Thesis (Ph. D.)--University of California, Riverside, 2009. / Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed March 10, 2010). Includes bibliographical references. Also issued in print.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2010. / Härtill 3 uppsatser.

No description available.

This PhD thesis investigates the transport and distribution of short-lived halogenated organic substances in the tropical tropopause layer (TTL) in the Pacific Ocean. Short-lived halocarbons are one of the major groups of the ozone depleting substances as they provide a source for the active halogens which decrease ozone in the atmosphere. The TTL serves as the primary gateway of tropospheric air to enter the stratosphere. The air which enters the stratosphere is distributed all over the globe. Thus, the research on which tropospheric air masses go into the TTL, its structure and composition and the transport within is crucial. This thesis uses the UK Meteorological Office Lagrangian particle dispersion model NAME to (i) support the flight planning activities and achieve the multi aircraft coordination in CAST, CONTRAST, ATTREX 2014 campaigns, and (ii) quantify the amount and distribution of short-lived halocarbons in the TTL, and explain differences in these vertical distributions and transport characteristics. The halocarbons of interest are methyl iodide (CH3I), bromoform (CHBr3) and dibromomethane (CH2Br2). A new NAME procedure was developed and operated successfully to provide routine simulations and near real-time products suitable for guiding the CAST, CONTRAST and ATTREX aircraft in order to achieve their mission scientific objectives, and to make coordinated measurements. NAME was used post-campaign to analyse distribution of short-lived halocarbons in the TTL, identify their source regions and transport timescales. A new approach is proposed to investigate the TTL composition in terms of the boundary layer air influence, and subsequently quantify CH3I, CHBr3 and CH2Br2 by estimating their boundary layer and background contribution. The sums of these modelled estimates are in good agreement with the ATTREX 2014 and 2013 CH3I, CHBr3 and CH2Br2 observations. The quantification of the contribution of short-lived bromocarbons to the active bromine in the TTL was achieved, and the results lie within the range of the recent literature studies. The final focus of this thesis is on how well NAME represents the particle displacement via convection. Convection is the major transport pathway for the short-lived halocarbons to reach the TTL. The role of convection in transporting CH3I, CHBr3 and CH2Br2 to the TTL is assessed using the new convection scheme in NAME. A validation of the performance of this scheme is provided, showing that it yields improved and more realistic representation of the particle displacement via convection.

