Dissertations / Theses on the topic 'Compound identification'

This numerical study is divided into two main parts: In the first part a model for routing unsteady flows in compound channels, called RUFICC, is developed. The model accounts for flood plain contribution to system conveyance and also for lateral momentum transfer (LMT) between adjacent deep and shallow zones of compound flow fields. In the modeling approach composite channel sections are divided into representative deep and shallow zones. The resulting one-dimensional model equations, which are a modified form of the St. Venant equations, are solved using a four-point implicit finite difference scheme. Different procedures to account for LMT in the modeling process were considered. These included empirical models that were developed based on field and laboratory measurements under steady flow conditions. The effect of LMT was found to be insignificant in most of the applications considered. For a hypothetical channel with wide and rough flood plains LMT was found to be strongest at small flood plain depths and resulted in attenuation of the discharge hydrographs. In the simulation exercises included in this work RUFICC's performance was compared to those of two frequently-used conventional models, namely: the Off-Channel Storage Model (OCSM) and the Separate Channel Model (SCM). For the applications considered a better agreement was achieved between RUFICC's simulated hydrographs and the observed data. Applying the two conventional models resulted in a marked delay in the fall of the recession curve of the simulated hydrographs. The OCSM also underestimated stages and discharges by more than 25%, especially for fairly high flood plain flows. Flood routing exercises, which involve the solution of the St. Venant equations, require that the geometric and hydraulic properties of the river reach under study be known. This includes the cross-sectional area of flow as well as the channel boundary roughness coefficients for different flow depths. The second phase of this study concerned the testing of different optimization techniques to determine the most suitable optimization algorithm(s) in the estimation of flood routing data. The algorithms considered include Powell's and Rosenbrock's methods, and the Nelder and Meade Simplex algorithm. Regular channel data as well as compound channel data were used in these exercises. The solution of the unsteady flow equations requires only cross-sectional area (A) and conveyance (K) as functions of flow depth (y). Thus, instead of following the conceptual approach of optimizing upon a channel's geometric and hydraulic parameters, optimization was performed upon abstract parameters in assumed A(y) and K(y) relationships. These types of relationships in the so-called 'Black-Box' approach would obviously speed up the computations involved in solving the unsteady flow equations. Furthermore, the relative simplicity of such relationships resulted in decreased computer times and reduced amounts of required computer storage. Estimated data using the Rosenbrock and Simplex methods were then applied to route different flood events. Simulated peak stages and discharges were in good agreement with those estimated using actual routing data. (Abstract shortened by UMI.)

With the environmental problems caused by man-induced pollution by persistent toxic compounds, the importance of finding remediation solutions is immense. As an emerging field, microbial environmental biotechnology may provide the tools to achieve novel solutions. Microbial communities in the environment have biodegradation capacities which could be, and historically have been, exploited for bioremediation. The novelty lies in being able to access the capacity of the uncultured majority of the microbial community. Every day, more and more knowledge is gained in the field and thanks to new approaches such as metagenomics, along with the access to databases and archives where scientists share information and data, the quest becomes considerably facilitated. Microorganisms are highly diverse in metabolic pathways and some have become highly developed during evolution; detoxification and biotransformation of naturally occurring toxic compounds are therefore not novel concepts. The environmental problem occurs when synthetically manufactured compounds are less efficiently biodegraded. However, improved knowledge about the degradation potential in nature and the involved enzymes may help in developing bioremediation procedures. For this reason, an enzyme involved in catabolic pathways of chlorinated aromatic compounds, dienelactone hydrolase, which has been less well studied, was selected as a target. This study investigated the biogeographical distribution of the dienelactone hydrolase gene identified in metagenomes sampled from different environments globally in order to detect potential environmental patterns. Results may cast light on its significance for degradation of chlorinated aromatic compounds in nature. The results indicate a broad biogeographical distribution of dienelactone hydrolase in varying microbial habitats in the environment. The enzyme was found in environments ranging from water and soil habitats to hypersaline-, dechlorinating-, hot-spring- and other extremophillic habitats, in which the gene sequences shared high similarity within each group. A broad environmental distribution suggests that dienlactone hydrolase could be useful in bioremediation.

Thesis (PhD)--Stellenbosch University, 2012.
ENGLISH ABSTRACT: The wine industry is an important sector of agriculture and wine analysis forms the basis of assessing compliance of its commodities with regulatory standards and research in this field. Liquid chromatography (LC) is extensively used for the determination of a wide range of nonvolatile wine components, but conventional detectors impose performance limitations on the technique that prevents its application to sophisticated analytical problems. In particular, conventional detectors for LC often lack the sensitivity and specificity for the determination of many wine compounds, especially trace level analytes, and furthermore, do not possess spectral capabilities for compound identification or structure elucidation. The hyphenation of mass spectrometry (MS) to LC has led to the introduction of a range of detectors that confers high levels of sensitivity and selectivity to the technique. In addition, a wide variety of MS architectures are available that are inherently suited for targeted analysis or structure elucidation studies. In this dissertation, the potential benefits of liquid chromatography – tandem quadrupole mass spectrometry (LC-MS/MS) to solve analytical problems relevant to the wine industry are explored. LC-MS/MS is a particularly versatile analytical technique because both mass analysers can be operated in full-spectrum mode or selected-ion monitoring, which, together with optional fragmentation, gives rise to four modes of operation that may be used for highly specific and sensitive targeted analysis or spectral investigations. In multiple reaction monitoring (MRM) mode, both analysers are set at single ion frequencies specific for the compound under investigation and one or more of its product fragments, respectively. MRM mode is ideally suited for trace level analysis in complex mixtures, even in cases where the target components are not resolved from interferences. In this study, MRM detection was used to solve challenges relevant to the wine industry for the selective quantitation of target analytes that could not be analysed by conventional LC methods. The application of this approach for the analysis of natamycin, ethyl carbamate (EC) and 3-alkyl-2- methoxypyrazines (MPs) in wine is demonstrated. Natamycin is an antimicrobial preservative that is not permitted in wine in the European Union. A rapid and sensitive method for the determination of natamycin was developed, and has been used since 2009 to regulate this vitally important sector of the South African wine export industry. EC is a natural carcinogen that occurs at trace level amounts in alcoholic products. It also has the potential to accumulate in wines and can occur in very high concentrations in some fruit brandies. The determination of EC is complicated by its physicochemical properties, and available analytical methods suffer from drawbacks such as the requirement for elaborate extraction procedures and high solvent consumption. A novel method for the determination of EC in wines, fortified wines and spirits is described and it was applied to perform an audit of the South African industry as well as to investigate factors responsible for its accumulation in alcoholic beverages. This work forms an integral part of the food safety mandate of the State and it ensures that export products comply with international norms for trade. MPs are ultra-trace-level aroma compounds that contribute to the varietal character of Sauvignon blanc wines. Their analytical determination is challenging due to their low levels of occurrence. The loading capacity of LC combined with the sensitivity and resolving power of MS was exploited to analyse concentrated extracts, in order to achieve very low limits of detection. The performance of the LC-MS/MS method enabled the quantitation of these compounds at their natural levels of occurrence, including the first quantitation and spectral confirmation of 3- ethyl-2-methoxypyrazine in wine. Extensive data pertaining to South African Sauvignon blanc wines are reported and statistical analysis is performed, reporting the correlation of variables such as vintage and origin as well as wine parameters such as malic acid with wine MPs. Furthermore, the application of LC-MS/MS for structural elucidation and screening of target classes of analytes was demonstrated for the analysis of red wine anthocyanins. The anthocyanidin-glycosides are responsible for the colour of red grapes and wine, contribute to the sensory properties of wine, and are also of interest due to their beneficial biological properties. Their determination is complicated by their large numbers and structural diversity, further exacerbated by diverse reactions during wine ageing as well as the lack of reference standards for most members of this class of compounds. Tandem MS in scan mode was used for the highly selective detection of glycosylated anthocyanins and derivatives, exploiting the predictable elimination of the sugar moiety in neutral loss mode. Concurrent survey scan experiments were used to unambiguously identify neutral loss detected compounds. The method therefore follows a simplified and structured approach for unambiguous peak identification based on elution order and mass spectral information to impart a high level of certainty in compound identification. In summary, the work presented in this dissertation demonstrates that LC-MS/MS is a versatile and powerful analytical approach for the analysis of diverse compounds of relevance to the wine industry. The sensitivity and specificity of MRM mode, and the selectivity and spectral capabilities of neutral loss and survey scan modes of MS/MS detection, is amply demonstrated by the applications presented in the dissertation.
AFRIKAANSE OPSOMMING: Die wynbedryf is ‘n belangrike komponent van landbou en wyn-analise vorm ‘n integrale deel van gehalteversekering ten opsigte van toepaslike wetlike standaarde. Wyn-analise is ook belangrik in navorsing oor die samestelling van wyn. Vloeistofchromatografie word dikwels aangewend vir die bepaling van ‘n wye verskeidenheid nie-vlugtige wynkomponente, maar konvensionele detektors plaas beperkinge op die aanwending van die tegniek tot gesofistikeerde analitiese toepassings. Meer spesifiek, konvensionele detektors vir vloeistofchromatografie beskik nie oor die sensitiwiteit en selektiwiteit vir die bepaling van baie wynkomponente nie, veral in die geval van spoorvlakanalise, en beskik boonop ook nie oor spektrale vermoëns vir identifikasie van komponente en struktuurbepaling nie. Die koppeling van vloeistofchromatografie met massaspektrometrie het ‘n reeks detektors tot die tegniek toegevoeg wat hoë vlakke van sensitiwiteit en selektiwiteit bied. Verder bied die verskeidenheid van massaspektrometrie-konfigurasies ook instrumente wat inherent geskik is vir geteikende analise of struktuurbepaling, afhangende van die doel van die ondersoek. In hierdie dissertasie word die voordele ondersoek wat verbonde is aan die aanwending van vloeistofchromatografie – tandem kwadrupool massaspektrometrie om relevante analitiese vraagstukke in die wynbedryf op te los. Hiedie tegniek is besonder toepaslik aangesien beide massa-analiseerders in geselekteerde-ioon modus of in volle skandering gebruik kan word. Tesame met opsionele fragmentasie, gee hierdie uitleg aanleiding tot vier funksionaliteite wat vir hoogs sensitiewe geteikende analise of spektrale onledings gebruik kan word. Eerstens word beide massa analiseerders vir enkel-ioon frekwensies opgestel, spesifiek tot die teikenkomponent en een of meer van sy produkfragmente, wat verkry word deur komponentspesifieke fragmentasie. Hierdie modus is by uitstek geskik vir spoorvlakontleding van komplekse monsters, selfs wanneer die teikenkomponente nie chromatografies van die matriks geskei is nie. In hierdie studie is die tegniek aangewend vir die hoogs sensitiewe bepaling van spoorvlak komponente wat nie met konvensionele detektors gemeet kon word nie. Die aanwending van hierdie tegniek word gedemonstreer vir die spoorvlakbepaling van natamycin, etielkarbamaat en 3-alkiel-2-metoksiepierasiene in wyn. Natamycin is ‘n antimikrobiese preserveermiddel wat ontoelaatbaar is in wyn in die Europese Unie. ‘n Vinnige en sensitiewe metode vir die bepaling van natamycin is ontwikkel, en word reeds sedert 2009 aangewend om hierdie uiters belangrike sektor van die Suid-Afrikaanse wyn uitvoerbedryf te reguleer. Etielkarbamaat is ‘n karsinogeen wat natuurlik voorkom in spoorhoeveelhede in alkoholiese produkte. Dit kan ook onder sekere omstandighede akkumuleer in wyn en in hoë konsentrasies voorkom in vrugtebrandewyne. Die bepaling van etielkarbamaat word bemoeilik deur sy chemiese eienskappe, en gevolglik word analitiese metodes gekenmerk deur uitgebreide, arbeidsintensiewe monstervoorbereiding en die gebruik van groot hoeveelhede, meestal giftige, oplosmiddels. ‘n Nuwe metode vir die bepaling van etielkarbamaat in wyn, gefortifiseerde wyn en spiritualië word beskryf en word aangewend om die faktore vir vorming daarvan te ondersoek. Die metode word aangewend om die Suid-Afrikaanse bedryf te ouditeer in terme van die voedselveiligheid mandaat van die Staat, en om te verseker dat uitvoere voldoen aan standaarde vir internasionale handel. Metoksiepierasiene is vlugtige, ultraspoorvlak wynaromakomponente wat verantwoordelik is vir die kenmerkede kultivarkarakter van Sauvignon blanc wyne. Hul analitiese bepaling word bemoeilik deur hulle lae konsentrasies in wyn. Die ladingskapasiteit van vloeistofchromatografie tesame met die sensitiwiteit en selektiwiteit van massaspektrometrie was benut om hoogs gekonsentreerde ekstrakte te ontleed. Baie hoë vlakke van sensitiwiteit word sodoende verkry. Die verrigting van die metode was voldoende om hierdie komponente teen hulle natuurlike konsentrasies te kwantifiseer, insluitende die eerste kwantifisering en spektrale bevestiging van 3-etiel-2-metoksiepierasien. Omvattende data van die vlakke van hierdie komponente in Suid- Afrikaanse Sauvignon blanc wyne word getoon en statistiese ontleding is gedoen om korrelasies tussen veranderlikes soos oorsprong en oesjaar sowel as basiese wyn veranderlikes soos byvoorbeeld appelsuur, met metoksiepierasienvlakke te ondersoek. Verder was die toepassing van vloeistofchromatografie – tandem massaspektrometrie tot struktuurbepaling en skandering vir groepe van komponente gedemonstreer vir die ontleding van rooiwyn antosianiene. Die antosianien-glukosiede is verantwoordelik vir die kleur van rooi druiwe en wyn, dra by tot die sensoriese eienskappe daarvan, en is ook relevant as gevolg van die voordelige biologiese eienskappe daarvan. Die bepaling van hierdie komponente word gekompliseer deur hulle groot getalle en strukturele diversiteit, verder bemoeilik deur die wye verskeidenheid van reaksies wat hulle ondergaan tydens veroudering. Daar is ook ‘n gebrek aan beskikbaarheid van standaarde vir die meeste van die lede van hierdie klas van komponente. Tandem massaspektrometrie was in skanderingsmodus gebruik vir hoogs selektiewe deteksie van die antosianien-glukosiede deur die voorspelbare eliminasie van die suiker komponent in neutrale verliesskandering te benut. Gelyktydige skanderings van die komponente wat met neutraleverliesskandering waargeneem word, is gebruik vir ondubbelsinnige komponent identifikasie. Die metode volg daarom ‘n eenvoudige en gestruktureerde benadering vir piek identifikasie wat gebaseer is op chromatografiese orde, sowel as massaspektrale inligting, om ‘n hoë vlak van sekerheid aan die identifikasie van komponente te verleen. Samevattend, word daar getoon deur die werk wat in hierdie dissertasie uiteengesit is dat vloeistofchromatografie – tandem massaspektrometrie ‘n veelsydige en kragtige tegniek bied vir chemiese analise relevant tot die wynbedryf. Die sensitiwiteit, selektiwiteit en spektrale vermoëns van die tegniek word duidelik deur toepassings in die dissertasie getoon.

