Supramolecular chemistry and crystal engineering seek to control molecular packing in the solid state to influence the physical and chemical properties of crystalline solid materials. A goal of supramolecular chemistry that seeks to control molecular packing in the solid state focuses on exploiting non-covalent interactions to assemble molecules into desirable arrangements. Strategies implemented to control molecular packing rely on strong, directional interactions such as hydrogen bonding, halogen bonding, and metal coordination to direct localized arrangement of molecules in solids. In this context, small molecules can be used as linear templates in co-crystals to assemble reactive alkenes into specific geometries allowing reactivity in the solid state. A linear template method has been used to achieve [2+2] photocycloadditions of discrete assemblies containing alkenes to afford cyclobutanes in high stereospecificity and in quantitative yield. Herein, we describe the use of a nonlinear template, in the form of 1,4-butynediol (1,4-bd), to pre-organize alkenes in the solid state. The nonlinear template of 1,4-bd hydrogen-bonds to the alkene 1,2-bis(N-pyridyl)ethene (where N = 3 or 4) to form 1D hydrogen-bonded polymers. The hydrogen-bonded polymer chains form infinite stacks which are sustained by C-H···O interactions occurring between polymer chains. The stacked alkenes undergo a UV-induced [2+2] photocycloaddition to produce rctt-tetrakis(N-pyridyl)cyclobutane photoproducts (where N = 3 and 4) in non-quantitative yields. The yield of the photoreaction is increased to nearly quantitative by applying a supramolecular catalysis approach with the 1,4-bd template. Functional groups on reactant molecules can compete via non-covalent interactions with templates employed for the self-assembly process. One method to inhibit competition between functional groups involves chemically modifying a functional group employing a supramolecular protecting group. Here, we describe an acetyl supramolecular protecting group approach employed to mask alkenes containing phenolic and pyridyl functional groups. The acetyl protecting group prevents the phenolic substituents of the targeted alkene from participating in non-covalent interactions employed for the template-mediated self-assembly process. Thus, a cyclobutane molecule was obtained using the novel acetyl supramolecular protecting group strategy applied to a solid-state [2+2] photodimerization that affords a head-to-head cyclobutane. After deprotection, the resulting cyclobutane possessed tetrahedrally-disposed cis-hydrogen-bond-donor and cis-hydrogen-bond-acceptor groups. Thus, a purely organic three-dimensional hydrogen-bonded network based on a rare Michael O'Keeffe (mok) topology was constructed using an organic molecule synthesized in the organic solid state. The phenolic substituents of the cyclobutane adopt different orientations (syn-, anti-, and gauche-) to conform to the structural requirements of the mok net. A challenge surrounding template-directed solid-state reactivity requires alkenes to be lined with functional groups that coordinate (or bind through other non-covalent interactions) to the template. Herein, we describe a dual approach of supramolecular assistance to covalent bond formation that utilizes a combination of imine and metal-organic chemistry to generate cyclobutanes lined with aldehyde groups. Specifically, dynamic imine chemistry was implemented to install a temporary recognition site on an aldehyde-containing alkene of cinnamaldehyde for a template-directed [2+2] photocycloaddition in the solid state. The resulting modified alkene aligns using Ag(I) ions into desirable arrangements for the covalent-bond-forming [2+2] photocycloaddition. The result is a 1D coordination polymer undergoes a UV-induced, regio-controlled [2+2] photocycloaddition in the solid state. The photoreaction proceeds stereospecifically with quantitative yield of the corresponding aldehyde-functionalized photodimer, α-truxilaldehyde. Additionally, we investigate the influence of the Ag(I) counterions on the assembly of imine containing alkenes to generate reactive assemblies for the purpose of producing aldehyde-containing cyclobutanes. This dissertation also encompasses research pertaining to pharmaceutical solids and mechanical properties of organic molecular crystals. Specifically, we describe the discovery of two polymorphic co-crystals containing acetylsalicylic acid (aspirin) combined with 4,4’-bipyridine. The initial discovery of the form I polymorph was aided by mechanical dry-grinding, while an additional form II polymorph was revealed by rapid cooling in ethanol. The polymorphs differ by relative twists of carboxylic acid groups of the aspirin molecules and of the pyridyl rings of 4,4’-bipyridine. Additionally, the form I polymorph contains aspirin molecules that are linked via discrete catemeric methyl C-H···O interactions, while the form II polymorph is linked via both infinite methyl C-H···O catemers and centrosymmetric dimers. These results demonstrate the importance of dry mechanical grinding for the discovery of pharmaceutical co-crystals and polymorphs.

