Development of a bovine adenovirus type 2-based gene delivery vector /

ABSTRACT Recombinant adenoviruses are currently under intense investigation as potential gene delivery and gene expression vectors with applications in human and veterinary medicine. As part of our efforts to develop a bovine adenovirus type 2 (BAV2) based vector system, the nucleotide sequence of BAV2 was determined. Sixty-six open reading frames (ORFs) were found with the potential to encode polypeptides that were at least 50 amino acid (aa) residue long. Thirty-one of the BAV2 polypeptide sequences were found to share homology to already identified adenovirus proteins. The arrangement of the genes revealed that the BAV2 genomic organization closely resembles that of well-characterized human adenoviruses. In the course of this study, continuous propagation of BAV2 over many generations in cell culture resulted in the isolation of a BAV2 spontaneous mutant in which the E3 region was deleted. Restriction enzyme, sequencing and PCR analyses produced concordant results that precisely located the deletion and revealed that its size was exactly 1299 bp. The E3-deleted virus was plaque-purified and further propagated in cell culture. It appeared that the replication of such a virus lacking a portion of the E3 region was not affected, at least in cell culture. Attempts to rescue a recombinant BAV2 virus with the bacterial kanamycin resistance gene in the E3 region yielded a candidate as verified with extensive Southern blotting and PCR analyses. Attempts to purify the recombinant virus were not successful, suggesting that such recombinant BAV2 was helper-dependent. Ten clones containing full-length BAV2 genomes in a pWE15 cosmid vector were constructed. The infectivity of these constructs was tested by using different transfection methods. The BAV2 genomic clones did appear to be infectious only after extended incubation period. This may be due to limitations of various transfection methods tested, or biological differences between virus- and E. co//-derived BAV2 DNA.

Aspergillus flavus infections in Galleria mellonella : a pathogen-host model system for the study of emerging diseases

To study emerging diseases, I employed a model pathogen-host system involving infections of insect larvae with the opportunistic fungus Aspergillus flavus, providing insight into three mechanisms ofpathogen evolution namely de novo mutation, genome decay, and virulence factoracquisition In Chapter 2 as a foundational experiment, A. flavus was serially propagated through insects to study the evolution of an opportunistic pathogen during repeated exposure to a single host. While A. flavus displayed de novo phenotypic alterations, namely decreased saprobic capacity, analysis of genotypic variation in Chapter 3 signified a host-imposed bottleneck on the pathogen population, emphasizing the host's role in shaping pathogen population structure. Described in Chapter 4, the serial passage scheme enabled the isolation of an A. flavus cysteine/methionine auxotroph with characteristics reminiscent of an obligate insect pathogen, suggesting that lost biosynthetic capacity may restrict host range based on nutrient availability and provide selection pressure for further evolution. As outlined in Chapter 6, cysteine/methionine auxotrophy had the pleiotrophic effect of increasing virulence factor production, affording the slow-growing auxotroph with a modified pathogenic strategy such that virulence was not reduced. Moreover in Chapter 7, transformation with a virulence factor from a facultative insect pathogen failed to increase virulence, demonstrating the necessity of an appropriate genetic background for virulence factor acquisition to instigate pathogen evolution.

Biosynthesis of benzyliasoquinoline alkaloids

This research was carried out to obtain a convenient route for the synthesis of [7_ 14C]-p-hydroxy benzaldehyde. Section 1 of the thesis includes a route involving intermediates with protecting groups like benzyl and methyl ethers of the phenols. The benzyl ethers afforded the product in relatively better yield. The overall synthesis involves four steps. Section 2 describes the reactions carried out directly on phenols, and a three step pathway is obtained for the synthesis of p-hydroxy benzaldehyde, which was repeated on labelled compounds to obtain [7_14C]p- hydroxy benzaldehyde. The synthesis involves the reaction of p-bromophenol with Cu14CN to yield [7_ 14C]-p-cyano phenol, which is then reduced to the aldehyde by means of a simple and clean photolysis method. The same route was tried out to get 3,4-dihydroxybenzaldehyde and was found to work equally well for the synthesis of this compound. Section 3 deals with the isolation of labelled alkaloids, corydaline, protopine and reticu1ine from [2-3H,1-14C]-dopamine (3H/ 14C ratio = 4) fed Corydalis solida. 3H/14C ratios in the labelled alkaloids were determined. The uncorrected values showed almost 50% loss of 3H relative to 14C in reticuline, and roughly 75% loss of the 3H relative to 14C in corydaline and protopine.

