X-ray crystallography is an important analytical method for the characterisation of materials in the solid state. During the last decade, it has become important as a tool in the new field of photocrystallography. This combines both crystallography and photochemistry and is used to monitor the formation of light-induced metastable and transient species, so that structural information can be obtained during the change of a material. This is an important area of research as solid state chemistry can display new phenomena and reveal properties that are not possible in solution. Chapter 1 of this thesis commences with a brief introduction to the different methods used to achieve and measure the excitation within crystalline compounds, while Chapter 2 contains an introduction into diffraction methods. In Chapters 3-5 new photocrystallographic studies were performed on two series of compounds. The first one consists of a systematic study on metal complexes with different pyridylethylene ligands. The focus was to align complexes in the solid state so that they can undergo photo induced cycloaddition reactions. These solid state reactions are important as they present “green synthetic chemistry”. The second study involves the photoinduced linkage isomerisation of [Ni(L)2(NO2)2] complexes. Structural characterisation shows that the NO2 ligands change their coordination mode when irradiated with light of different wavelengths. Conditions for the metastable isomerisation were optimised by altering temperature and wavelengths. In Chapters 6 and 7 a systematic study of structural changes in a series of lanthanide complexes and their use as triboluminescence materials, is described. The proposed mechanism of triboluminescence for these complexes is discussed. To summarise, in this thesis, systematic investigations have been carried out in different aspects of crystallography using appropriate series of compounds. The nature of and the conditions required for the change to occur within the solid state have been established.

Single nucleotide polymorphisms (SNPs) are single base variations among groups of individuals. In order to study their properties in fine gene mapping, I considered their occurrence as transitions and transversions. The aim of the study was to classify each polymorphism depending upon whether it was a transition or transversion and to calculate the proportions of transitions and transversions in the SNP data from the public databases. This ratio was found to be 2.35 for data from the Whitehead Institute for Genome Research database, 2.003 from the Genome Database, and 2.086 from the SNP Consortium database. These results indicate that the ratio of the numbers of transitions to transversions was very different than the expected ratio of 0.5. To study the effect of different transition to transversion ratios in fine gene mapping, a simulation study was performed to generate nucleotide sequence data. The study investigated the effect of different transition to transversion ratios on linkage disequilibrium parameter (LD), which is frequently used in association analysis to identify functional mutations. My results showed no considerable effect of different transition to transversion ratios on LD. I also studied the distribution of allele frequencies of biallelic SNPs from the Genome Database. My results showed that the most common SNPs are normally distributed with mean allele frequency of 0.7520 and standard deviation of 0.1272. These results can be useful in future studies for simulating SNP behavior. I also studied the simulated data provided by the Genetic Analysis Workshop 12 to identify functional SNPs in candidate genes by using the genotype-specific linkage disequilibrium method.

Plant cell walls determine cellular shape and provide structural support for the entire plant. Polysaccharides, comprising the major components of the wall, are actively remodelled throughout development. Xyloglucan endotransglucosylase (XET)/hydrolase (XTH, EC 2.4.1.207) cleaves xyloglucan (XyG), the donor substrate, and attaches a portion to another XyG chain, the acceptor substrate. Recently, a novel transglucosylase called mixed-linkage β-glucan (MLG) : XyG endotransglucosylase (MXE) was discovered in horsetails (Equisetum spp.) that could attach a portion of MLG to XyG, resulting in a hetero-polymer product. My aims were to further investigate the nature of this activity, biochemically characterize the enzyme, and explore its physiological role. MXE activity was attributable to an enzyme unlike Equisetum XTHs. MXE had a p1 of 4.1 (XTHs were 6.6-9), a pH optimum of 6.3 (XTHs preferred 5.5), and had higher activity using smaller oligosaccharide acceptor substrates like XXXGol (XTHs were more active using XLLGol). Importantly, the MXE protein was shown to utilize both MLG and XyG as donor substrates, and therefore have both MXE and XET activity. Also, the enzyme was capable of using various glucan oligosaccharides (O) as substrates, including MLGO, XyGO, and cello-O, but not laminari-O. By using a novel ex vivo approach, the proportion of extractable MXE product to XET product was found to increase in older tissues. Transglucosylase products were localized in sclerenchyma and structural parenchyma by in situ assays, implying a strenghening function for MXE. Surprisingly, another novel activity was discovered that could covalently attach cellulose to XyG, and termed cellulose : xyloglucan endotransglucosylase (CXE). This activity was attributed to the MXE enzyme, implying that the protein is a promiscuous endotransglucosylase. The presence of CXE in other plants has not yet been tested. Besides being a novel discovery in plant cell biology, the modification of cellulose has applications in a number of industries.