ALENCAR, Poliana de Oliveira Cavalcante. Polissacarídeos obtidos da alga marinha vermelha Gracilaria caudata j. agardh: estudo químico-estrutural e avaliação de atividade antioxidante. 2016. 94 f. Dissertação (Mestrado em Bioquímica) - Universidade Federal do Ceará, Fortaleza-CE, 2016. / Submitted by Eric Santiago (erichhcl@gmail.com) on 2016-07-19T15:04:04Z No. of bitstreams: 1 2016_dis_pocalencar.pdf: 1106975 bytes, checksum: a8651f16465608b575a1c479fca0b598 (MD5) / Approved for entry into archive by José Jairo Viana de Sousa (jairo@ufc.br) on 2016-08-02T20:30:51Z (GMT) No. of bitstreams: 1 2016_dis_pocalencar.pdf: 1106975 bytes, checksum: a8651f16465608b575a1c479fca0b598 (MD5) / Made available in DSpace on 2016-08-02T20:30:51Z (GMT). No. of bitstreams: 1 2016_dis_pocalencar.pdf: 1106975 bytes, checksum: a8651f16465608b575a1c479fca0b598 (MD5) Previous issue date: 2016 / Red algae are natural sources of sulfated polysaccharides, which are widely used in the food and pharmaceutical industries. This study aims to obtain the total sulfated polysaccharides from the red seaweed Gracilaria caudata (PSG) through enzymatic extraction, determine their chemical structure and their antioxidant potential. Chemical analysis revealed that the obtained extract is comprised of 85% total sugars and 1% of contaminating proteins. Through Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES), the PSG showed a percentage of 0.9% sulfur atoms and a degree of sulfation of 0.14%. The average molar mass of PSG was determined through gel permeation chromatography (GPC) and was determined as 116.51 kDa. The total sulfated olysaccharides were subjected to structural characterization tests through infrared Fourier transform spectroscopy and C13 and H1 Nuclear Magnetic Resonance (NMR) analysis, identifying the PSG as galactan from the agaran type. The in vitro antioxidant activity of PSG was determined using tests such as elimination of DPPH radical, chelation of ferrous ion and total antioxidant capacity. The results indicated that such polysaccharides have the capacity to scavenge free radicals significantly and in a concentration-dependent maner. The in vivo antioxidant activity of PSG was valuated in an oxidative stress model induced by 2,2'-azobis- -amidinopropane (AAPH) in rats, with subsequent dosage of antioxidant enzyme system markers, such as catalase (CAT) and superoxide dismutase (SOD), and the quantitation of oxidative damage markers such as nitrite and thiol. The results showed an improvement in the redox imbalance through increased CAT activity and increased SOD activity with the best response found at a dose of 3 mg / kg. Because of these results, the sulfated polysaccharide obtained from seaweed Gracilaria caudata shows potential for their being used in the food and pharmaceutical industry. / Algas marinhas do filo Rhodophyta são fontes naturais de polissacarídeos sulfatados que são amplamente utilizados na indústria alimentícia e na indústria farmacêutica. O presente trabalho teve como finalidade obter os polissacarídeos sulfatados totais da alga marinha vermelha Gracilaria caudata (PSG) por extração enzimática, determinar a sua estrutura química e testar o seu potencial antioxidante. As análises químicas revelaram a presença de 85% de açúcares totais e 1% de proteínas contaminantes no extrato obtido. Através de espectrometria de emissão óptica com plasma (ICP-OES), os PSG apresentaram 0,9% de átomos de enxofre e um grau de sulfatação de 0,14%. A massa molar média dos PSG foi determinada por cromatografia em permeação em gel (GPC) e mostrou ser da ordem de 116,51 kDa. Os polissacarídeos sulfatados totais foram submetidos a testes de caracterização estrutural através da análise por espectroscopia de infravermelho com transformada de Fourier e ressonância magnética nuclear (RMN) de próton (1H) e carbono (13C), identificando os PSG como galactana do tipo agarana. A atividade antioxidante in vitro dos PSG foi avaliada através de testes, tais como, ensaios de eliminação do radical DPPH, quelação do íon ferroso e capacidade antioxidante total. Os resultados indicaram que tais polissacarídeos possuem capacidade de sequestrar radicais livres de maneira significativa e concentração-dependente. A atividade antioxidante in vivo dos PSG foi avaliada em modelo de estresse oxidativo induzido pelo 2,2’-azobis-2-amidinopropano (AAPH) em ratos, com posterior dosagem de marcadores do sistema antioxidante enzimático, como catalase (CAT) e superóxido desmutase (SOD), além da quantificação de marcadores de dano oxidativo, como nitrito e tiol. O resultado demonstrou uma melhora no desequilíbrio redox pelo aumento da atividade da CAT e aumento da atividade da SOD, com melhor resposta na dose de 3 mg/kg. Devido a estes resultados, os polissacarídeos sulfatados obtidos a partir da alga marinha Gracilaria caudata mostram potencial de virem a ser utilizados na indústria alimentícia e farmacêutica.