The study of natural variation is a principle component of biology. One process that affects levels of natural variation is meiotic recombination—the process by which homologous chromosomes break and interchange genetic information with one another during the formation of gametes. Surprisingly, this factor that shapes levels of natural variation across the genome itself presents with a great deal of variation. That variation manifests itself at many levels: within genomes, between individual organisms, across populations, and among species. The factors and mechanisms responsible for the non-random patterning of recombination events across the genome remain particularly elusive in most cases. Herein, I utilize a combination of bioinformatic and molecular genetic approaches to better explain recombination patterning. I explore several factors that are now known to contribute to the distribution of recombination events across genomes. In particular, I demonstrate that transcriptional activity during meiosis is associated with, and partially predictive of crossing over events in Drosophila melanogaster. Additionally, I present a model which is capable of accounting for approximately 40% of the variation in crossover rates in Drosophila based on the localization of several previously identified DNA motifs. Lastly, I present preliminary data describing how recombination patterns are altered under naturally stressful conditions, a key insight that is necessary for uniting our findings at one level of variation with the many others. These findings support a multifactorial model for crossover distribution that includes both genetic and epigenetic factors and will further progress the field in developing a comprehensive understanding of recombination localization.

Selection of HIV-1 variants resistant to antiretroviral therapy is well documented. However, the selection in vivo of HIV-1 mutant species that can escape host immune system HLA class I restricted cytotoxic T-lymphocyte responses has, to date, only been documented in a few individuals and its clinical importance is not well understood. This thesis analyses the observed diversity of the HIV-1 reverse transcriptase protein in a well characterised, stable, HLA-diverse cohort of HIV-1 infected patients with over two thousand patient-years of observation. The results show that HIV-1 polymorphism is selected within functional constraints and is associated with specific HLA class I alleles. Furthermore, these associations significantly cluster along the sequence and tend to occur within known corresponding HLA-restricted epitopes. Absence of polymorphism is also HLA-specific and more often seen with common HLA alleles. Knowledge of HLA specific viral polymorphisms can be used to model an individual’s viral load from their HLA type and viral sequence. These results suggest that cytotoxic T-lymphocyte escape mutation in HIV-1 is critical to the host at an individual and population level as well as to short and long term viral evolution. This work provides new insights into viral-host interactions and has clinical implications for individualisation of HIV-1 therapy and vaccine design.

Spectroscopy is increasingly used to investigate and monitor the solid state forms of pharmaceutical materials and products. Spectroscopy�s speed, nondestructive sampling, compatibility with fibre optics and safety also make it attractive for in-line monitoring. In this thesis, the spectroscopic techniques Fourier transform Raman spectroscopy, terahertz pulsed spectroscopy and second harmonic generation were used to characterise and quantify polymorphism and crystallinity of pharmaceutical compounds. Where possible, the multivariate analysis technique partial least squares was used for quantitative analysis. Fourier transform Raman spectroscopy detects polarisability changes mainly associated with molecular vibrations. Terahertz pulsed spectroscopy is a new spectroscopic technique that operates between the infrared and microwave regions of the electromagnetic spectrum and detects dipole moment changes mainly associated with crystalline phonon vibrations in the solid state. Second harmonic generation is a nonlinear optical phenomenon that depends on the dipole moment in crystals and crystal symmetry. Several materials capable of existing in different solid state forms were used. FT-Raman spectroscopy was able to differentiate carbamazepine forms I and III, enalapril maleate forms I and II and γ-crystalline and amorphous indomethacin. Combined with partial least squares the technique could quantify binary mixtures of CBZ forms I and III with a limit of detection as low as 1%, and mixtures of enalapril maleate with a limit of detection of as low as 2%. Terahertz pulsed spectroscopy obtained very different spectra for carbamazepine forms I and III, enalapril maleate forms I and II, γ-crystalline and amorphous indomethacin, crystalline and supercooled thermotropic liquid crystalline fenoprofen calcium, three forms of lactose, and five forms of sulphathiazole. At present the modes in the spectra cannot be attributed to specific phonon modes. Quantitation of binary mixtures of different forms of a compound using partial least squares analysis usually resulted in a limit of detection of about 1%. Second harmonic generation was used to quantify binary mixtures of different forms of enalapril maleate and lactose, as well as binary mixtures of enalapril maleate form II and polyvinylpyrrolidone. A quantitative relationship was present for each of the mixtures, however the limits of detection were usually above 10%. The high value is probably due to the machine being a prototype and univariate analysis associated with a single output variable. Future improvements to the apparatus and measurement parameters are likely to reduce the limits of detection. Ranitidine hydrochloride polymorphs could also be differentiated using second harmonic generation, however γ-crystalline and amorphous indomethacin and forms I and III of carbamazepine could not. The methods used in this thesis were successfully used for qualitative and quantitative analysis of polymorphism and crystallinity of pharmaceutical compounds. TPS and SHG are useful additions to the range of experimental techniques that can be used to investigate and monitor properties of pharmaceutical solids.