Rhodococcus is a soil bacterium, member of the Actinobacteria, and a close relative of the prolific small molecule producer Streptomyces. Recent interest in Rhodococcus as an under investigated source of possible bioactive secondary metabolites is sparked by the discovery of many polyketide synthase and non-ribosomal peptide synthetase genes of unknown function from sequenced Rhodococcus genomes. Rhodococcus species strain MTM3W5.2 was recently shown to produce a strong inhibitory compound with activity against most strains of Rhodococcus and closely related genera. A goal of this investigation is to discover the gene(s) required to synthesize this inhibitory molecule. The engineered Rhodococcus transposon, pTNR, was used to generate random insertional mutations in the genome of MTM3W5.2. The transposon insertion sites for 8 non-producing mutants were cloned and sequenced. Genes that encode polyketide synthases usually form parts of large biosynthetic gene clusters responsible for the production of small polyketide molecules.

The Web is a vast repository of data, and information on almost any subject can be found with the aid of search engines. Although the Web is international, the majority of research on finding of information has a focus on languages such as English and Chinese. In this thesis, we investigate information retrieval techniques for Indonesian. Although Indonesia is the fourth most populous country in the world, little attention has been given to search of Indonesian documents. Stemming is the process of reducing morphological variants of a word to a common stem form. Previous research has shown that stemming is language-dependent. Although several stemming algorithms have been proposed for Indonesian, there is no consensus on which gives better performance. We empirically explore these algorithms, showing that even the best algorithm still has scope for improvement. We propose novel extensions to this algorithm and develop a new Indonesian stemmer, and show that these can improve stemming correctness by up to three percentage points; our approach makes less than one error in thirty-eight words. We propose a range of techniques to enhance the performance of Indonesian information retrieval. These techniques include: stopping; sub-word tokenisation; and identification of proper nouns; and modifications to existing similarity functions. Our experiments show that many of these techniques can increase retrieval performance, with the highest increase achieved when we use grams of size five to tokenise words. We also present an effective method for identifying the language of a document; this allows various information retrieval techniques to be applied selectively depending on the language of target documents. We also address the problem of automatic creation of parallel corpora --- collections of documents that are the direct translations of each other --- which are essential for cross-lingual information retrieval tasks. Well-curated parallel corpora are rare, and for many languages, such as Indonesian, do not exist at all. We describe algorithms that we have developed to automatically identify parallel documents for Indonesian and English. Unlike most current approaches, which consider only the context and structure of the documents, our approach is based on the document content itself. Our algorithms do not make any prior assumptions about the documents, and are based on the Needleman-Wunsch algorithm for global alignment of protein sequences. Our approach works well in identifying Indonesian-English parallel documents, especially when no translation is performed. It can increase the separation value, a measure to discriminate good matches of parallel documents from bad matches, by approximately ten percentage points. We also investigate the applicability of our identification algorithms for other languages that use the Latin alphabet. Our experiments show that, with minor modifications, our alignment methods are effective for English-French, English-German, and French-German corpora, especially when the documents are not translated. Our technique can increase the separation value for the European corpus by up to twenty-eight percentage points. Together, these results provide a substantial advance in understanding techniques that can be applied for effective Indonesian text retrieval.