nÃo hà / Algas marinhas do filo Rhodophyta sÃo fontes naturais de polissacarÃdeos sulfatados que sÃo amplamente utilizados na indÃstria alimentÃcia e na indÃstria farmacÃutica. O presente trabalho teve como finalidade obter os polissacarÃdeos sulfatados totais da alga marinha vermelha Gracilaria caudata (PSG) por extraÃÃo enzimÃtica, determinar a sua estrutura quÃmica e testar o seu potencial antioxidante. As anÃlises quÃmicas revelaram a presenÃa de 85% de aÃÃcares totais e 1% de proteÃnas contaminantes no extrato obtido. AtravÃs de espectrometria de emissÃo Ãptica com plasma (ICP-OES), os PSG apresentaram 0,9% de Ãtomos de enxofre e um grau de sulfataÃÃo de 0,14%. A massa molar mÃdia dos PSG foi determinada por cromatografia em permeaÃÃo em gel (GPC) e mostrou ser da ordem de 116,51 kDa. Os polissacarÃdeos sulfatados totais foram submetidos a testes de caracterizaÃÃo estrutural atravÃs da anÃlise por espectroscopia de infravermelho com transformada de Fourier e ressonÃncia magnÃtica nuclear (RMN) de prÃton (1H) e carbono (13C), identificando os PSG como galactana do tipo agarana. A atividade antioxidante in vitro dos PSG foi avaliada atravÃs de testes, tais como, ensaios de eliminaÃÃo do radical DPPH, quelaÃÃo do Ãon ferroso e capacidade antioxidante total. Os resultados indicaram que tais polissacarÃdeos possuem capacidade de sequestrar radicais livres de maneira significativa e concentraÃÃo-dependente. A atividade antioxidante in vivo dos PSG foi avaliada em modelo de estresse oxidativo induzido pelo 2,2â-azobis-2-amidinopropano (AAPH) em ratos, com posterior dosagem de marcadores do sistema antioxidante enzimÃtico, como catalase (CAT) e superÃxido desmutase (SOD), alÃm da quantificaÃÃo de marcadores de dano oxidativo, como nitrito e tiol. O resultado demonstrou uma melhora no desequilÃbrio redox pelo aumento da atividade da CAT e aumento da atividade da SOD, com melhor resposta na dose de 3 mg/kg. Devido a estes resultados, os polissacarÃdeos sulfatados obtidos a partir da alga marinha Gracilaria caudata mostram potencial de virem a ser utilizados na indÃstria alimentÃcia e farmacÃutica. / Red algae are natural sources of sulfated polysaccharides, which are widely used in the food and pharmaceutical industries. This study aims to obtain the total sulfated polysaccharides from the red seaweed Gracilaria caudata (PSG) through enzymatic extraction, determine their chemical structure and their antioxidant potential. Chemical analysis revealed that the obtained extract is comprised of 85% total sugars and 1% of contaminating proteins. Through Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES), the PSG showed a percentage of 0.9% sulfur atoms and a degree of sulfation of 0.14%. The average molar mass of PSG was determined through gel permeation chromatography (GPC) and was determined as 116.51 kDa. The total sulfated olysaccharides were subjected to structural characterization tests through infrared Fourier transform spectroscopy and C13 and H1 Nuclear Magnetic Resonance (NMR) analysis, identifying the PSG as galactan from the agaran type. The in vitro antioxidant activity of PSG was determined using tests such as elimination of DPPH radical, chelation of ferrous ion and total antioxidant capacity. The results indicated that such polysaccharides have the capacity to scavenge free radicals significantly and in a concentration-dependent maner. The in vivo antioxidant activity of PSG was valuated in an oxidative stress model induced by 2,2'-azobis- -amidinopropane (AAPH) in rats, with subsequent dosage of antioxidant enzyme system markers, such as catalase (CAT) and superoxide dismutase (SOD), and the quantitation of oxidative damage markers such as nitrite and thiol. The results showed an improvement in the redox imbalance through increased CAT activity and increased SOD activity with the best response found at a dose of 3 mg / kg. Because of these results, the sulfated polysaccharide obtained from seaweed Gracilaria caudata shows potential for their being used in the food and pharmaceutical industry.

PhD (Chemistry) / Department of Chemistry

<div> <div> <div> <p>As a major part of the dietary fiber classification, plant polysaccharides often have chemically complex structures which may differ by genera and species, and perhaps even by genotype and growing environment. Arabinoxylans from cereal cell walls are known to differently impact human gut microbiota composition and fermentation metabolites due to variability in chemical structure, though specificities of structure to these functions are not known at the level of genotype ́ environment. In the first study, corn bran arabinoxylan (CAX) extracted from 4 genotypes ́ 3 growing years at the Purdue Agronomy Farm was compared in human fecal fermentations to test the hypotheses that, 1) CAXs extracted from brans from different corn genotypes and grown over different years (environments) show distinct structures, and 2) these cause differences in gut microbiota response and fermentation metabolites. Monosaccharides and linkage analysis revealed that CAXs had different structures and the differences were genotype-specific, but not significantly due to environment. PCA analysis revealed that both short chain fatty acid production and the microbial community shifted also in a genotype-specific way. Thus, small structural changes, in terms of sugar and linkage compositions, cause significant changes in fermentation response showing very high specificity of structure to gut microbiota function. </p> <p>Insoluble fermentable cell wall matrix fibers have been shown to support beneficial butyrogenic Clostridia, but have restricted use in food products due to their insoluble character.</p></div></div> </div> <div> <div> <div> <p>In the second study, a soluble fiber matrix was developed that exhibited a similar fermentation effect as fermentable insoluble fiber matrices. Low arabinose/xylose ratio CAX was extracted with two concentrations of sodium hydroxide to give soluble polymers with relatively low and high residual ferulic acid (CAX-LFA and CAX-HFA). After laccase treatment to make diferulate crosslinks, soluble matrices were formed with average size of 3.5 to 4.5 mer. In vitro human fecal fermentation of CAX-LFA, CAX-HFA, soluble crosslinked ~3.5 mer CAX-LFA (SCCAX- LFA), and ~4.5 mer SCCAX-HFA revealed that the SCCAX matrices had slower fermentation property and higher butyrate proportion in SCCAX-HFA. 16S rRNA gene sequencing showed that SCCAX-HFA promoted OTUs associated with butyrate production including Unassigned Ruminococcaceae, Unassigned Blautia, Fecalibacterium prausnitzii, and Unassigned Clostridium. This is the first work showing the fabrication of soluble crosslinked fiber matrices that favors growth of butyrogenic bacteria. </p> <p>Moreover, these same SCCAXs exhibited an interesting gel forming property on simple pH reduction, which is similar in gelling property to low acyl gellan gum, though is differently readily soluble in water. Both of the SCCAXs formed gels at pH 2, with SCCAX-HFA forming the stronger gel. Gels showed shear-thinning behavior and a thermal and pH reversible property. A gel forming mechanism was proposed involving noncovalent crosslinking including hydrogen bonds and hydrophobic interaction among the SCCAX complexes. This mechanism was supported by structural characterization of SCCAX complexes using a Zeta-sizer and FT-IR spectroscopy. SCCAX-HFA could be used in low sugar gels and has the above property of promoting butyrogenic bacteria in the gut. </p> <p>In conclusion, gut microbiota responds differentially to CAXs with various fine structures. This probably due to dietary fiber-gut microbiota relationships have been evolved over time to be highly specific. Forming soluble fiber matrices could be a good strategy to promote butyrogenic bacteria and improve gut health, in a readily usable form in beverages.</p></div></div></div>