Characterization of the phosphorylation of thylakoid membrane proteins from cyanobacterium synechococcus sp. PCC 6301 in light state 1 and light state 2

The distribution of excitation energy between the two photosystems (PSII and PSI) of photosynthesis is regulated by the light state transition. Three models have been proposed for the mechanism of the state transition in phycobilisome (PBS) containing organisms, two involving protein phosphorylation. A procedure for the rapid isolation of thylakoid membranes and PBS fractions from the cyanobacterium Synechococcus m. PCC 6301 in light state 1 and light state 2 was developed. The phosphorylation of thylakoid and soluble proteins rapidly isolated from intact cells in state 1 and state 2 was investigated. 77 K fluorescence emission spectra revealed that rapidly isolated thylakoid membranes retained the excitation energy distribution characteristic of intact cells in state 1 and state 2. Phosphoproteins were identified by gel electrophoresis of both thylakoid membrane and phycobilisome fractions isolated from cells labelled with 32p orthophosphate. The results showed very close phosphoprotein patterns for either thylakoid membrane or PBS fractions in state 1 and state 2. These results do not support proposed models for the state transition which required phosphorylation of PBS or thylakoid membrane proteins.

Development of packaging cell lines for rescuing BAV2 viral vectors

The construction of adenovirus vectors for cloning and foreign gene expression requires packaging cell lines that can complement missing viral functions caused by sequence deletions and/or replacement with foreign DNA sequences. In this study, packaging cell lines were designed to provide in trans the missing bovine adenovirus functions, so that recombinant viruses could be generated. Fetal bovine kidney and lUng cells, acquired at the trimester term from a pregnant cow, were tranfected with both digested wild type BAV2 genomic DNA and pCMV-EI. The plasmid pCMV-EI was specifically constructed to express El of BAV2 under the control of the cytomegalovirus enhancer/promoter (CMV). Selection for "true" transformants by continuous passaging showed no success in isolating immortalised cells, since the cells underwent crisis resulting in complete cell death. Moreover, selection for G418 resistance, using the same cells, also did not result in the isolation of an immortalised cell line and the same culture-collapse event was observed. The lack of success in establishing an immortalised cell line from fetal tissue prompted us to transfect a pre-established cell line. We began by transfecting MDBK (Mardin-Dardy bovine kidney) cells with pCMV-El-neo, which contain the bacterial selectable marker neo gene. A series of MDBK-derived cell lines, that constitutively express bovine adenoviral (BAV) early region 1 (El), were then isolated. Cells selected for resistance to the drug G418 were isolated collectively for full characterisation to assess their suitability as packaging cell lines. Individual colonies were isolated by limiting dilution and further tested for El expression and efficiency of DNA uptake. Two cell lines, L-23 and L-24, out of 48 generated foci tested positive for £1 expression using Northern Blot analysis. DNA uptake studies, using both lipofectamine and calcium phosphate methods, were performed to compare these cells, their parental MDBK cells, 8 and the unrelated human 293 cells as a benchmark. The results revealed that the new MDBKderived clones were no more efficient than MDBK cells in the transient expression of transfected DNA and that they were inferior to 293 cells, when using lacZ as the reporter gene. In view of the inherently poor transfection efficiency of MDBK cells and their derivatives, a number of other bovine cells were investigated for their potential as packaging cells. The cell line CCL40 was chosen for its high efficiency in DNA uptake and subsequently transfected with the plasmid vector pCMV El-neo. By selection with the drug G418, two cell lines were isolated, ProCell 1 and ProCell 2. These cell lines were tested for El expression, permissivity to BAV2 and DNA uptake efficiency, revealing a DNA uptake efficiency of 37 % , comparable to that of CCL40. Attempts to rescue BAV2 mutants carrying the lacZ gene in place of £1 or £3 were carried out by co-transfecting wild type viral DNA with either the plasmid pdlElE-Z (which contains BAV2 sequences from 0% to 40.4% with the lacZ gene in place of the £1 region from 1.1% to 8.25%) or with the plasmid pdlE3-5-Z (which contains BAV2 sequences from 64.8% to 100% with the lacZ gene in place of the E3 region from 75.8% to 81.4%). These cotransfections did not result in the generation of a viral mutant. The lack of mutant generation was thought to be caused by the relative inefficiency ofDNA uptake. Consequently, cosBAV2, a cosmid vector carrying the BAV2 genome, was modified to carry the neo reporter gene in place of the £3 region from 75.8% to 81.4%. The use of a single cosmid vector earring the whole genome would eliminate the need for homologous recombination in order to generate a viral vector. Unfortunately, the transfection of cosBAV2- neo also did not result in the generation of a viral mutant. This may have been caused by the size of the £3 deletion, where excess sequences that are essential to the virus' survival might have been deleted. As an extension to this study, the spontaneous E3 deletion, accidently discovered in our viral stock, could be used as site of foreign gene insertion.

