Bridging the Scale Gap from Leaf to Canopy in Biosphere-Atmosphere Gas and Particle Exchanges

Terrestrial ecosystems, occupying more than 25% of the Earth's surface, can serve as

`biological valves' in regulating the anthropogenic emissions of atmospheric aerosol

particles and greenhouse gases (GHGs) as responses to their surrounding environments.

While the signicance of quantifying the exchange rates of GHGs and atmospheric

aerosol particles between the terrestrial biosphere and the atmosphere is

hardly questioned in many scientic elds, the progress in improving model predictability,

data interpretation or the combination of the two remains impeded by

the lack of precise framework elucidating their dynamic transport processes over a

wide range of spatiotemporal scales. The diculty in developing prognostic modeling

tools to quantify the source or sink strength of these atmospheric substances

can be further magnied by the fact that the climate system is also sensitive to the

feedback from terrestrial ecosystems forming the so-called `feedback cycle'. Hence,

the emergent need is to reduce uncertainties when assessing this complex and dynamic

feedback cycle that is necessary to support the decisions of mitigation and

adaptation policies associated with human activities (e.g., anthropogenic emission

controls and land use managements) under current and future climate regimes.

With the goal to improve the predictions for the biosphere-atmosphere exchange

of biologically active gases and atmospheric aerosol particles, the main focus of this

dissertation is on revising and up-scaling the biotic and abiotic transport processes

from leaf to canopy scales. The validity of previous modeling studies in determining

iv

the exchange rate of gases and particles is evaluated with detailed descriptions of their

limitations. Mechanistic-based modeling approaches along with empirical studies

across dierent scales are employed to rene the mathematical descriptions of surface

conductance responsible for gas and particle exchanges as commonly adopted by all

operational models. Specically, how variation in horizontal leaf area density within

the vegetated medium, leaf size and leaf microroughness impact the aerodynamic attributes

and thereby the ultrane particle collection eciency at the leaf/branch scale

is explored using wind tunnel experiments with interpretations by a porous media

model and a scaling analysis. A multi-layered and size-resolved second-order closure

model combined with particle

uxes and concentration measurements within and

above a forest is used to explore the particle transport processes within the canopy

sub-layer and the partitioning of particle deposition onto canopy medium and forest

oor. For gases, a modeling framework accounting for the leaf-level boundary layer

eects on the stomatal pathway for gas exchange is proposed and combined with sap

ux measurements in a wind tunnel to assess how leaf-level transpiration varies with

increasing wind speed. How exogenous environmental conditions and endogenous

soil-root-stem-leaf hydraulic and eco-physiological properties impact the above- and

below-ground water dynamics in the soil-plant system and shape plant responses

to droughts is assessed by a porous media model that accommodates the transient

water

ow within the plant vascular system and is coupled with the aforementioned

leaf-level gas exchange model and soil-root interaction model. It should be noted

that tackling all aspects of potential issues causing uncertainties in forecasting the

feedback cycle between terrestrial ecosystem and the climate is unrealistic in a single

dissertation but further research questions and opportunities based on the foundation

derived from this dissertation are also brie

y discussed.

The Synthesis of Novel N-Heterocyclic Scaffolds and Diazirine-Based Molecular Tags

N-Heterocycles are ubiquitous in biologically active natural products and pharmaceuticals. Yet, new syntheses and modifications of N-heterocycles are continually of interest for the purposes of expanding chemical space, finding quicker synthetic routes, better pharmaceuticals, and even new handles for molecular labeling. There are several iterations of molecular labeling; the decision of where to place the label is as important as of which visualization technique to emphasize.

Piperidine and indole are two of the most widely distributed N-heterocycles and thus were targeted for synthesis, functionalization, and labeling. The major functionalization of these scaffolds should include a nitrogen atom, while the inclusion of other groups will expand the utility of the method. Towards this goal, ease of synthesis and elimination of step-wise transformations are of the utmost concern. Here, the concept of electrophilic amination can be utilized as a way of introducing complex secondary and tertiary amines with minimal operations.