A síndrome de Marfan (MFS) é uma doença autossômica dominante do tecido conjuntivo que afeta o coração, vasos sanguíneos, pulmões, olhos, ossos e os ligamentos. Mutações no gene codificante da fibrilina 1 (FBN1) causam a síndrome de Marfan e doenças relacionadas do tecido conjuntivo. Fibrilina 1 é o componente principal das microfibrilas de 10-12nm encontradas na matriz extracelular (ECM). A ECM tem um papel estrutural na organização específica do tecido e participa na regulação de várias citocinas e fatores de crescimento. Uma quantidade crescente de evidências demonstra um relacionamento entre fibrilina 1 e o receptor do fator de transformação do crescimento (TGF-). A Homologia entre fibrilina 1 e TGF- latente (LTGF) permite que os microfibrilas sirvam de reservatório para esta citocina. Recentemente foram descritos nos pacientes com MFS, mutações nos genes receptores I e II do TGF- (TGFBRI/II). O objetivo deste estudo foi analisar a heterogeneidade genética da síndrome de Marfan. Nós realizamos análises de ligação para 6 marcadores dos gene FBN1 e TGFBRII em 34 famílias e sequenciamos o TGFBRI e TGFBRII. A análise de ligação dos haplótipos em relação aos marcadores do gene FBN1 indicou co-segregação em 70,58%, exclusão em 17,64% e homozigozidade em 11,76%; em relação aos marcadores do gene TGFBRII indicou co-segregação em uma família. Conseguimos demonstrar a heterogeneidade de lócus e a utilidade do teste diagnóstico na assistência das famílias pré-sintomáticas com manifestações atípicas ou ambíguas da MFS. / Marfan syndrome is an autosomal dominant disorder of connective tissue that can affect the heart, blood vessels, lungs, eyes, bones, and ligaments. Mutations in the gene encoding fibrillin 1 (FBN1) cause Marfan syndrome (MFS), and related connective tissue disorders. Fibrillin-1 is the main component of the 10-12 nm microfibrils found in the extracellular matrix (ECM). ECM displays a structural role in the tissue-specific organization and takes part in the regulation of various cytokines and growth factors. A growing body of evidence supports a narrow relationship between fibrillin 1 and TGF-beta. Homology between fibrillin 1 and latent TGF-beta (LTGF) allows microfibrils to be a reservoir for this cytokine. Recently, mutations in the gene for transforming growth factor-beta (TGF-) receptor type I and II (TGFBRI/II) have been described in patients with MFS. The aim of this study was to analyze the genetic heterogeneity of Marfan syndrome. We have performed linkage analysis for 6 FBN1 and TGFBRII gene markers in 34 families and sequenced both TGFBRI and TGFBRII. The haplotype linkage analysis concerning the FBN1 gene markers indicated co-segregation at 70.58%, exclusion at 17.64% and homozygosity at 11.76%; in relation to the TGFBRII gene markers, it indicated co-segregation in one family. We were able to demonstrate the heterogeneity of locus and the utility of the diagnostic test in the assistance of the daily pre-symptomatic families with atypical or ambiguous manifestations of MFS.