<p>Leber´s hereditary optic neuropathy (LHON), a disease affecting vision, is caused by several point mutations in mitochondrial DNA. Mutations leading to a defect NADH ubiquinone oxidoreductase protein will affect the respiratory chain and cause a disturbed ATP production. It is still unknown why this defect leads to the degeneration of retinal ganglion cells and cells in the opticus nerve as well as demyelination of axons in these areas. Analysis of mitochondrial DNA is an important tool in the diagnosis of the disease. At the present time analysis is based on cleavage by restriction enzymes, which only detects two of the most frequent mutations: m.3460G>A and m.11778G>A. This is far too few considering that more than 30 mutations are known to be associated with LHON. Therefore a new analysis method is requested. Here we describe a method based on the sequencing of the mitochondrial genes MT-ND1, MT-ND4 and MT-ND6, which will detect more than 15 different point mutations associated with the disease. To validate the analysis, DNA from 31 patients with LHON symptoms were sequenced; of these 10 were found to be positive for a LHON mutation. This result indicates that the sequencing analysis will be more effective in diagnosis of LHON than restriction enzymes.</p> / <p>Lebers hereditära optikus neuropati (LHON) är en sjukdom som beror på genetiska förändringar i arvsmassan som leder till att cellens energiomsättning rubbas. Detta gör att nervceller i ögat och synnerven bryts ned vilket leder till en synnedsättning. En patient som drabbas av LHON har inga symptom fram till dess att synen börjar försämras. Sjukdomsförloppet går snabbt och på bara några veckor är patienten ofta helt blind. Diagnostik av LHON idag utgörs av flera undersökningar av öga och synfält. Diagnosen bekräftas av en analys av arvsmassan som finns i mitokondrien, cellens energifabrik. Här beskriver vi en ny förbättrad analysmetod baserad på DNA sekvensering, dvs. bestämning av baserna i mitokondriella arvsmassan. För att utvärdera analysen har vi undersökt 31 patienter med misstänkt LHON - av dessa visade sig 10 bära på en sjuklig förändring. Resultatet visar att sekvensering med fördel kan ersätta den tidigare analysmetoden då fler sjukliga förändringar kan påvisas och utförandet av analysen är mer användarvänligt.</p>

<p>In this thesis we attempted to elicit patterns of gene expression that influence phenotype, and that may also have been altered by thousands of years of domestication and selection, between red junglefowl and White Leghorn chickens. Red junglefowl are the wild ancestor to all domesticated chickens, and poultry in general are highly valued as a research animal and food resource. The project was also begun in order to complement an earlier study of an intercross between White Leghorn and red junglefowl, which identified several regions that were linked with phenotypic differences between the two birds.</p><p>We began by creating our own cDNA microarray via generating four cDNA libraries from red junglefowl/White Leghorn brain and testis. We generated 12,549 unique transcripts. This included 400 new putative transcripts specific to chickens, and 180 transcripts that were not found in any other database. When investigating polymorphisms between White Leghorn and red junglefowl we found a SNP rate of 1.9/kb coding region, and a synonymous and non-synonymous percentage for these SNPs of 80 and 20% respectively.</p><p>In the last two studies we used the cDNA microarray to measure gene expression differences between White Leghorn and red junglefowl in both hypothalamus/thalamus and liver. We found that there appears to be a significant number of genes down-regulated in White Leghorn hypothalamus/thalamus, plus an over-representation of up-regulated genes from well-known pathways, as compared with red junglefowl. We hypothesize that domestication/selection may be connected with this characteristic. We also found that the p-arm of chicken chromosome 4, which is an ancestral microchromosome, was over represented with differentially expressed genes in hypothalamus/thalamus. A number of differentially expressed genes are shared between the two tissues, and these genes are expressed in same manner between red junglefowl and White Leghorn.</p>