Mercapturic acids are urinary metabolites which signal exposure to genotoxic compounds. Carefully designed hapten-protein conjugates and a judicious screening strategy has enabled the generation of compound and class-specific antibodies which bind mercapturic acids. S-phenylmercapuric acid (S-PMA) is a highly specific and sensitive marker of benzene exposure. A monoclonal antibody reactive with S-PMA has been generated. The immobilised antibody retains immunoreactivity and can be used to enrich S-PMA from the urine of benzene exposed workers. The performance of the immunoaffinity column has been validated by comparison with data obtained from GC/MS analysis of urine from benzene exposed workers (range 12-168ug/1. corr. coeff. 0.98, n=23). Furthermore immunoaffinity chromatography facilitates the quantitative determination of urinary S-PMA by HPLC. Bioconcentration of S-PMA from the urine of benzene exposed workers has permitted the quantification of S-PMA by HPLC at 8 hour Time Weighted Average exposures of around 1ppm. Monoclonal antibodies to low molecular weight mercapturic acids (eg. S-(2-hydroxyethyl)mercapturic acid) were generally of too low affinity for practical application. As an alternative approach antibodies to adducted protein were investigated. Antibody 4D3 binds the adducted N-terminal heptapeptide released from the alpha-chain of haemoglobin by trypsin hydrolysis. Initial studies suggest antibody 4D3 can bind the adducted heptapeptide in whole haemoglobin. This may facilitate the determination of adducted haemoglobin in biomonitoring studies.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous, toxic contaminants that are released to the environment from various petrogenic and pyrogenic sources. In an effort to more clearly identify and trace sources of PAHs in the environment, purification and compound specific isotope analysis methods were developed to accurately measure the stable carbon isotope ratio of individual PAHs. Development of the method included improving accuracy and precision of the isotopic measurement by producing highly pure extracts using various chromatographic techniques. The method was refined by improving compound separations using purification techniques and high resolution chromatographic columns. The purification method consists of alumina/silica gel column chromatography, gel permeation chromatography and thin layer chromatography. The mean recovery of PAHs after the purification procedure was approximately 80 %. Sample purities after purification were verified by GC/FID and full scan mass spectrometry. To better resolve peaks and provide more accurate stable carbon isotope measurements, various gas chromatographic conditions were evaluated. The precision of the method ranged between 0.08 and 0.43 . The analytical protocols were evaluated to confirm compositional and stable isotopic integrity during purification and stable isotopic analysis. To confirm the utility of the purification and isotope analysis methods, various environmental samples from marine, land and lacustrine environments were analyzed. The isolates were analyzed for the composition and the stable carbon isotope ratios of PAHs. The stable carbon isotope ratio was measured by GC/IRMS and the results, along with quantitative compound compositions, were used to characterize and identify the contaminant sources. The sources of the PAHs in the study areas were differentiated by PAH molecular ratios and confirmed by stable carbon isotope ratios. This study confirms that compound specific isotope analysis of pollutants by GC/IRMS can be used to identify PAH sources in environmental samples. The study also confirms that the purification and stable carbon isotope analysis methods that were developed can be used to accurately measure the stable carbon isotope ratios of PAHs in environmental samples for the purpose of source identification. GC/IRMS measurement of stable isotopic compositions can be an effective fingerprinting method when used in conjunction with traditional molecular composition methods.

Thesis (M.S.) -- University of Maryland, College Park, 2005.
Thesis research directed by: Civil Engineering. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

The 90-KDa heat shock protein (Hsp90) is part of the molecular chaperone family, and as such it is involved in the regulation of protein homeostasis within cells. Specifically, Hsp90 aids in the folding of nascent proteins and re-folding of denatured proteins. It also plays an important role in the prevention of protein aggregation. Hsp90’s functionality is attributed to its several staged, multi-conformational ATPase cycle, in which associated client proteins are bound and released. Hsp90 is known to be associated with a wide array of client proteins, some of which are thought to be involved in multiple oncogenic processes. Indeed Hsp90 is known to be directly involved in perpetuating the stability and function of multiple mutated, chimeric and over-expressed signalling proteins that are known to promote the growth and survival of cancer cells. Hsp90 inhibitors are thus thought to be promising therapeutic agents for cancer treatment. A lack of a 3D structure of human Hsp90 however has restricted Hsp90 inhibitor development in large to in vivo investigations. This study, aims to investigate and calculate hypothetical homology models of the full human Hsp90 protein, and to probe these structural models for novel drug target sites using several in silico techniques. A multi-template homology modelling methodology was developed and in conjunction with protein-protein docking techniques, two functionally important human Hsp90 structural models were calculated; the nucleotide free “v-like” open and nucleotide bound closed conformations. Based on the conservation of ligand binding, virtual screening experiments conducted on both models using 316 natural compounds indigenous to South Africa, revealed three novel putative target sites. Two binding pockets in close association with important Hsp90-Hop interaction residues and a single binding pocket on the dimerization interface in the C-terminal domain. Targeted molecular docking experiments at these sites revealed two compounds (721395-11-5 and 264624-39-7) as putative inhibitors, both showing strong binding affinities for at least one of the three investigated target sites. Furthermore both compounds were found to only violate one Lipinski’s rules, suggesting their potential as candidates for further drug development. The combined work described here provides a putative platform for the development of next generation inhibitors of human Hsp90.

The MS-818 compound is used in the proliferation process of neuronal cells and many biological activities that accompany this process such as astrocyte differentiation, inhibition of neuronal apoptosis, and fraction repairs. We do know the effects of this compound, but the mechanism of action remained uncertain until now. To determine the pathway of this compound, NT2 cells were cultured and lysed to isolate the proteins. Affinity Chromatography was performed in order to immobilize the MS-818 compound to a Hi-Trap NHS column. The NT2 protein sample was injected through the column and eluted with a MS-818 concentrated, high salt content elution buffer. SDS-PAGE was then performed to isolate the proteins that bound to MS-818. The gel was visualized using Coomassie Blue. The results indicate that there are two proteins associated in the mechanism of this compound. A standard protein marker ranging from 10 kDa to 250 kDa was used to compare the bands. The findings indicate that one of the protein bands is slightly less than 250kDa and the other is between 50-75 kDa. When the proteins are confirmed by mass spectrometry sequencing, this will help to promote this compound as a drug candidate.
B.S.
Bachelors
Medicine
Molecular Biology and Microbiology

In the European Union an environmental risk assessment is required for the registration of new chemicals, biocides, pesticides and pharmaceuticals. In order to avoid the release of potential hazardous substances, various ecotoxicity tests are performed, including acute and chronic fish tests. As a consequence of the new program of the European Union “Registration, Evaluation and Authorisation of Chemicals” (REACH) the number of animal experiments for environmental risk assessment is expected to increase remarkably within the next years. On the other hand there is a strong societal demand for reducing the number of animal tests by using alternative in vitro models. According to EU directives, investigations using non-human vertebrate embryos are considered pain free in vitro methods and are therefore accepted as alternatives to animal experiments. For the acute fish test, the Danio rerio embryo test (DarT) has been established as a replacement method and included in national regulations at least for waste water (German Waste Water Dues Law). However, no alternatives for chronic fish tests are currently available. The overall goal of this thesis was to work towards such a replacement by extending DarT zu Gene-DarT. Toxicants will initially interact at the molecular level with consequences for physiology, fitness and survival. The analysis of gene expression patterns may unravel elements of these molecular events before any phenotypic changes are visible. The hypothesis of this thesis therefore was that chemical-sensitive genes in embryos exposed in a conventional DarT may indicate toxic impact of substances at sub-acute concentrations and thus enhance the sensitivity of the embryo toxicity test. Furthermore, unlike the conventional DarT-endpoints, gene expression analysis will provide insights into mechanistic processes underlying toxicity. The 3,4-dichloroaniline (3,4-DCA), which is used as a reference compound in the DarT, was selected as model chemical in this thesis. In a first step, differentially expressed genes in embryos exposed to 3,4-DCA were identified by microarray technology and RT-PCR techniques. Six dose-dependent significant differentially expressed genes were identified. These genes were involved in biotransformation pathways (cyp1a, ahr2), stress response (nrf2, maft, ho-1) and cell cycle control (fzr1). Differential expression upon 3,4-DCA exposure was detected below the LOEC (lowest observed effect concentration = 6.2 µM) of survival or developmental disorders of the embryo test (0.78 µM and above). For the validation of stage specific sensitivity, genes were also analysed in post-hatched stages. Extension of exposure to post-hatched stages resulted in a differential expression at lower concentrations as for the embryonic stages, indicating an improved sensitivity due to stage-specific sensitivity or exposure time. To confirm the adaptive function of the 3,4-DCA-sensitive genes, embryonic mRNA abundance was experimentally manipulated by knock down and overexpression. By injection of sense (mRNA) or antisense (siRNA) RNA in one-cell-stages of embryos, the transcript levels of genes were transiently enhanced or repressed in embryos exposed to 3,4-DCA. mRNA injection of the genes cyp1a, ho-1 and nrf2 reduced the number of embryos with 3,4-DCA-induced malformations. In contrast, siRNA injections for the same genes led to an increase in the severity and frequency of developmental disorders. The results clearly indicate the adaptive functions of the investigated genes or their corresponding proteins. This study demonstrates that the analysis of chemical-sensitive gene expression shows the potential to increase the sensitivity of conventional toxicity tests. The analysis of gene expression also provides additional mechanistic information for toxic action, e.g. in the presented study, the involvement of Ah-receptor regulated pathways as an adaptive response. Furthermore, the presented data indicate that functional manipulations, using mRNA and siRNA-injection, are suitable to evaluate the role of differentially expressed genes for toxicity.