Intramolecular carbenoid insertion : reactions of [alpha] -diazoketones derived from benzothienyl, pyrolyl and indolyl alkanoic acids with rhodium (II) acetate

Recent studies have shown that the rhodium (II) acetate decomposition chemistry observed for a-diazoketones tethered to thienyl, furanyl, and benzofuranyl moieties is dependent not only on the nature of the heteroatom but also on the length of the aliphatic tether linking the diazoketone moiety with the aromatic fragment. The present thesis expands on these results and focuses on a-diazoketones tethered to benzothiophenes, pyrroles and indoles by a methylene linker. In the case of benzothiophenes, it was shown that the rhodium catalyst decomposition of I-diazo-4-(3-benzothienyl)-2-butanone (146) and 1-diazo-4-(3benzothienyl)- 2-butanone (152) allow for the isolation of 1,2,3a,3b-tetrahydro-3Hbenzo[ b]cyclopenta[1,3]cyclopropa- [1 ,2-d]thiophen-3-one (147) and 1,2,3a,3btetrahydro- 3H-benzo[b]cyclopenta[1,3]cyclopropa[1,2-d]thiophen-3-one (153). However treatment of 1-diazo-3-(3-Benzothienyl)-2-Propanone (165) with Rh(II) acetate results in the formation of 2,3-Dihydro-1H-benzo[b]cyclopenta[d]thiophen-2-one (159), while 1diazo- 3-(2-Benzothienyl)-2-Propanone with the same condition gives 5,5-bis( 1benzothiophen- 2-ylmethyl)-2(5H)-furanone (166) along with the tricycle 159. The chemistry of the pyrrolyl and the indolyl moieties linked to terminal adiazoketone systems was also investigated. The decomposition of I-diazo-(2-pyrrolyl)-2propanone (173) results in the formation of two products; the N-H insertion product IHpyrrolizin- 2(3H)-one (176) and the alkylation product 4,6-dihydrocyclopenta[b]pyrrol5( 1 H)-one (180). When 1-Diazo-3-(3-indoly)-3-propanone (194) is treated with catalytic amount of Rh (II) 3,4-dihydrocyclopenta[b]indol-2(1H)-one (193) is isolated quantitatively. The later reaction when monitored using IH NMR the intermediate 200 can be seen whose structure was confirmed by the comparison to series of model compounds. The mechanisms underlying these reactions as well as their synthetic utility is discussed.

Studies of nucleophilic attack on tris (pentafluorophenyl) phosphine and its oxides