Objects can be said to be structured when their representation also contains their parts. While OWL in general can describe structured objects, description graphs are a recent, decidable extension to OWL which support the description of classes of structured objects whose parts are related in complex ways. Classes of chemical entities such as molecules, ions and groups (parts of molecules) are often characterised by the way in which the constituent atoms of their instances are connected via chemical bonds. For chemoinformatics tools and applications, this internal structure is represented using chemical graphs. We here present a chemical knowledge base based on the standard chemical graph model using description graphs, OWL and rules. We include in our ontology chemical classes, groups, and molecules, together with their structures encoded as description graphs. We show how role-safe rules can be used to determine parthood between groups and molecules based on the graph structures and to determine basic chemical properties. Finally, we investigate the scalability of the technology used through the development of an automatic utility to convert standard chemical graphs into description graphs, and converting a large number of diverse graphs obtained from a publicly available chemical database. / Computer Science (School of Computing) / M. Sc. (Computer Science)

Au cours de ce travail de thèse, nous nous sommes intéressés aux études taxonomiques des deux souches TN17 et Fr10 qui sont deux nouvelles espèces du genre Streptomyces dont nous avons proposé les nomenclatures suivantes : Streptomyces lilaceus sp. TN17 et Streptomyces microflavus sp. Fr10. A partir de la souche Streptomyces lilaceus sp. TN17, trois molécules on été purifiées et identifiées par le biais de plusieurs techniques spectroscopiques, il s’agit d’un dérivé de DKP (L-Leu, L-Arg), un dérivé de phtalate le di-(2-éthylhexyl) phtalate et un tértrapeptide cyclique : le 1 - [2 -(cyclopentanecarbonyl-3-phenylpropionyl] – pyrrolidine-2-carboxylique (1-carbamoyl-propyl)-amide. Ces trois molécules présentent des activités antibactériennes et antifongiques. Suite au criblage des souches de bactéries lactiques productrices de bactériocines de la collection de notre laboratoire et leurs caractérisations, nous avons identifié une nouvelle souche de Lactobacillus nommée Lactobacillus plantarum sp.TN635 qui produit une bactériocine « BacTN635 » de 3,8 KDa. Cette dernière a été purifiée à homogénéité, elle possède un spectre d’action très large contre les bactéries à Gram+, à Gram- et contre les champignons filamenteux et unicellulaires. BacTN635 a un effet bactéricide contre Listeria ivanovii BUG 496 et fongistatique contre Candida tropicalis R2 CIP203. / In This Thesis, we are interested in taxonomic studies of two strains TN17 and Fr10 which are two new species of the genus Streptomyces, and we have proposed the following names: Streptomyces lilaceus sp. TN17 and Streptomyces microflavus sp. Fr10. From Streptomyces lilaceus strain sp. TN17, three molecules have been purified and identified by means of several spectroscopic techniques, it is a derivative of DKP (L-Leu, Larg), a derivative of phthalate di-(2-ethylhexyl) phthalate and cyclic peptide 1 - [2 - (cyclopentanecarbonyl-3-phenylpropionyl] - pyrrolidine-2-carboxylic acid (1-carbamoylpropyl)- amide. All three molecules exhibit antibacterial and antifungal activities. A novel strain of lactic acid bacteria was isolated and characterized from a collection of our laboratory. It’s identified as a new strain of Lactobacillus, named Lactobacillus plantarum sp.TN635 producing a new bacteriocin "BacTN635" of 3.8 kDa, purified to homogeneity and spectrum with a very broad action against Gram + and Gram-, filamentous and unicellular fungi. BacTN635 has a bactericidal effect against Listeria ivanovii BUG 496 and fungistatic against Candida tropicalis R2 CIP203.