The growing concern for environmental problems underlines the importance of correctly predicting the fate of pollutants released into the environment. In the case of VOCs, this is a complex task due to the large number of VOCs with different reactivity's present in ambient air (Atkinson, 1990). In Cape Town and the Vaal Triangle brown haze layers develops in ambient air during windless days in the wintertime. This leads to the build-up of pollutants emitted into the atmosphere. The haze is usually most intense in the early mornings, gradually dispersing during the day. The aim of the study was the identification, quantification and comparison of VOCs in Cape Town and the Vaal Triangle. Different sampling techniques have been used during intensive field campaigns in Cape Town and the Vaal Triangle. Three different sampling techniques were used, namely: 6 litre TO canisters, CarbotrapTM 300 tubes and 75 mm Carboxen-PDMS SPME fibres. Samples were also taken at different altitudes in the lower troposphere, because the pollution layers are formed at different altitudes. Background corrections were also carried out. A Supelco (Cat no: 41900-U) calibration standard, was used as external standard. Samples were analysed by a Hewlett Packard Agilent 6890 gas chromatograph (GC) and Micromass Autospec-TOF mass spectrometer (MS) according to the EPA TO-14a compendium method. The samples were concentrated on a Perkin-Elmer Turbo matrix thermal desorber. A temperature program was used and VOCs not present in the Supelco standard were identified using the MS data system library (NIST). SMPE was only used as a qualitative comparison to the other techniques. A large number of VOCs were identified and quantified at ground level and at different altitudes in ambient air in both Cape Town and in the Vaal Triangle region. The aim was identifying and quantifying manmade emissions. The total VOC profile may differ from these since oxygenated species have not been focussed on. In the Cape Town study more unsaturated VOCs and longer chain HCs were detected during the night than during the day. The number of ketones present also seemed to be higher during the day. In the city centre and Khayelitsha a wide range of halogenated hydrocarbons was detected at ground level. Chlorinated HCs do not take part in photochemical reactions and the concentrations of these VOCs did not to change very much in the day and night samples. It appeared that the concentration of the VOCs at different altitudes in some cases differ significantly. This correlated with the brown haze that forms visible layers and it seemed that the concentration of VOCs in layers differ. The VOCs found at ground level were in most cases related to petroleum products while the VOCs detected at higher altitudes are compounds that remained in the atmosphere and can be transferred from their source over great distances, or photochemical products. In the Vaal Triangle study a very wide variety of VOCs that included a large range of halogenated VOCs were detected. The north-east wind prevailing on the day of sampling diluted the VOCs sampled in the Vaal Triangle. The comparison of the two study regions showed that in both regions the toluene had the highest concentrations of all the measured VOCs. The reported daytime benzene concentrations at Goodwood, Table View and the city centre and the nighttime levels in Khayelitsha exceeded 1.6 ppb (5 pg.m-3). The low benzene concentration levels in the Vaal Triangle are mainly due to the wind diluting pollution at the time of sampling. A wider variety of VOCs were detected in the Vaal Triangle than in Cape Town. Pollutants detected in the Vaal Triangle had very low concentrations, mostly even below the detection limits. This was due to the strong wind that is typical for August in the Vaal Triangle. BVOCs were detected in both regions. In both areas the influence of photochemical processes is evident and secondary products of photochemical reactions were found. A large range of halogenated VOCs was found in the ground level samples in the Vaal Triangle and at higher altitudes in the Cape region. Halogenated VOCs were also detected in the city centre in Cape Town and in Khayelitsha. In both regions a large range of complex benzene derivates were found. The comparison of the values obtained using canisters and the CarbotrapTM 300 tubes showed differences that cannot be explained unambiguously. VOCs sampled with SPME correlated with the above-mentioned techniques but the identification of the unknown compounds was much easier in samples taken with the SPME than with the other techniques used. SPME proved to be a handy "screening" tool for the identification of VOCs. A comparison of the two different regions investigated gave insight into the concentrations and the fate of VOCs on a regional and global scale in South Africa. It followed from the results reported in this study that VOC emissions in Cape Town and in the Vaal Triangle would most definitely play a significant role in the formation of photochemical smog.
Thesis (Ph.D. (Chemistry))--North-West University, Potchefstroom Campus, 2006.

In the European Union an environmental risk assessment is required for the registration of new chemicals, biocides, pesticides and pharmaceuticals. In order to avoid the release of potential hazardous substances, various ecotoxicity tests are performed, including acute and chronic fish tests. As a consequence of the new program of the European Union “Registration, Evaluation and Authorisation of Chemicals” (REACH) the number of animal experiments for environmental risk assessment is expected to increase remarkably within the next years. On the other hand there is a strong societal demand for reducing the number of animal tests by using alternative in vitro models. According to EU directives, investigations using non-human vertebrate embryos are considered pain free in vitro methods and are therefore accepted as alternatives to animal experiments. For the acute fish test, the Danio rerio embryo test (DarT) has been established as a replacement method and included in national regulations at least for waste water (German Waste Water Dues Law). However, no alternatives for chronic fish tests are currently available. The overall goal of this thesis was to work towards such a replacement by extending DarT zu Gene-DarT. Toxicants will initially interact at the molecular level with consequences for physiology, fitness and survival. The analysis of gene expression patterns may unravel elements of these molecular events before any phenotypic changes are visible. The hypothesis of this thesis therefore was that chemical-sensitive genes in embryos exposed in a conventional DarT may indicate toxic impact of substances at sub-acute concentrations and thus enhance the sensitivity of the embryo toxicity test. Furthermore, unlike the conventional DarT-endpoints, gene expression analysis will provide insights into mechanistic processes underlying toxicity. The 3,4-dichloroaniline (3,4-DCA), which is used as a reference compound in the DarT, was selected as model chemical in this thesis. In a first step, differentially expressed genes in embryos exposed to 3,4-DCA were identified by microarray technology and RT-PCR techniques. Six dose-dependent significant differentially expressed genes were identified. These genes were involved in biotransformation pathways (cyp1a, ahr2), stress response (nrf2, maft, ho-1) and cell cycle control (fzr1). Differential expression upon 3,4-DCA exposure was detected below the LOEC (lowest observed effect concentration = 6.2 µM) of survival or developmental disorders of the embryo test (0.78 µM and above). For the validation of stage specific sensitivity, genes were also analysed in post-hatched stages. Extension of exposure to post-hatched stages resulted in a differential expression at lower concentrations as for the embryonic stages, indicating an improved sensitivity due to stage-specific sensitivity or exposure time. To confirm the adaptive function of the 3,4-DCA-sensitive genes, embryonic mRNA abundance was experimentally manipulated by knock down and overexpression. By injection of sense (mRNA) or antisense (siRNA) RNA in one-cell-stages of embryos, the transcript levels of genes were transiently enhanced or repressed in embryos exposed to 3,4-DCA. mRNA injection of the genes cyp1a, ho-1 and nrf2 reduced the number of embryos with 3,4-DCA-induced malformations. In contrast, siRNA injections for the same genes led to an increase in the severity and frequency of developmental disorders. The results clearly indicate the adaptive functions of the investigated genes or their corresponding proteins. This study demonstrates that the analysis of chemical-sensitive gene expression shows the potential to increase the sensitivity of conventional toxicity tests. The analysis of gene expression also provides additional mechanistic information for toxic action, e.g. in the presented study, the involvement of Ah-receptor regulated pathways as an adaptive response. Furthermore, the presented data indicate that functional manipulations, using mRNA and siRNA-injection, are suitable to evaluate the role of differentially expressed genes for toxicity.

La mammite est une inflammation de la mamelle, le plus souvent, en réponse à une invasion d’origine bactérienne. L’utilisation d’antibiotiques pour le traitement de cette pathologie n’est pas la solution idéale. Outre les problèmes engendrés pour la qualité du lait, l’apparition de résistance et l’inefficacité des traitements nécessitent de développer des méthodes alternatives. L’objectif de ces travaux de thèse était de vérifier si l’utilisation d’huile de tournesol ozonée comme moyen de lutte alternatif contre les mammites est envisageable. Dans un premier temps, l’effet des conditions d’ozonation sur la composition et sur l’activité antibactérienne de l’huile ozonée a été étudié pour déterminer les conditions optimales de synthèse d’un agent antibactérien. Les résultats ont montré que l’ajout d’eau et l’augmentation de la durée de la réaction permettaient l’obtention de valeurs d’indice de peroxyde plus élevées et d’une meilleure activité antibactérienne mettant en évidence la relation existant entre ces deux paramètres. Par la suite, l’activité antibactérienne d’huile de tournesol ozonée a été évaluée in vitro sur 59 espèces bactériennes isolées de cas déclarés de mammites chez des brebis. Le produit testé a prouvé son efficacité contre toutes les souches étudiées avec des concentrations minimales inhibitrices de croissance comprises entre 0,625 et 20 mg/mL. L’homologation de l’huile de tournesol ozonée comme préparation vétérinaire requiert d’avoir des données sur sa stabilité thermique et d’identifier les molécules actives. Les travaux menés ont montré que la composition de l’huile de tournesol ozonée stockée à −20 °C ou à +4 °C n’évoluait pas pendant une durée d’un an. Au contraire, des températures de stockage plus élevées entrainaient rapidement une diminution de l’indice de peroxyde et une augmentation de l’acidité. Cependant, ces modifications n’ont pas eu d’effet sur l’activité antibactérienne qui a gardé une valeur constante. Ces observations ont permis d’émettre des hypothèses sur l’identité des molécules actives. L’activité antibactérienne des huiles ozonées serait due à la présence d’ozonides, d’hydroperoxydes et d’acides nonanoïque et azélaïque. L’étude de la réaction d’ozonolyse sur un composé modèle, l’oléate de méthyle, a permis d’affiner ces hypothèses. En effet, l’activité antibactérienne spécifique de différentes fractions obtenues après purification d’oléate de méthyle ozoné a été évaluée. Toutefois, les ozonides purifiés et caractérisés par RMN n’ont pas montré d’activité dans la gamme de concentration testée. L’activité antibactérienne de l’huile de tournesol ozonée peut donc être attribuée aux hydroperoxydes, aux aldéhydes et aux acides carboxyliques à chaines courtes
Mastitis is an inflammation of the udder, usually in response to a bacterial invasion. The use of antibiotics for the treatment of this disease is not the ideal solution. In addition to the problems caused to the quality of milk, the development of resistance and ineffective treatments require to focus on alternative methods. The aim of this work was to verify if the use of ozonized sunflower oil as an alternative means of fight against mastitis could be possible. Firstly, the effect of the ozonation conditions on the composition and the antibacterial activity of ozonized oils was studied to determine the optimum conditions for the synthesis of an antibacterial agent. The results showed that the addition of water and increasing the duration of the reaction allowed to obtain higher peroxide index values and improved antibacterial activity highlighting the relationship between these two parameters. Afterwards, the antibacterial activity of ozonized sunflower oil was assessed in vitro against 59 bacterial species isolated from reported cases of mastitis in ewes. The tested product has proved its efficiency against all the strains studied with minimum inhibitory concentrations between 0.625 and 20 mg/mL. The registration of ozonized sunflower oil as a veterinary preparation requires to obtain data on its thermal stability and to identify the active molecules. The work carried out has shown that the composition of ozonized sunflower oil stored at −20 °C or +4 °C did not evolve for a period of one year. On the contrary, higher storage temperatures quickly led to a decrease of the peroxide index and an increase in acidity. However, these changes had no effect on the antibacterial activity that kept a constant value. These observations allowed speculating on the identity of active molecules. The antibacterial activity of ozonized oils could be due to the presence of ozonides, hydroperoxides and nonanoic acid and azelaic acid. The study of the ozonolysis reaction on a model compound, methyl oleate, helped to refine these assumptions. Indeed, specific antibacterial activity of various fractions obtained after purification of ozonized methyl oleate was evaluated. However, purified ozonides, characterized by NMR, showed no activity in the tested concentration range. The antibacterial activity of ozonized sunflower oil can therefore be attributed to hydroperoxides, aldehydes and short chain carboxylic acids