The reaction of tris(pentafluorophenyl)phosphine [5] with the nucleophiles dimethyl formamide (DMF), hexamethylphosphoric triamide (HMPA), diethyl formamide (DEF), hexaethylphosphoric triamide (HEPA), hydrazine, N,N-dimethyl hydrazine (in presence and/or absence of KF), phenylhydrazine, ammonium hydroxide, formamide, aniline, sodium hydrogen sulfide, and hexaethylphosphorous triamide was investigated. The reaction of [5] with DMF and HMPA gave the same product, namely tris-[4-(N,N-dimethylamino)-2,3,5,6-tetrafluorophenyl]phosphine [12] but in higher yield in the case of HMPA. Compound (5] also reacted with DEF to give tris[4-(N,N-diethylamino)-2,3,5,6-tetrafluorophenyl] phosphine [14]. When [51 was treated with HEPA, it gave a mixture of bis(pentafluorophe~yl)-(N,N-diethylamino-tetrafluorophenyl)phosphine, pentafluorophenyl-bis-(N,N-diethylamino-tetrafluorophenyl)phosphine and tris (N,N-diethylamino-tetrafluorophenyl)phosphine. Treatment of [5] with aqueeus hydrazine solution in excess ethanol gave tris(4-hydrazo-2,3,4,6-tetrafluorophenyl)phosphine [1s1 in high yield while reaction with aqueous hydrazine led to C-P cleavage and production of tetrafluorophenyl hydrazine. With N,N-dimethyl hydrazine, [5] gave tris(4-N,N-dimethylhydrazine-2,3,5,6-tetrafluorophenyl) phosphine {20j. The latter could be obtained in higher yield and shorter reaction time, by the addition of KF. The reaction of compound {51 with phenylhydrazine in THF gave bis(pentafluorophe~yl)-4-S-phenylhydrazino- 2,3,5,6-tetrafluorophenyl phosphine [22] in low yield. Reaction of [5] with ammonium hydroxide in THF at high pressure in the presence of KF gave tris-~4-amino-2,3,5,6-tetrafluorophenyl)phosphine [25]. Similarly, formamide led to a mixture of (C6F4NHZ)3P, (C6F4NHZ)ZPC6FS, (C6F4NHZ)ZPC6F4NHCHO, and C6F4NHZP(C6Fs)(C6F4NHCHO). When [5] was treated with aniline, a mixture of mono-, di-, and tri-substituted products was obtained. Sodium hydrogen sulfide in ethylene glycol/ pyridine led to C-P cleavage and the isolation of pentafluorobenzene and tetrafluorothiophenol. Reaction of [5] and its oxide [35] with different alkoxides in the corresponding alcohols led mainly to C-P bond cleavage products, with the exception of one case where sodium methoxide was used in ether, and which led to tris-(4-methoxy-2,3,9,6-tetrafluorophenyl)phosphine [37]. On the basis of various spectroscopic data, it was concluded that the para position in compound [5] was generally the favoured site of attack.

An exploratory study for the discovery of non-invasive hepatocellular carcinoma biomarkers among high-risk hepatitis C virus infected patients