The grain amaranths (Amaranthus hypochondriacus L., A. cruentus L., and A. caudatus L.) are important pseudocereals native to the Americas that have received increased attention for their nutritional content, specifically their balance of amino acids. The objective of this project was to produce and characterize a set of highly informative, reproducible microsatellite markers for the grain amaranths. A total of 1457 clones were sequenced from three genomic libraries enriched for the microsatellite motifs AAC, AAT and AC. Of these, 353 (24%) contained unique microsatellites. An additional 29 microsatellite loci were identified among 728 BAC-end sequences of a newly developed amaranth BAC library. Flanking primers were designed for 319 of the microsatellite loci and all were screened on a panel of diverse amaranths, including grain and weedy Amaranthus species. A total of 179 (56%) microsatellites were polymorphic across accessions from the three grain amaranths. Among these polymorphic microsatellite loci, a total of 731 alleles were identified with average of four alleles per locus. Heterozygosity values ranged from 0.14 to 0.83 with a mean value of 0.62. Thirty-seven (21%) of the markers were polymorphic between the parents of a segregating population and were shown to be inherited in a normal Mendelian fashion based on chi-squared analysis, demonstrating the utility of these markers for linkage mapping of the amaranth genome. Phylogenetic analysis using the marker data showed A. hybridus accessions in two of the three major grain amaranth clades, suggesting the polyphyletic evolution of the three cultivated species from different A. hybridus ancestors. The microsatellite markers reported here will be useful for further evaluating the relationships among the grain amaranths and their relatives and are an ideal resource for use in marker-assisted breeding programs, germplasm analysis and varietal identification. The transferability of these markers to A. hybridus, A. powellii, and A. retroflexus as reported here suggests that the markers may be useful to other species with the genus Amaranthus, including economically important weeds, vegetable amaranths, and ornamentals.

Barley is an economically important cereal crop throughout most of the world. The study and elucidation of the genetic complex of this plant will add to its extensive usefulness to man, and will also provide valuable information for similar research projects on other crop plants.

This thesis mainly examines inflectional morphology of verbal paradigms in Laki, which is considered as one of the Southern varieties of Kurdish language. The association of form and content of morphological markings are viewed from a realizational angle, in which exponents (morphological forms) are associated with the morphosyntactic properties via the application of rules of exponence, appealed by paradigm functions (Stump 2001) and ordered into rule blocks (Anderson 1992). In particular, I applied the paradigm linkage theory proposed and fully developed by Stump (2002 and 2016) to account for Laki verbal paradigms. In this study, it is claimed that alignment pattern and the syntagmatic combination of some of the inflectional exponents such as agreement markers are sensitive to preterite property. Hence, I argue in favor of considering two distinct morphotactic patternings in Laki. As the result of this assumption, depending on whether the inflectional markers attach to a preterite or a non-preterite stem, we should define two separate sets of affix position in this language. Moreover, I examine Laki polyfunctional agreement markers through the consideration of the morphotactics of this language. Applying Stump's analysis (to appear) of Swahili verbal concords, I consider two distinct types of content for these agreement markers: intrinsic content, and positional content. Their positional content is what the morphotactics of the language determines.

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.

Barley (Hordrium sp.) is the most important spring sown cereal crop in Utah, both in acreage and in yield of total digestible nutrients per unit area. It also rates high as a feed crop in the United States. For this reason it is important that varieties are available which are high in yield, high in quality, and disease resistant, along with other desirable characteristics. In order to work toward this end most efficiently, it is first necessary that the genetics of the barley plant be worked out. Barley offers the plant breeders and geneticists a valuable material to use in the study of genetics. The fact that it has many easily distinguishable characters, that it is easy to grow large F2 populations, and that it has a low chromosome number make it desirable for this type of study. That all interspecific crosses are fertile make it all the more desirable for the plant breeder. This study is a by-product of the cereal breeding and improvement program being carried on at the Utah Experiment Station. Recently the study of translocations induced by X0rays and other means has gained wide interests among plant breeders, geneticists, and cytologists alike. Translocations or interchanges consist of the exchange of segments of non-homologous chromosomes. As a result semisterility occurs in plants which are heterozygous for the interchange. the objective of this study is to calculate any linkage which may be found in different crosses involving translocated stocks in barley in order to determine which linkage groups are involved in the translocation; and to note any characters now linked as a result of a translocation which were not linked in normal barley stocks. The ratios and interactions which occur in any of the characters found in this study will be calculated.

Barley, during the past three decades, has been used considerably for the study of linkage groups and character inheritance. The commercial varieties are diploids, having seven pairs of chromosomes. Six linkage groups have been established. According to studies on interchange by Kramer et al. (1954), two linkage groups, formerly designated as III and VII, may be separate arms of the same chromosome. They are now generally considered as one linkage group.