Consumption of cocoa and dark chocolate products has been associated with positive health outcomes including reduced onset of cardiovascular disease, inflammation, diabetes, obesity, and platelet disorders. Cocoa polyphenols, putatively responsible for these beneficial activities, are highly impacted by cocoa variety, agronomic effects and processing history. However, the difference in polyphenol concentration and composition between cocoa products originating from different hybrid clones (selected for high yield) or from different fermentation conditions is not fully understood. Detailed polyphenol characterization including determination of total polyphenol and total procyanidin concentrations, and qualitative and quantitative analysis of (mean) degree of polymerization was conducted. Significant differences in total polyphenol and procyanidin concentrations were observed between five genetic clones grown by the USDA-ARS Cocoa Germplasm Repository located in Mayagüez, Puerto Rico. To facilitate cocoa fermentation research in laboratories distant from cocoa harvesting sites, a laboratory-scale cocoa fermentation model system was developed in this study. This model system used dried, unfermented, cocoa beans and simulated pulp medium as the starting material. The model system supported growth of the essential succession of cocoa fermenting microorganisms and generated similar chemical changes to those observed in on-farm cocoa fermentation. Using this model system, the impact of inoculation with proprietary yeast strains Saccharomyces cerevisiae Lev F and Saccharomyces cerevisiae Lev B on cocoa polyphenol concentration and composition was evaluated. Inoculation with both yeast strains resulted in increased fermentation rate and Lev B inoculation resulted in higher total polyphenol and procyandin contents at the end of fermentation. Overall, the present work addressed the influence of cocoa variety selection and fermentation process conditions on the composition and concentration of polyphenols. These findings will contribute to continued efforts to develop cocoa products with optimized bioactivity and maximum disease preventative effects.
PHD

La qualité des eaux-de-vie est un paramètre associé à la composition en composés volatils d’arôme. Cette composition résulte de la combinaison de différents facteurs dont la nature et le traitement des matières premières, mais surtout des transformations ayant lieu lors des phases de fermentation, distillation et, dans la plupart de cas, vieillissement.La distillation est une opération de séparation pratiquée depuis des millénaires, avec une technologie assez mature. Cependant, dans le domaine des eaux-de-vie, elle s’appuie essentiellement sur des connaissances empiriques. L’objectif de ce doctorat fut de contribuer à une meilleure compréhension du comportement des composés volatils d’arôme au cours de différents modes de distillation et de fournir des bases scientifiques à la conduite des unités par le biais de modules de simulation. L’attention a été portée sur la distillation d’Armagnac et de Calvados dans des colonnes multiétagées en régime stationnaire.Les modules de simulation ont été construits avec le logiciel ProSimPlus®. La première partie des travaux a été consacrée à l’acquisition de données d’équilibre liquide-vapeur des composés volatils d’arôme en milieu hydroalcoolique pour l’identification du modèle NRTL, en suivant trois approches complémentaires : recherche dans la littérature, détermination expérimentale et prédiction théorique avec les modèles UNIFAC et COSMO. Grâce à la connaissance acquise sur les volatilités relatives par rapport à l’éthanol et à l’eau, les composés volatils d’arôme ont pu être classés en trois groupes : composés légers, composés intermédiaires et composés lourds. La deuxième partie des travaux a porté sur la construction et la validation des modules de simulation, après réconciliation des données issues de la caractérisation expérimentale des unités de distillation. Cette investigation démontre que la simulation est un outil d’ingénierie performant dans le domaine des eaux-de-vie. Les résultats de la simulation ont permis d’affiner la classification des composés intermédiaires en trois catégories supplémentaires selon leur profil de concentration dans la colonne et leur taux de récupération dans le distillat. Enfin, cet outil a mis en évidence que certains paramètres opératoires, notamment l’augmentation de la teneur en éthanol du distillat ainsi que l’extraction de queues, favorisent la séparation préférentielle de certaines espèces de volatilité faible ou intermédiaire par rapport à l’éthanol
The quality of spirits is a parameter related to the composition of volatile aroma compounds. This composition results from the combined production process of raw material extraction, subsequent fermentation, distillation and, in many cases, ageing.Distillation is a very old and the most important industrial separation technology. However, in spirits production, this operation relies essentially on empirical knowledge. The aim of this PhD was to contribute to a better understanding of the volatile aroma compounds behaviour in spirits distillation and to provide a scientific basis for the process through computer simulation. The study was focused on Armagnac and Calvados production by continuous multistage distillation.The simulation modules were built using the software ProSimPlus®. The first part of this research was dedicated to the acquisition of vapor-liquid equilibrium data of the volatile aroma compounds in ethanol-water solutions, in order to estimate the binary interaction parameters of the NRTL model.Three complementary approaches of data acquisition were used: literature compilation, experimental measurements and predictions with UNIFAC and COSMO models.According to their relative volatilities with respect to ethanol and water, the volatile aroma compounds can be classified in three groups: light compounds, intermediary compounds and heavy compounds. The second part of this research dealt with the creation and validation of simulation modules, by using reconciled experimental data from the distillation units. The results prove that simulation is a powerful tool in spirits distillation. The simulation data enables a more precise classification of the intermediary compounds in three categories, by considering their composition profiles in the distillation column and their recovery ratios from feed to distillate. Finally, the analysis of some operating parameters, including ethanol concentration in the distillate as well as tails extractions, demonstrates that the distillate composition can be modified by virtue of a selective separation of intermediary and heavy compounds with respect to ethanol

Reactions of different alcohols with 2-hydroxy - 1- trifluoromethyl -1,2,2-trifluoroethanesulfonic acid sultone were studied. Six new esters were prepared: C6F5OC(O)CF(CF3)SO2F, CH3CH2OC(O)CF(CF3)SO2F, CF3CH2OC(O)CF(CF3)SO2F, (CF3)2CHOC(O)CF(CF3)SO2F, CH2=CHCH20C(O)CF(CF3)SO2F, (CH2OC(O)CF(CF3)SO2F)2. Analytical data, infrared, nmr and mass spectra are presented supporting the proposed structures for these new compounds.

Tras la infección por VIH-1, el establecimiento de un depósito de células T en reposo infectadas latentemente con VIH impide la erradicación del virus en pacientes. Para lograr la erradicación, la terapia retroviral existente debe combinarse con medicamentos que reactiven los virus latentes. Previamente, nuestro grupo describió un nuevo compuesto químico, MMQO (8-metoxi-6-metilquinolin-4-ol) que es capaz de reactivar la transcripción viral a través de un mecanismo desconocido. El objetivo de este proyecto fue identificar los proteínas que interaccionan con MMQO e investigar su papel en la reactivación del VIH-1. Hemos establecido que MMQO es capaz de inducir la transcripción de minigenomas provirales que carecen de genes para los componentes virales, lo que nos permite plantear la hipótesis de que el compuesto funciona principalmente a través de factores del huésped. La caracterización de los perfiles de transcripción de MMQO mediante microarrays de expresión nos permitió identificar numerosos rasgos provocados por el compuesto. MMQO muestra una robusta naturaleza inmunosupresora que afecta a la proliferación celular debido a la disminución de los niveles proteicos de cMyc y Bcl-2 y la desregulación de genes sensibles a acetilación. Estas características indican que MMQO imita las lisinas acetiladas de histonas y funciona como un inhibidor de bromodominio y dominio extraterminal (BET). Análisis adicionales de la expresión génica y proteómica confirmaron esta hipótesis y demostramos que MMQO desplaza de la cromatina a Brd4, un miembro de la familia BET y antagoniza el papel pro-latente de Brd4 cerca del sitio de inicio de la transcripción de VIH-1. Modelos computacionales de docking también confirmaron la especificidad de MMQO hacia los bromodominios de la familia BET y un ensayo in vitro mediante FRET contra los miembros de la familia, identificó que MMQO tiene una mayor afinidad hacia la proteína Brd9. Por último, hemos establecido que la inhibición de Brd9 tiene un mínimo efecto sobre la expresión proviral, lo que sugiere que la principal función de MMQO sobre VIH-1 se puede atribuir al desplazamiento de Brd4. Debido a la amplia gama de propiedades de los inhibidores de la familia BET, estas moléculas se están evaluando actualmente en ensayos clínicos contra diversos tipos de cáncer y afecciones inmunitarias. MMQO, con un funcionamiento dual, es un nuevo miembro de esta clase de medicamentos. La estructura minimalista de MMQO puede ser muy prometedora ya que puede ser modificada para optimizar la afinidad hacia Brd9 / 4 y, potencialmente, podría ser de utilidad en la investigación contra una gran variedad de enfermedades, incluyendo el VIH.
Upon HIV-1 infection, a reservoir of HIV latently infected resting T cells prevents the eradication of the virus from patients. To achieve eradication, the existing virus suppressing antiretroviral therapy must be combined with drugs that reactivate the dormant viruses. Our group previously described a novel chemical scaffold compound, MMQO (8-methoxy-6-methylquinolin-4-ol), which is capable of reactivating viral transcription through an unknown mechanism. The objective of this project was to identify the molecular binding partners of MMQO and elaborate their role in the reactivation of HIV-1. We established that MMQO is capable of inducing HIV-1 independently of viral proteins by inducing transcription from proviral minigenomes lacking genes for viral components, allowing us to hypothesize that the compound primarily functions through host factors. Characterizing MMQO’s transcriptional profiles with total mRNA expression microarrays, we were able to identify numerous traits provoked by the drug. MMQO displayed a robust immunosuppressive nature, it affected cell proliferation by diminishing cMyc and Bcl-2 protein levels and increased the dysregulation of acetylation sensitive genes. These hallmarks indicated that MMQO mimics acetylated lysines of core histones and functions as a bromodomain and extraterminal domain (BET) protein family inhibitor. Further gene expression and proteomic analysis confirmed this supposition and we demonstrated that MMQO deposes of the BET family member Brd4 from global chromatin and antagonizes the pro-latent role of Brd4 near the transcription start site of HIV-1. Computational docking models also confirmed MMQO’s specificity towards the BET family bromodomains and an in vitro screening against the family members by FRET identified MMQO to have the highest affinity towards the Brd9 protein. Finally, we established that the inhibition of Brd9 had minimal effect on the proviral expression, suggesting that the primary function of MMQO on HIV-1 can be attributed to the displacement of Brd4. Due to the broad range of properties characteristic to BET family inhibitors, these molecules are currently being evaluated in clinical trials against various types of cancers and immune conditions. The dual functioning scaffold compound MMQO is a new member of this class of drugs. The minimalistic structure of MMQO shows promise for it to be further optimized for higher affinities towards Brd9 / 4 and could potentially be of use in research against a variety of diseases, including HIV.