Hepatocellular Carcinoma (HCC) is a major healthcare problem, representing the third most common cause of cancer-related mortality worldwide. Chronic infections with Hepatitis B virus (HBV) and/or Hepatitis C virus (HCV) are the major risk factors for the development of HCC. The incidence of HBV -associated HCC is in decline as a result of an effective HBV vaccine; however, since an equally effective HCV vaccine has not yet been developed, there are 130 million HCV infected patients worldwide who are at a high-risk for developing HCC. Because reliable parameters and/or tools for the early detection of HCC among high-risk individuals are severely lacking, HCC patients are always diagnosed at a late stage where surgical solutions or effective treatment are not possible. Using urine as a non-invasive sample source, two different approaches (proteomic-based and genomic-based approaches) were pursued with the common goal of discovering potential biomarker candidates for the early detection of HCC among high-risk chronic HCV infected patients. Urine was collected from 106 HCV infected Egyptian patients, 32 of whom had already developed HCC and 74 patients who were diagnosed as HCC-free at the time of initial sample collection. In addition to these patients, urine samples were also collected from 12 healthy control individuals. Total urinary proteins, Trans-renal nucleic acid (Tr-NA) and microRNA (miRNA) were isolated from urine using novel methodologies and silicon carbide-loaded spin columns. In the first, "proteomic-based", approach, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to identify potential candidates from pooled urine samples. This was followed by validating relative expression levels of proteins present in urine among all the patients using quantitative real time-PCR (qRT-PCR). This approach revealed that significant over-expression of three proteins: DJ-1, Chromatin Assembly Factor-1 (CAF-1) and 11 Moemen Abdalla HCC Biomarkers Heat Shock Protein 60 (HSP60), were characteristic events among HCC-post HCV infected patients. As a single-based HCC biomarker, CAF-1 over-expression identified HCC among HCV infected patients with a specificity of 90%, sensitivity of 66% and with an overall diagnostic accuracy of 78%. Moreover, the CAF-lIHSP60 tandem identified HCC among HCV infected patients with a specificity of 92%, sensitivity of 61 % and with an overall diagnostic accuracy of 77%. In the second genomic-based approach, two different approaches were processed. The first approach was the miRNA-based approach. The expression levels of miRNAs isolated from urine were studied using the Illumina MicroRNA Expression Profiling Assay. This was followed by qRT-PCR-based validation of deregulated expression of identified miRNA candidates among all the patients. This approach shed the light on the deregulated expression of a number of miRNAs, which may have a role in either the development of HCC among HCV infected patients (i.e. miR-640, miR-765, miR-200a, miR-521 and miR-520) or may allow for a better understanding of the viral-host interaction (miR-152, miR-486, miR-219, miR452, miR-425, miR-154 and miR-31). Moreover, the deregulated expression of both miR-618 and miR-650 appeared to be a common event among HCC-post HCV infected patients. The results of the search for putative targets of these two miRNA suggested that miR-618 may be a potent oncogene, as it targets the tumor-suppressor gene Low density lipoprotein-related protein 12 (LPR12), while miR-650 may be a potent tumor-suppressor gene, as it is supposed to downregulate the TNF receptor-associated factor-4 (TRAF4) oncogene. The specificity of miR-618 and miR-650 deregulated expression patterns for the early detection of HCC among HCV infected patients was 68% and 58%, respectively, whereas the sensitivity was 64% and 72%, respectively. When the deregulated expression of both miRNAs was combined as a tandem biomarker, the specificity and the sensitivity were 75% and 58% respectively. 111 Moemen Abdalla HCC Biomarkers In the second, "Trans-renal nucleic acid-based", approach, the urinary apoptotic nucleic acid (uaNA) levels of 70ng/mL or more were found to be a good predictor of HCC among chronic HCV infected patients. The specificity and the sensitivity of this diagnostic approach were 76% and 86%, respectively, with an overall diagnostic value of 81 %. The uaNA levels positively correlated to HCC disease progression as monitored by epigenetic changes of a panel of eight tumor-suppressor genes (TSGs) using methylation-sensitive PCR. Moreover, the pairing of high uaNA levels (:::: 70 ng/mL) and CAF-1 over-expreSSIOn produced a highly specific (l 00%) multiple-based HCC biomarker with an acceptable sensitivity of 64%, and with a diagnostic accuracy of 82%. In comparison to the previous pairing, the uaNA levels (:::: 70 ng/mL) in tandem with HSP60 over-expression was less specific (89%) but highly sensitive (72%), resulting in a diagnostic accuracy of 64%. The specificities of miR-650 deregulated expression in combination with either high uaNA content or HSP 60 over-expression were 82% and 79%, respectively, whereas, the sensitivities of these combinations were 64% and 58%, respectively. The potential biomarkers identified in this study compare favorably with the diagnostic accuracy of the a-fetoprotein levels test, which has a specificity of 75%, sensitivity of 68% and an overall diagnostic accuracy of 70%. Here we present an intriguing study which shows the significance of using urine as a noninvasive sample source for the identification of promising HCC biomarkers. We have also introduced new techniques for the isolation of different urinary macromolecules, especially miRNA, from urine. Furthermore, we strongly recommend the potential biomarkers indentified in this study as focal points of any future research on HCC diagnosis. A larger testing pool will determine if their use is practical for mass population screening. This explorative study identified potential targets that merit further investigation for the development of diagnostically accurate biomarkers isolated from 1-2 mL urine samples that were acquired in a non-invasive manner.

Enantiodivergent chemoenzymatic synthesis of Balanol and approaches to the synthesis of (+)-Codine

The present thesis reviews the development of a formal enantiodivergent synthesis of the (+)- and (-)-isomers of balanol. This approach commences from a cis-dihydrodiol derived from the enzymatic dihydroxylation of bromobenzene. The stereochemistry of the diol is used to direct the synthesis of two different aziridines, each used in the formal synthesis of one enantiomer of balanol. Also described are several enantioselective approaches to (+ )-codeine. Each strategy begins with the enzymatic dihydroxylation of p-bromoethylbenzene and involves a Mitsunobu inversion and intramolecular Heck reaction as key steps.

Chemoenzymatic synthesis of amaryllidaceae alkaloids and their C-1 analogues : symmetry based approach to total synthesis of thebaine

Described herein is the chemoenzymatic total synthesis of several Amaryllidaceae constituents and their unnatural C-I analogues. A new approach to pancratistatin and related compounds will be discussed along with the completed total synthesis of 7 -deoxypancratistatin and trans-dihydrolycoricidine. Evaluation of all new C-l analogues as cancer cell growth inhibitory agents is described. The enzymatic oxidation of dibromobenzenes by Escherichia coli 1M 109 (pDTG60 1) is presented along with conversion of their metabolites to (-)-conduritol E. Investigation into the steric and functional factors governing the enzymatic dihydroxylation of various benzoates by the same organism is also discussed. The synthetic utility of these metabolites is demonstrated through their conversion to pseudo-sugars, aminocyclitols, and complex bicyclic ring systems. The current work on the total synthesis of some morphine alkaloids is also presented. Highlighted will be the synthesis of several model systems related to the efficient total synthesis of thebaine.