Molecular tags should be on or adjacent to an N-heterocycle as they are normally the motifs implicated at the binding site of enzymes and receptors. The labeling techniques should be useful to a chemical biologist, but should also in theory be useful to the medical community. The two types of labeling that are of interest to a chemist and a physician would be positron emission tomography (PET) and magnetic resonance imaging (MRI).

Coincidentally, the 3-positions of both piperidine and indole are historically difficult to access and modify. However, using electrophilic amination techniques, 3-functionalized piperidines can be synthesized in good yields from unsaturated amines. In the same manner, 3-labeled piperidines can be obtained; the piperidines can either be labeled with an azide for biochemical research or an 18F for PET imaging research. The novel electrophiles, N-benzenesulfonyloxyamides, can be reacted with indole in one of two ways: 3-amidation or 1-amidomethylation, depending on the exact reaction conditions. Lastly, a novel, hyperpolarizable 15N2-labeled diazirine has been developed as an exogenous and versatile tag for use in magnetic resonance imaging.

Asymmetric oxidation of sulfides

This review discusses synthesis of enantiopure sulfoxides through the asymmetric oxidation of prochiral sulfides. The use of metal complexes to promote asymmetric sulfoxidation is described in detail, with a particular emphasis on the synthesis of biologically active sulfoxides. The use of non-metal-based systems, such as oxaziridines, chiral hydroperoxides and peracids, as well as enzyme-catalyzed sulfoxidations is also examined.

Peptidomic approach identifies cruzioseptins, a new family of potent antimicrobial peptides in the splendid leaf frog, Cruziohyla calcarifer

Phyllomedusine frogs are an extraordinary source of biologically active peptides. At least 8 families of antimicrobial peptides have been reported in this frog clade, the dermaseptins being the most diverse. By a peptidomic approach, integrating molecular cloning, Edman degradation sequencing and tandem mass spectrometry, a new family of antimicrobial peptides has been identified in Cruziohyla calcarifer. These 15 novel antimicrobial peptides of 20–32 residues in length are named cruzioseptins. They are characterized by having a unique shared N-terminal sequence GFLD– and the sequence motifs –VALGAVSK– or –GKAAL(N/G/S) (V/A)V– in the middle of the peptide. Cruzioseptins have a broad spectrum of antimicrobial activity and low haemolytic effect. The most potent cruzioseptin was CZS-1 that had a MIC of 3.77 μM against the Gram positive bacterium, Staphylococcus aureus and the yeast Candida albicans. In contrast, CZS-1 was 3–fold less potent against the Gram negative bacterium, Escherichia coli (MIC 15.11 μM). CZS-1 reached 100% haemolysis at 120.87 μM. Skin secretions from unexplored species such as C. calcarifer continue to demonstrate the enormous molecular diversity hidden in the amphibian skin. Some of these novel peptides may provide lead structures for the development of a new class of antibiotics and antifungals of therapeutic use.

Dispositifs optoélectroniques à base de semi-conducteurs organiques en couches minces

