control of nucleic acids leads to the regulation of genetic information flow and gene expression. Meanwhile, many non-coding RNAs are in-volved in signal transduction directly. Moreover, nucleic acid-based therapeutic strategies have been lead to drug candidates and are effective tools in drug discovery and disease study at the molecular level as well as the genetic level. Consequently, the 3D crystal structure study and related functional research on natural and unnatural nucleic acids have become very popular area, expanding their potential appli-cation in medicinal and biological chemistry. Since oxygen, sulfur, selenium and tellurium are in the same elemental family (VIA) in the peri-odic table, we anticipate that oxygen atoms in nucleic acids can most likely be replaced with the other chalcogen atoms without causing significant perturbations. Owing to the special K edge and unique properties of selenium, our lab has completed the chemical and enzymatic synthesis of unnatural nucle- ic acids with selenium substitutions at various positions. The selenium functionality in nucleic acid is es-sential for nucleic acids’ structural determination at the atomic level. Additionally this novel elemental feature (atomic size and electronic nature) provides nucleic acids with unique properties. In addition, the selenium derivatization can facilitate crystal growth. Other chalcogen elements are applicable as well to modify nucleic acid, generating some special biofunctions, like the application of phosphorthioate oligonucleotide in gene therapy. This dissertation will outline the chalcogen elements (especially selenium) modifications of nucleic acids, including syntheses strategies, structure studies and potential therapeutic applications. Our research work here tries to show that (1) Selenium functionality is able to facilitate the crystal structure determination, by both helping solve phase problem and accel-erating crystal growth; (2) Selenium functionality can generate special capability to nucleic acids, like improved base pair fidelity, novel atomic interactions and feasibility to be biological chemistry probe; (3) Selenium derivatized oligonucleotides are extraordinary good candidates for gene therapy discovery, considering its stability under nuclease environment. In general, these atom-specific replacements gen-erate a new paradigm of nucleic acids. INDEX WORDS: Nucleic acid, Selenium, X-ray crystal structure, Biofunction, Therapeutics

Despite previous extensive study of the widely-employed ruthenium-catalysed olefin metathesis reaction, the finer mechanistic details have not been elucidated. An area that is noticeably lacking is spectroscopic exploration of the relevant complexes. In this work, organometallic ruthenium complexes of importance to olefin metathesis have been investigated using Ru K-edge X-ray absorption spectroscopy. The lowest energy feature in the Ru K-edge spectrum has been unambiguously assigned as due to Ru 4d←1s transitions. These electric-dipole-forbidden transitions are extremely sensitive to geometry. For centrosymmetric complexes, the pre-edge feature has very low intensity because it is limited by the weak electric quadrupole mechanism. By contrast, non-centrosymmetric complexes exhibit a substantial increase in pre-edge intensity because Ru 5p-4d mixing introduces electric-dipole-allowed character to the Ru 4d←1s transitions. The energy of the edge feature in the Ru K-edge spectrum corresponds to ionisation of 1s electrons and is a good indicator of the charge on the metal centre. Unexpectedly, we found that the first-generation (L = PCy₃) Grubbs precatalyst (1) has a higher 1s ionisation energy than the second-generation (L = H₂IMes) complex (2). This effect provides a compelling rationale for the unexplained differences in phosphine dissociation kinetics for complexes 1 and 2: the phosphine dissociation rate of 2 is slower than 1 because the metal centre is more electron-deficient in 2. Density functional theory calculations confirm the charge differences and offer some insight into the nature of bonding in these complexes, particularly with regard to the N-heterocyclic carbene and trialkylphosphine ligands. On the basis of these results, we propose that, for this system, the NHC ligand is a weaker σ-charge donor than the phosphine ligand, and that the NHC accepts significant π-electron density from the metal; both interactions function to reduce the electron density on the ruthenium centre. An ultimate goal is to investigate reactive species in the olefin metathesis mechanism; accordingly, we have made considerable progress toward collecting XAS data for a metallacyclobutane species, and we are pursuing methods to trap the four-coordinate intermediate in the metathesis cycle.

The study was conducted to develop a technique that measures the amount of gadolinium based contrast agent accumulated in a head tumour by x-ray fluorescence, while a patient is exposed to neutrons or during external beam radiotherapy planning. In this research, measurements of the gadolinium concentration in a vessel simulating a brain tumour located inside a head phantom, by the x-ray fluorescence method were taken, where the Magnevist contrast medium which has gadolinium atom, in the tumour vessel, was excited by a 36 GBq (0.97 Ci) 241Am source that emits gamma rays of 59.54 keV, in 35.7 % of it’s decays, resulting the emission of characteristic fluorescence of gadolinium at 42.98 keV that appeared in the X-ray fluorescence spectrum. A Cadmium Telluride (CdTe) detector was used to evaluate and make an analysis of the gadolinium concentration. Determinations of the gadolinium content were obtained directly from the detector measurements of XRF from gadolinium in the exposed tumour vessel. The intensity measured by the detector was proportional to the gadolinium concentration in the tumour vessel. These concentrations of gadolinium were evaluated for dose assessment. The positioning of the head phantom was selected to be in the lateral and vertex positions for different sizes of tumour vessels. Spherical tumour vessels of 1.0, 2.0, 3.0 cm and an oval tumour vessel of 2.0 cm diameter and 4.0 cm length, containing the gadolinium agent, contained concentration between 5.62 to 78.63 mg/ml. They were placed at different depths inside a head phantom at different positions in front of the detector and the source for the measurements. These depths ranged from 0.5 cm to 5.5 cm between the center of the tumour and interior wall of the head phantom surface. The total number of measurements in all four sizes of the tumour vessel was 478; 78 examinations of a 1.0 cm spherical tumour vessel, 110 examinations of a 2.0 cm spherical tumour vessel, 150 examinations of a 3.0 cm spherical tumour vessel and 140 examinations of a 2.0 x 4.0 cm ellipsoid tumour vessel. To measure the size and the shape of the tumour by the alternative radiographic method, a general x-ray machine with radiograph film was used. Based on that, the appropriate shape of concentration could be selected for therapy. The differences of optical density in the x-ray films showed that the noise was increased with low concentration of the Gd. Because radiographic film may be subjected to different chemical processes where the darkness will be affected, these measurements would be very hard to be quantitative. Accordingly it is difficult to use the film for Gd concentrations. The obtained data show that the method works very well for such measurements.

Thesis ( Ph.D.) -- McMaster University, 1998. / Includes bibliographical references (leaves 237-246). Also available via World Wide Web.

Thesis (Ph.D.)--McMaster University (Canada), 1994. / Source: Dissertation Abstracts International, Volume: 56-08, Section: B, page: 4314. Adviser: R. F. Childs.

Licentiatavhandling (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 3 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 3 uppsatser.