Malaria, caused by the parasite Plasmodium falciparum, has a long history as a global health threat. The vector-borne disease causes millions of deaths yearly, especially in developing countries with tropical climates that facilitate transmission. Compounding the problem is the emergence of drug-resistant strains due to overuse of outdated treatments. New compounds with antiplasmodial activity are needed to be developed as effective drugs against malaria. The hypothesis for this project is that marine microorganisms have a high likelihood of yielding novel antiplasmodial chemotypes because of their high diversity, which has not yet been explored for antimalarial development. In this project, microbes harvested and fermented by the Harbor Branch Oceanographic Institute in Fort Pierce, Florida were explored as sources for antiplasmodial natural products. Using a SYBR Green I fluorescence-based assay, 1,000 microbial extracts were screened for inhibition of the multidrug-resistant Plasmodium falciparum strain Dd2. Dose-response analysis was performed on 46 fractions from isolates whose extracts demonstrated greater-than or equal to] 70% inhibition of Dd2 at 1 micro]g/mL. To evaluate cytotoxicity, the MTS cell viability assay was used to calculate IC50 of extracts from active isolates in NIH/3T3 embryonic mouse fibroblasts. Several extracts demonstrated low IC50 in Dd2 and high IC50 in 3T3, suggesting that they contain potential lead antimalarial compounds. Extracts with high selectivity indices (potent plasmodial inhibition with low mammalian toxicity) have been prioritized for dereplication, with the goal of identifying novel active components that can be developed as antimalarial drugs.
B.S.
Bachelors
Burnett School of Biomedical Sciences
Molecular Biology and Microbiology

Consumers view natural antioxidants as a safe means to reduce spoilage in foods. In addition, these compounds have been reported to be responsible for human health benefits. Identification of these compounds in peanut skins may enhance consumer interest, improve sales, and increase the value of peanuts. This study evaluated analytical methods which have not been previously incorporated for the analysis of peanut skins. Toyopearl size-exclusion chromatography (SEC) was used for separating phenolic size-classes in raw methanolic extract from skins of Gregory peanuts. This allowed for an enhanced analysis of phenolic content and antioxidant activity based on compound classes, and provided a viable preparatory separation technique for further identification. Toyopearl SEC of raw methanolic peanut skin extract produced nine fractions based on molecular size. Analysis of total phenolics in these fractions indicated Gregory peanut skins contain high concentrations of phenolic compounds. Further studies revealed the fractions contained compounds which exhibited antioxidant activities that were significantly higher than that of butylated hydroxyanisole (BHA), a common synthetic antioxidant used in the food industry. This indicates peanut skin extracts are a viable antioxidant source, and that synthetic antioxidants can be replaced with those naturally-derived from peanut by-products. Structures contained in each fraction were identified using high performance liquid chromatography (HPLC) coupled with electrospray ionization (ESI) ion trap mass spectrometry (MSn). Prior to this study, approximately 20 compounds have been identified in peanut skins. The combination of Toyopearl SEC with ESI-HPLC-MSn allowed for the identification of 314 phenolic-based compounds, most of which are newly discovered compounds in peanut skins. Many compounds identified are known to have powerful antioxidant effects, and also have been reported to exhibit numerous beneficial chemical and biological activities, including the treatment of various human health-related conditions. It is evident that peanut skins may be a potential untapped source for the extraction of natural food antioxidants, nutracueticals, and even pharmaceuticals. Because peanut skins are largely a wasted resource to peanut processors, the novel polyphenols identified in this research could have a significant financial impact on the peanut industry.
Ph. D.

Thesis (Ph.D.)--Kent State University, 2007.
Title from PDF t.p. (viewed Mar. 11, 2009). Advisor: Miguel Quiñones-Mateu. Keywords: HIV/AIDS, drug discovery, small molecule library screening, characterization of new antiretroviral drugs, highly active antiretroviral therapy. Includes bibliographical references (p. 180-200).

The physicochemical parameters of fifteen honey samples from a wide range of botanical origins were characterized to identify the influence of composition on the formation of alpha-dicarbonyl compounds during heating. Color, pH, moisture content, water activity, hydroxymethylfurfural (HMF), sugar and amino acid content were determined before and after storage at various time and temperatures. The effects of storage time and temperature on the formation of Maillard reaction product were also investigated. Analysis of the data has indicated that they have a significant impact on the rate of production of Maillard related compounds such as alpha-dicarbonyls and HMF. The content of free amino acids was also decreased 'over time with concomitant increase in color intensity. Furthermore, nine alpha-dicarbonyl compounds were detected in honey samples. The analysis of these compounds after derivatization with o-diaminobenzene resulted in the identification of three previously unreported derivatives in honey such as 3-deoxypentulose, 1,4-dideoxyhexulose and 3,4dideoxyglucosone-3-ene. More importantly, the detection of 5-hydroxycyclohexane-1,2,4-trione was to our knowledge the first cyclic alpha-dicarbonyl compound ever reported in literature. Characterization of this molecule by different mass spectrometric techniques and spiking experiments provided evidence that supported the precursor, the structure and proposed mechanism of formation.

Carissa lanceolata (conkerberry) is a perennial woody shrub used in traditional medicine by indigenous communities in Western Australia, the Northern Territory and Queensland for various medical conditions such as toothache, respiratory infections and the cleaning of sores, which all strongly indicate an antibacterial activity. A literature review revealed that the wood of this plant possesses significant antibacterial activity, which was found to be related to the presence of eudesmane type sesquiterpenes. C. edulis and C. carandus are frequently used in other traditional systems of medicine in different parts of the world, and thus have also been investigated for bioactive compounds and pharmacological properties. Some of these were found to be in line with the main findings of this work. Carissa lanceolata root was shown to exhibit significant antibacterial activity against both Gram negative and Gram positive organisms. A micro-broth dilution assay was performed on 96-well plates using resazurin as an indicator for microbial growth of Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. Bioassays carried out in this work showed that crude extracts of root bark and wood, particularly their polar constituents were more active against the four strains of bacteria tested.
Chemical investigation of the root bark revealed that it contains a volatile oil, which was isolated by steam distillation as well as solid phase micro extraction. It was found to consist of a single compound, which was identified as 2'-hydroxy acetophenone. The identity of this compound was confirmed by GC/MS and 1H NMR spectroscopy. Furthermore, the eudesmane-type sesquiterpene, carissone, was isolated from the root bark DCM and root wood hexane extracts. Its chemical identity was confirmed by IR, 1 [superscript] H and 13 [superscript] C NMR spectroscopy. The lignan, carinol, on the other hand, was isolated from the moderately polar fractions of the root wood MeOH extract. The obtained IR and 1 [superscript] H NMR data as well as Rf values all correspond to the literature. Two other yet unidentified compounds were isolated, but further studies into their chemistry and antibacterial activity were not possible in this current study. The antibacterial activity of the isolated compounds was considerable, with 2'-hydroxy acetophenone exhibiting the strongest effect, followed by carinol and then carissone.