Molybdenum (IV) imido silylamido and hydride complexes : stoichiometric and catalytic reactivity, mechanistic aspects of hydrosilation reactions

This thesis describes the synthesis, structural studies, and stoichiometric and catalytic reactivity of novel Mo(IV) imido silylamide (R'N)Mo(R2)(173_RIN-SiR32-H)(PMe3)n (1: Rl = tBu, Ar', Ar; R2 = Cl; R32 = Me2, MePh, MeCl, Ph2, HPh; n = 2; 2: R' = Ar, R2 = SiH2Ph, n = 1) and hydride complexes (ArN)Mo(H)(R)(PMe3)3 (R = Cl (3), SiH2Ph (4». Compounds of type 1 were generated from (R'N)Mo(PMe3)n(L) (5: R' = tBu, Ar', Ar; L = PMe3, r/- C2H4) and chlorohydrosilanes by the imido/silane coupling approach, recently discovered in our group. The mechanism of the reaction of 5 with HSiCh to give (ArN)MoClz(PMe3)3 (8) was studied by VT NMR, which revealed the intermediacy of (ArN)MCh(172 -ArN=SiHCl)(PMe3)z (9). The imido/silyl coupling methodology was transferred to the reactions of 5 with chlorine-free hydrosilanes. This approach allowed for the isolation of a novel ,B-agostic compound (ArN)Mo(SiHzPh)(173 -NAr-SiHPhH)(PMe3) (10). The latter was found to be active in a variety of hydrosilation processes, including the rare monoaddition of PhSiH3 to benzonitrile. Stoichiometric reactions of 11 with unsaturated compounds appear to proceed via the silanimine intermediate (ArN)M(17z-ArN=SiHPh)(PMe3) (12) and, in the case of olefins and nitriles, give products of Si-C coupling, such as (ArN)Mo(R)(173 -NAr-SiHPh-CH=CHR')(PMe3) (13: R = Et, R' = H; 14: R = H, R' = Ph) and (ArN)Mo(172-NAr-SiHPh-CHR=N)(PMe3) (15). Compound 13 was also subjected to catalysis showing much improved activity in the hydrosilation of carbonyls and alkenes. Hydride complexes 3 and 4 were prepared starting from (ArN)MoCh(PMe3)3 (8). Both hydride species catalyze a diversity of hydrosilation processes that proceed via initial substrate activation but not silane addition. The proposed mechanism is supported by stoichiometric reactions of 3 and 4, kinetic NMR studies, and DFf calculations for the hydrosilation of benzaldehyde and acetone mediated by 4.

Spectral Reflectance Characteristics of Kimberlite Indicator Minerals and Other Selected Mineral Grains

High chromium content in kimberlite indicator minerals such as pyrope garnet and diopside is often correlated with the presence of diamonds. In this study, kimberlite indicator minerals were examined using visible light reflectance spectroscopy to determine if chromium content can be correlated with spectral absorption features. The depth of absorption features in the visible spectral region were correlated with the molecular percentage of chromium and other first series transition metal elements obtained by electron microprobe data. In the visible part of the spectrum, chromium is evident by 3 absorption features in the pyrope reflectance spectrum; one isolated and narrow feature at the wavelength 689 nm was used to correlate with the chromium mol %. The isolation of this feature in the pyrope spectra is advantageous since it is not directly affected by other proximal absorption bands that could be caused by other transition metals. Analysis of the feature indicates that as grain volume increases the depth of the absorption feature will also increase. Clustering grain volumes into fractions yields better correlation between absorption depth and mol % chromium. Other types of garnet (almandine, grossular, spessartine) and kimberlite indicator minerals (olivine, diopside, chromite, ilmenite) were analyzed to determine if other absorption features could be used to predict the proportion of specific transition metal elements. Diopside in particular illustrates the same isolated chromium absorption feature as pyrope and may indicate mol percent but needs further study with larger sample sets.