A primary goal of population genetics is to identify the role of microevolutionary forces in producing observed patterns of molecular and phenotypic variation. I conducted four studies in the northern leopard frog, Rana pipiens, to determine just how mutation, migration, genetic drift, and selection influenced, genetic structure of mitochondrial DNA (mtDNA), nuclear DNA, and a single locus polymorphism that determines dorsal coloration. In the first study, I surveyed the literature concerning color and pattern polymorphisms in anurans. I conclude that anuran polymorphisms remain a rich but largely unexploited system for studying the evolution of phenotypic variation in nature. In the second study, I compared mitochondrial DNA variation from 35 populations distributed across the species' range. A phylogenetic analysis indicated R. pipiens is split into two deeply divergent mtDNA groups, a western group and an eastern group. Phylogeographic and demographic analyses indicated that although restricted gene flow with isolation by distance explained the majority of the processes influencing current genetic structure, population bottlenecks and expansions also played an important role. In the third study, I investigated mtDNA and microsatellite variation in Pacific Northwest populations of R. pipiens, where a recent range contraction had occurred. I found that peripheral populations had reduced levels of genetic variation compared to more interior populations. Moreover, I found that historic samples from peripheral population already had reduced levels of genetic variation. Therefore, low diversity in the remnant populations could not be ascribed to the recent range contraction. In the fourth study, I compared genetic structure from a suite of putatively neutral molecular markers with that derived from the color polymorphism locus. Genetic structure at the color locus, assessed both spatially and temporally, was indistinguishable from structure at neutral loci. This study exemplifies the importance of investigating for evidence of selective maintenance before studies attempt to measure the selective mechanisms maintaining a polymorphism. Overall, my research helps to elucidate how biogeographic and microevolutionary forces influence a wide-spread North American species, R. pipiens. / Graduation date: 2004

Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2007.

Males of the Mexican lizard Sceloporus minor (Phrynosomatidae) exhibit striking variation in dorsal coloration, both within and among populations, which may have arisen by sexual selection. The possible significance of this trait was investigated through a combination of observational and experimental approaches. This research revealed that males in one population (La Manzana) in NW Hidalgo exhibit three discrete color morphs (blue, yellow, red) each characterized by morphological, physiological and behavioral differences. Furthermore, these morphs can be identified by an objective approach to color assessment (spectroradiometry). In addition, males in a second population (Escalerillas) from SE San Luis Potosí were also found to occur in at least two color morphs (yellow and red), suggesting that color polymorphism may be general in this species. The hypothesis of sensory exploitation by male contest competition was tested for S. minor from Escalerillas; however, no support for this hypothesis was found. Overall, results from this study are consistent with the hypothesis of alternative reproductive tactics in S. minor.

The human cytomegalovirus (HCMV) viral chemokine gene, UL146, shows a high degree of variability in clinical isolates. The UL146-produced viral chemokine, vCXCL-1, has homology to CXC chemokines and is predicted to be an immune modulator that may contribute to the pathogenesis of HCMV infections. In the analysis of clinical isolates from congenitally infected infants, we found 11 distinct vCXCL-1 clades. Although the four cysteine residues that create two disulfide bonds providing the essential structure for CXC chemokines,are conserved, the N-loop region, which is important for receptor binding and activation, was hypervariable. One clade also contained a modified glutamic acid-leucine-arginine (ELR) motif (asparagine-glycine-arginine / NGR), which regulates binding to CXCR1 and CXCR2 receptors. Based on this sequence information, we hypothesize that these proteins differentially activate neutrophils, which may have a role in HCMV pathogenesis. To address these functional differences, we produced representative vCXCL-1 proteins from each of the 11 clades using a baculovirus protein expression system. Using competition binding assays, we have examined their binding affinities to either CXCR1 or CXCR2 expressed on HEK293 cells. All vCXCL-1s bound to CXCR2 with different binding affinities. Interestingly, only three vCXCL-1s bound to CXCR1 while the others demonstrated did not. We analyzed functional differences between the vCXCL-1s in calcium mobilization, adhesion molecule induction, and chemotaxis on human peripheral blood neutrophils (PBNs). Although the binding affinities to CXCR2 and/or CXCR1 were variable, all vCXCL-1s were capable of inducing intracellular calcium mobilization in PBNs and upregulating adhesion molecules on the surface of PBNs to similar levels as human CXCL1. However, the potency of the vCXCL-1s in the chemotaxis of neutrophils varied and was affinity independent. We also examined secondary chemokine production upon vCXCL-1 treatment on neutrophil-like HL60 T2 cells using real-time PCR. The results showed CCL22 induction was affinity dependent. Taken together, these results provide insights into the potential role of vCXCL-1 in HCMV pathogenesis and how the variability in these chemokines can affect neutrophil function.