Thesis (MSc)--Stellenbosch University, 2014.
ENGLISH ABSTRACT: Phytoestrogens are perceived as a safer alternative to conventional hormone replacement therapy (HRT) for the alleviation of menopausal symptoms as they present a decreased side-effect profile. The Cyclopia subternata (honeybush) methanol extract, SM6Met, displays estrogenic attributes desirable for the development of an phytoestrogenic nutraceutical, namely, estrogen receptor (ER) α antagonism, ERβ agonism, and antagonism of 17β-estradiol (E2)-induced breast cancer cell proliferation. Activity-guided fractionation was employed in an attempt to isolate and identify the compounds inducing the specific estrogenic profile of SM6Met. Fractions were evaluated for estrogenic attributes and major polyphenols present. Initial liquid-liquid fractionation of SM6Met yielded a polar fraction (PF) and a non-polar fraction (NPF), with the estrogenic attributes of interest retained and concentrated in NPF. Subsequent high performance counter-current chromatography (HPCCC) fractionation of NPF yielded three fractions (F1-F3). Interestingly, the fractions revealed separation of the previously demonstrated positive estrogenic attributes of NPF into separate fractions, with F1 and F2 acting as ERα antagonists, only F2 inducing antagonism of E2-induced breast cancer cell proliferation and only F3 retaining ERβ agonist activity. Although ERβ agonism displayed by F3 was robust and significantly higher than that of 10-11 M E2, it also displayed weak ERα agonism. Fractionation also for the first time in the study revealed ERβ antagonism, as induced by F1. In terms of major polyphenols HPCCC fractionation resulted in a divergence with F1 emerging as the dihydrochalcone-rich fraction and F2 as the flavanone and benzophenone-rich fraction, while the xanthones, flavones and phenolic acids were retained in F3. In addition, a preliminary absorption study was conducted using the ex vivo flow-through diffusion assay whereby the permeability of porcine small and large intestine for polyphenols in SM6Met was evaluated. The major compounds present in SM6Met were not able to penetrate the large intestinal mucosa, but small intestinal permeation of all major compounds in SM6Met ensued, with apparent permeability coefficient (Papp) values ranging from 1.91-3.74 x 10-6 cm.s-1, indicative of good intestinal absorption. Open source programs used for theoretical prediction of absorption gave conflicting results, emphasising the need to confirm predictions experimentally. ACD/Labs predicted poor intestinal absorption of SM6Met compounds based on physicochemical profiling, while OSIRIS and ChemAxon anticipated good absorption. In conclusion, activity-guided fractionation results suggest that retention of all the positive estrogenic attributes of the original SM6Met in one fraction is not an attainable goal. This suggests that several of the polyphenols present in SM6Met or NPF, through antagonistic, synergistic, or additive effects, may together be conferring these desired estrogenic traits. Thus production or isolation of a mixture of compounds, i.e. an “intelligent” mixture, should serve as a superior strategy in designing a nutraceutical product tailored to user demand of estrogenic activity.
AFRIKAANSE OPSOMMING: Fitoestrogene word beskou as ‘n veiliger alternatief vir konvensionele hormoon-vervangingsterapie (HVT) vir die verligting van simptome geassosiaeer met menopause aangesien dit ‘n verminderde newe-effek profiel vertoon. Die metanol ekstrak van Cyclopia subternata (heuningbos), SM6Met, vertoon estrogeniese eienskappe wat wenslik is vir die ontwikkeling van ‘n fitoestrogeen nutraseutiese middel, naamlik, estrogeen reseptor (ER) α antagonisme en ERβ agonisme, asook antagonisme van 17β-estradiol (E2) geïnduseerde proliferasie van borskankerselle. Aktiwiteit-begeleide fraksionering (ABF) is gebruik om die verbindings wat die spesifieke estrogeniese profiel aan SM6Met verleen te probeer isoleer en identifiseer. Fraksies is ge-evalueer vir estrogeniese eienskappe, asook vir die hoof polifenole teenwoordig. Aanvankilike vloeistof-vloeistof fraksionering van SM6Met het ‘n polêre fraksie (PF) en ‘n nie-polêre fraksie (NPF) opgelewer met behoud en konsentrering van die wenslike estrogeniese eienskappe in NPF. Daaropeenvolgende hoë werkverrigting teen-vloei chromatografie (HPCCC) van NPF het drie fraksies (F1-F3) opgelewer. Interessant genoeg het hierdie fraksies ‘n verdeling van die wenslike estrogeniese eienskappe van NPF in die individuele fraksies teweeggebring, deurdat F1 en F2 ERα antagonisme getoon het, F2 E2-geïnduseerde proliferasie van borskankerselle antagoniseer het, en net F3 ERβ agonis-aktiwiteit behou het. Alhoewel die ERβ agonis-aktiwiteit van F3 betekenisvol hoër was in vergelyking met die aktiwiteit van 10-11 M E2, het dit ook swak ERα agonisme getoon. Verder het fraksionering, vir die eerste keer in hierdie studie, ERβ antagonisme meegebring soos getoon deur F1. HPCCC het ook ‘n skeiding van die hoof polifenole veroorsaak, waarvolgens F1 as die dihidrogalkoon-ryke fraksie, F2 as die bensofenoon-ryke en flavanoon-ryke fraksie, en F3 as die xantoon-, flavoon- en fenoliese suur-ryke fraksie tevoorskyn gekom het. ‘n Voorlopige absorpsie studie, wat gebruik gemaak het van die ex vivo deurvloei diffusie toetssisteem, is uitgevoer om die deurlaatbaarheid van vark dik- en dunderm vir SM6Met polifenole te evalueer. Die hoof verbindings van SM6Met kon nie die dikderm mukosa penetreer nie, maar die deurlaatbaarheid van die dunderm vir alle SM6Met hoof polifenole is aangetoon, met skynbare deurlaatbaarheidskoëffisiënt (Papp) waardes wat strek vanaf 1.91 tot 3.74 x 10-6 cm.s-1, ooreenstemmend met goeie intestinale absorpsie. Oopbron programme, wat gebruik is vir die teoretiese voorspelling van absorpsie deur gebruik te maak van fisiese-chemiese profilering van verbindings, het teenstellende resultate opgelewer wat daarop dui dat hierdie voorspellings eksperimenteel bevestig moet word. ACD/Labs, wat van die fisiese-chemiese eienskappe van die verbinding gebruik maak, het swak intestinale absorpsie van die polifenole voorspel, terwyl OSIRIS en ChemAxon goeie absorpsie voorspel het. Ten slotte, resultate van aktiwiteit-begeleide fraksionering het getoon dat behoud van al die gewensde estrogeniese eienskappe van SM6Met in een fraksie nie ‘n haalbare doelwit is nie. Hierdie bevinding dui daarop dat verskeie van die polifenole teenwoordig in SM6Met of NPF saam, deur middel van antagonistiese, sinergistiese of additiewe effekte, die wenslike estrogeniese eieskappe verleen. Die ontwikkeling of isolering van ‘n mengsel van verbindings, met ander woorde ‘n ―intelligente‖ mengsel is dus ‘n beter strategie vir die ontwerp van ‘n estrogeniese nutraseutiese produk om die verbruikers-aanvraag van estrogeniese aktiwiteit te voorsien.

Thesis (Ph.D.)--Kent State University, 2008.
Title from PDF t.p. (viewed Dec. 14, 2009) Advisor: Miguel E. Quinones-Mateu. Keywords: biomedical research, cellular biology, molecular biology, virology. Includes bibliographical references (p. 201-228)

Tapura fischeri is a member of the family Dichapetalaceae and the only other member of this family naturally occurring in South Africa is Dichapetalum cymosum. Poisoning by D. cymosum results in the deaths of many domestic livestock each year due to the presence of fluoroacetate. The aim of the study was to determine if monofluoroacetate or another fluorinated compound is present in T. fischeri, and the possible role endophytes might play in the production of these compounds. Through NMR and GCMS studies it was established that trifluoroacetate is present in T. fischeri. Bacterial endophytes were isolated from plant material and shown to produce a fluorinated compound other than mono and trifluoroacetate. Since trifluoroacetic acid is extremely volatile, and evaporate from the plant extract over time, column chromatography, together with NMR was employed to isolate and identify other compounds responsible for antibacterial activity against the bacterium Enterococcus faecalis previously observed on TLC plates. Two compounds were isolated, and identified with NMR as a fatty acid and a fatty acid attached to glycerol. The names of the compounds could not be established with GCMS due to insufficient derivatization of the compounds. The antibacterial activity of the compounds were also analyzed using 96 well microtitre plates in liquid media, where it was determined that the compounds do not have antibacterial activity against E. faecalis. This indicated that previous results on TLC plates were false positives due to the hydrophobic nature of the fatty acid compounds. Transmission electron microscopy was done on leaf material to determine the presence of bacterial endophytes in the intracellular spaces of plant material, but none was detected. These results suggest a possitive correlation between the plant, its endophytes and the production of the fluorinated compound.
Dissertation (MSc)--University of Pretoria, 2014.
tm2015
Plant Science
MSc
Unrestricted