Informing the structure of subjective well-being through examining changes in life satisfaction, positive affect, and negative affect

Subjective well-being (SWB) refers to how individuals evaluate and experience their lives in positive ways, and encompasses global judgments of life satisfaction (LS), as well as the frequency of positive and negative affect (PA and NA, respectively) in one’s life. To inform the current ambiguity concerning the structure of SWB, the aim of this Masters thesis was to evaluate the structure of SWB based on whether the three components of SWB change together or independently naturally, over time and following experimental manipulation. In Study 1, associations among changes in LS, PA, and NA were evaluated using a longitudinal approach tracking natural changes in the components over periods of three months and three years. Results indicated that change in one component was related to change in the other two components. In Study 2, an experimental design was used to manipulate each SWB component individually, and evaluate changes in all three components following each manipulation. Manipulation materials designed to target LS only were effective (i.e., led to heightened focus on LS, and not PA or NA) and created an increase in both LS and PA. Manipulation materials designed to target PA and NA only were not effective (i.e., led to heightened focus on the target component, as well as on LS). Furthermore, in both studies the strength of an individual’s SWB (assessed in terms of structural consistency and structural ambivalence in Study 1 and Study 2, along with subjective ambivalence in Study 2) did not consistently moderate the degree to which changes in the components were associated with one another. Together, these findings indicate that the structure of SWB may be complex and dynamic, rather than static. Alternatively, the components of SWB may not be easily manipulated in isolation of one another. Implications for existing structural models of SWB are discussed.

Chemoenzymatic Total Synthesis of Morphine alkaloids: Synthesis of Dihydrocodeine and Hydrocodone via a Double Claisen Strategy and ent-Hydromorphone via an Oxidative Dearomatization/intramolecular [4+2] Cycloaddition

This thesis describes the chemoenzymatic synthesis of three morphine alkaloids. The total synthesis of dihydrocodeine and hydrocodone was accomplished starting from bromobenzene in 16 and 17 steps, respectively. The key steps included a microbial oxidation of bromobenzene by E. coli JM109 (pDTG601A), a Kazmaier-Claisen rearrangement of glycinate ester to generate C-9 and C-14 stereo centers, a Johnson-Claisen rearrangement to set the C-13 quaternary center, and a C-10/C-11 ring closure via a Friedel-Crafts reaction. In addition, the total synthesis of ent-hydromorphone starting from β-bromoethylbenzene in 12 steps is also described. The key reactions included the enzymatic dihydroxylation of β-bromoethylbenzene to the corresponding cis-cyclohexadienediol, a Mitsunobu reaction, and an oxidative dearomatization followed by an intramolecular [4+2] cycloaddition.

Systematic analysis of protein complexes involved in the human RNA polymerase II machinery

La transcription, la maturation d’ARN, et le remodelage de la chromatine sont tous des processus centraux dans l'interprétation de l'information contenue dans l’ADN. Bien que beaucoup de complexes de protéines formant la machinerie cellulaire de transcription aient été étudiés, plusieurs restent encore à identifier et caractériser. En utilisant une approche protéomique, notre laboratoire a purifié plusieurs composantes de la machinerie de transcription de l’ARNPII humaine par double chromatographie d’affinité "TAP". Cette procédure permet l'isolement de complexes protéiques comme ils existent vraisemblablement in vivo dans les cellules mammifères, et l'identification de partenaires d'interactions par spectrométrie de masse. Les interactions protéiques qui sont validées bioinformatiquement, sont choisies et utilisées pour cartographier un réseau connectant plusieurs composantes de la machinerie transcriptionnelle. En appliquant cette procédure, notre laboratoire a identifié, pour la première fois, un groupe de protéines, qui interagit physiquement et fonctionnellement avec l’ARNPII humaine. Les propriétés de ces protéines suggèrent un rôle dans l'assemblage de complexes à plusieurs sous-unités, comme les protéines d'échafaudage et chaperonnes. L'objectif de mon projet était de continuer la caractérisation du réseau de complexes protéiques impliquant les facteurs de transcription. Huit nouveaux partenaires de l’ARNPII (PIH1D1, GPN3, WDR92, PFDN2, KIAA0406, PDRG1, CCT4 et CCT5) ont été purifiés par la méthode TAP, et la spectrométrie de masse a permis d’identifier de nouvelles interactions. Au cours des années, l’analyse par notre laboratoire des mécanismes de la transcription a contribué à apporter de nouvelles connaissances et à mieux comprendre son fonctionnement. Cette connaissance est essentielle au développement de médicaments qui cibleront les mécanismes de la transcription.