The high composition of fruits and vegetables in the daily diet is associated with cognitive well-being, especially in the elderly population. The phytonutrients are shown to have effects as antioxidants that neutralize oxidative stressors and can interact with molecular pathways to signal neuron survival. Adult hippocampal neurogenesis is a dynamic lifelong process of generating functional newborn neurons in the granular layer of the dentate gyrus from adult precursor cells. This process contributes to brain plasticity and plays a role in learning and memory. External stimuli such as environmental enrichment and physical activity are known to positively regulate this process. However, the role of nutrition and whether nutritional compounds have pro-neurogenic effects on adult hippocampal precursor cells are still elusive. In this study, I investigated the impact of dietary compounds in apples, a significant source of phytonutrients in our food, on adult hippocampal neurogenesis. I demonstrated that quercetin, the most abundant polyphenol in apple, induces cell cycle exit and differentiation of adult hippocampal precursor cells in monolayer culture. Furthermore, this compound also increases the number of surviving cells upon differentiation in vitro, through the activation of endogenous antioxidants in the Nrf2-Keap1 pathway and the prosurvival Akt pathway. Quercetin supplementation in vivo is also shown to significantly increase the number of surviving cells and new neurons in the dentate gyrus. To search for other potential active compounds in apple, I performed bioassay-guided fractionation whereby the flesh extract from apples of the Pinova cultivar was subjected to liquid- and solid phase separation and the active fraction was determined using primary neurosphere assays using cells derived from adult mouse dentate gyrus. Using mass spectometry, we revealed that the active compounds in the apple flesh extract are dihydroxybenzoate glycosides, which are non-flavonoid benzoic acid derivatives. I also confirmed that the isomers of these compounds; 2,3- and 3,5 dihydroxybenzoic acids significantly increase the number of neurospheres. Interestingly, 3,5 dihdroxybenzoic acid is an agonist of lactate receptor hydroxycarboxylic acid receptor 1 (HCAR1), with an even higher affinity than lactate. This receptor is suggested to mediate neurotrophic actions such as increasing production and release of BDNF. I also demonstrated for the first time that this receptor is presence in adult hippocampal precursor cells. To observe whether customary fruits or fruit-related products consumption affects adult hippocampal neurogenesis, I performed an experiment giving apple juice supplementation ad libitum to mice. I did not find a significant increase in net neurogenesis or the performance in the Morris water maze after apple juice supplementation. This is likely due to the low concentration of active compounds in apple juice failing to reach an effective concentration in the body. I conclude that apples provide potential proneurogenic compounds that can influence adult hippocampal neurogenesis through the activation of endogenous antioxidant mechanisms and molecular pathways for cell survival. Further studies are necessary to investigate the role of HCAR1 activation on adult hippocampal neurogenesis, which is a potential new mechanism to explain the health benefits of fruit and vegetable consumption
Eine Ernährung die täglich reich an Obst und Gemüse ist, hat insbesondere bei älteren Menschen einen positiven Einfluss auf kognitive Fähigkeiten. Pflanzeninhaltsstoffe wirken als natürliche Antioxidantien, indem sie oxidative Stressoren neutralisieren. Weiterhin beeinflussen pflanzliche Nährstoffe molekulare Signalwege welche beim Überleben von Neuronen eine Rolle spielen. Die adulte hippocampale Neurogenese ist ein dynamischer, lebenslanger Prozess, bei dem aus Vorläuferzellen funktionelle neue Neuronen in der Körnerzellschicht des Gyrus dentatus gebildet werden. Dieser Prozess trägt zur Plastizität des Gehirns bei und spielt eine bedeutende Rolle beim Lernen und für das Gedächtnis. Externe Stimuli wie zum Beispiel eine reizreiche Umgebung und körperliche Aktivität wirken als positive Regulatoren und begünstigen die adulte hippocampale Neurogenese. Welche Rolle die Ernährung dabei spielt und ob Nahrungsbestandteile einen proneurogenen Effekt auf adulte hippocampale Vorläuferzellen haben ist kaum bekannt. In diesem Projekt habe ich den Effekt von Nahrungsbestandteilen aus Äpfeln, welche eine bedeutende Quelle von pflanzlichen Nährstoffen in unserer Ernährung darstellen, auf die adulte hippocampale Neurogenese untersucht. Ich habe gezeigt, dass Querzetin, das am reichlichsten in Äpfeln enthaltende Polyphenol, in der Monolayer-Zellkultur den Austritt aus dem Zellzyklus induziert und die Differenzierung von adulten hippocampalen Vorläuferzellen fördert. Des Weiteren steigert Querzetin nach der Differenzierung in vitro die Anzahl an überlebenden Zellen. Dies geschieht durch die Aktivierung von endogenen Antioxidantien des Nrf2-Keap1-Signalweges und des für das Überleben von Zellen förderlichen Akt-Signalweges. Die Verabreichung von Querzetin in vivo als Nahrungsergänzungsmittel führte ebenfalls zu einem signifikanten Anstieg der Anzahl an überlebenden Zellen und neu gebildeten Nervenzellen im Gyrus dentatus. Um weitere potentiell aktive Wirkstoffe von Äpfeln zu bestimmen, habe ich eine Bioassay-ausgerichtete Fraktionierung durchgeführt, wobei der Fruchtfleischextrakt von Äpfeln der Sorte Pinova einer Fest-/ Flüssig-Separation unterzogen wurde. Die aktive Fraktion wurde anhand der primären Neurosphäre-Assay-Methode mit Zellen aus dem Gyrus dentatus adulter Mäuse ermittelt. Mittels spektrometrischer Analyse habe ich gezeigt, dass die aktiven Wirkstoffe im Fruchtfleischextrakt von Äpfeln zur Gruppe der Dihydroxybenzol-Glykosiden gehören, welche den nicht-flavonoiden Benzoesäure-Derivaten zuzuordnen sind. Im in vitro Neurosphäre-Assay habe ich zudem gezeigt, dass die Isomere dieser Wirkstoffe, die 2,3- und die 3,5-Dihydroxybenzoesäuren, die Anzahl der Neurosphären signifikant erhöhen. Interessanterweise ist die 3,5-Dihydroxybenzoesäure ein Agonist des Laktatrezeptors Hydroxycarboxylic acid receptor 1 (HCAR1) und weist sogar eine noch höhere Affinität als Laktat auf. Es wird suggeriert, dass dieser Rezeptor neurotrophische Wirkungen vermittelt, wie zum Beispiel eine erhöhte Produktion von BDNF und dessen Ausschüttung. Zudem habe ich das Vorkommen dieses Reporters erstmalig bei adulten hippocampalen Vorläuferzellen nachgewiesen. Um zu untersuchen, ob der Konsum handelsüblicher Obstprodukte die adulte hippocampale Neurogenese beeinflusst, habe ich Mäusen Apfelsaft ad libitum verabreicht. Nach der Gabe von Apfelsaft sah ich keinen signifikanten Anstieg der Gesamtneurogenese und keine Verbesserung der Leistungsfähigkeit im Morris-Wasserlabyrinth-Test. Dies ist bedingt durch eine zu geringe Konzentration der aktiven Wirkstoffe im Apfelsaft wodurch die wirksame Konzentration im Körper nicht erreicht wird. Ich schlussfolgere, dass in Äpfeln potentielle pro-neurogene Inhaltsstoffe enthalten sind, welche die adulte hippocampale Neurogenese beeinflussen. Dies wird insbesondere durch die Aktivierung endogener antioxidativer Mechanismen und molekularer Signalwege vermittelt, die für das Überleben von Zellen von Bedeutung sind. Weitere Studien sind nötig, um zu bestimmen wie sich die Aktivierung von HCAR1 auf die adulte hippocampale Neurogenese auswirkt. Dies stellt einen potentiellen neuen Wirkmechanismus dar, welcher die gesundheitlichen Vorteile von Obst- und Gemüsekonsum belegt

Phosphorus (P) regulates trophic status in most aquatic systems. However, only bioavailable P contributes to primary production. In most lakes and shallow seas, mineralisation of sediment P into its bioavailable form and its release to the water column is important for maintaining primary production. Sediment organic P forms a substantial proportion of this P to be mineralised and can originate from different sources on land (farmland, forests, etc.) or from primary production in the lake. These organic P forms can thus be expected to have differing composition, degradability and recyclable P content. Knowledge of the chemical structure of sediment organic P compounds is scarce, mainly due to lack of appropriate analytical techniques. The commonly used 31P-nuclear magnetic resonance (31P-NMR) technique, only identifies P binding groups, so a mass spectrometric (MS) analysis method was developed that allows individual sediment organic P compounds to be identified. EDTA as pre-extractant resulted in the highest P yield in subsequent NaOH extraction. Extracted organic P compound groups were identified using 31P-NMR. For identification of specific P compounds with MS, a sample preparation method prior to electrospray tandem mass spectrometry (ESI-MS/MS) analysis was developed. Liquid chromatography (LC) with porous graphitic carbon prior to ESI-MS/MS enhanced sensitivity and selectivity, enabling several of the ions detected to be identified as nucleotides. 31P-NMR analysis showed P monoesters to be the most stabile P compounds throughout a lake sediment profile. The developed LC-ESI-MS/MS analysis method revealed that some monoester-P (nucleotides) were labile, while other P compounds increased in concentration with Baltic Sea sediment depth and were therefore considered stabile. Differences in patterns of P compounds detected were also shown depending on catchment characteristics in relation to Baltic Sea sediment age. For cost-effective management of eutrophication, knowledge of the sources of degradable organic P forms, contributing to internal loading, is needed. This thesis showed the developed LC-ESI-MS/MS analysis method to be a powerful analytical tool for this purpose.

Although some progress has been made in the treatment of cancer over the last sixty years, the majority of chemotherapeutics has fallen short. Because general chemotherapies that target DNA replication have only a limited efficacy and significant non-target side-effects, a new paradigm for cancer drug development has been adopted. Using a molecular targeted approach, new gene and protein targets have been identified and the development of chemotherapies that are specific to these targets has already begun. In this study, compounds that interact with two key cancer targets, the G-quadruplex of the c-Myc promoter and p-glycoprotein, have been investigated. By developing such compounds, improvements in treatment efficacy is anticipated with an aspiration for decreased mortality attributable to cancer.Formation of DNA secondary structures, such as the G-quadruplex, in the NHE III1 region of the c-Myc promoter has been shown to repress c-Myc transcription. Because c-Myc is an oncogene that is overexpressed in a variety of cancers, stabilization of the G-quadruplex by small molecules would be advantageous in cancer treatment. Using Fluorescence Resonance Energy Transfer, with Taq Polymerase Stop assays for confirmation, a group of compounds were identified that stabilize the c-Myc G-quadruplex structure. Using a colon cancer model, two compounds were shown to decrease c-Myc gene and protein expression. Also, exposure to the compounds for 48 hours results in an induction of caspase-3, indicative of apoptosis. Furthermore, surface plasmon resonance suggests that compound-induced stabilization of the c-Myc G-quadruplex can prevent sustained binding of the regulatory protein NM23-H2 by increasing its dissociation from the G-quadruplex. This may subsequently prevent unraveling of the G-quadruplex.Because resistance to chemotherapy reduces its effectiveness, development of multidrug resistance (MDR) modulators was also studied. Psorospermin is a topoisomerase II-directed DNA alkylating agent active against MDR cell lines. In a study examining the mechanism of psorospermin's P-glycoprotein modulation, Flow Cytometry demonstrated that doxorubicin-resistant multiple myeloma cells pre-treated with psorospermin enhanced intracellular retention of doxorubicin. Because neither transcription of mdr1 nor translation of P-glycoprotein was downregulated by psorospermin, resistance reversal is most likely due to a direct interaction between the side chain of psorospermin and P-glycoprotein, inhibiting drug efflux.