Les petites molécules de type p à bandes interdites étroites sont de plus en plus perçues comme des remplaçantes possibles aux polymères semi-conducteurs actuellement utilisés conjointement avec des dérivés de fullerènes de type n, dans les cellules photovoltaïques organiques (OPV). Par contre, ces petites molécules tendent à cristalliser facilement lors de leur application en couches minces et forment difficilement des films homogènes appropriés. Des dispositifs OPV de type hétérojonction de masse ont été réalisés en ajoutant différentes espèces de polymères semi-conducteurs ou isolants, agissant comme matrices permettant de rectifier les inhomogénéités des films actifs et d’augmenter les performances des cellules photovoltaïques. Des polymères aux masses molaires spécifiques ont été synthétisés par réaction de Wittig en contrôlant précisément les ratios molaires des monomères et de la base utilisée. L’effet de la variation des masses molaires en fonction des morphologies de films minces obtenus et des performances des diodes organiques électroluminescentes reliées, a également été étudié. La microscopie électronique en transmission (MET) ou à balayage (MEB) a été employée en complément de la microscopie à force atomique (AFM) pour suivre l’évolution de la morphologie des films organiques minces. Une nouvelle méthode rapide de préparation des films pour l’imagerie MET sur substrats de silicium est également présentée et comparée à d’autres méthodes d’extraction. Motivé par le prix élevé et la rareté des métaux utilisés dans les substrats d’oxyde d’indium dopé à l’étain (ITO), le développement d’une nouvelle méthode de recyclage eco-responsable des substrats utilisés dans ces études est également présenté.

Perturbations in Blood Phosphatidylcholine and Sphingomyelin Fatty Acid Composition in a Sample Population of Cigarette Smokers

Docosahexaenoic (DHA) and arachidonic acids (AA) are polyunsaturated fatty acids (PUFAs), major components of brain tissue and neural systems, and the precursors of a number of biologically active metabolites with functions in inflammation resolution, neuroprotection and other actions. As PUFAs are highly susceptible to peroxidation, we hypothesised whether cigarette smokers would present altered PUFAs levels in plasma and erythrocyte phospholipids. Adult males from Indian, Sri-Lankan or Bangladeshi genetic backgrounds who reported smoking between 20 and 60 cigarettes per week were recruited. The control group consisted of matched non-smokers. A blood sample was taken, plasma and erythrocyte total lipids were extracted, phospholipids were separated by thin layer chromatography, and the fatty acid content analysed by gas chromatography. In smokers, dihomo-gamma-linolenic acid, the AA precursor, was significantly reduced in plasma and erythrocyte phosphatidylcholine. AA and DHA were significantly reduced in erythrocyte sphingomyelin. Relatively short term smoking has affected the fatty acid composition of plasma and erythrocyte phospholipids with functions in neural tissue composition, cell signalling, cell growth, intracellular trafficking, neuroprotection and inflammation, in a relatively young population. As lipid peroxidation is pivotal in the pathogenesis of atherosclerosis and neurodegenerative diseases such as Alzheimer disease, early effects of smoking may be relevant for the development of such conditions.

Antibacterial activity of the marine sponge Ircinia Campana collected at Punta Uva Limón against Staphylococcus Aureus

The sponges are simple multicellularorganisms; they inhabit in marine environments from the polar seas to the tropical waterswhere they are more abundant. These species are exposed to large populations of microbes, reason that explains their complex morphological and cellular defense mechanism, which are used by these organisms to fight against pathogens. The purpose of this study was to evaluate the antibacterial activity of the marine sponge Ircinia campana, whichinhabits in the south of the Caribbean coast of Costa Rica against  Sthapylococcus aureus gram-positive bacteria. Sampleswere collected in Punta Uva in Limónduring July of 2007. The active compounds were obtainedby extraction with acetone (crude extract); and subsequently, chromatographic extracts were obtained using fractions 1:4 hexane: ethyl acetate. The antibacterial activities of the different fractions, including the  crude extract were tested.Our results suggest a zone of inhibition of 14.60 ±0.25 mm for the crude extract and18.70±0.25mm for the most active fraction separated by chromatography. The metabolite responsible for the antibacterial activity was isolated by High Performance Liquid Chromatography (HPLC)and preliminarily characterized through ultraviolet (UV) and infrared (IR) spectroscopy.

Modyfikacja aglikonu Josamycyny z wykorzystaniem regioselektywnej substytucji nukleofilowej typu SN1’ i dipolarnej cykloaddycji Huisgena

Wydział Chemii: Zakład Syntezy i Struktury Związków Organicznych

Utilização de bagaço de maçã como ingrediente alimentar em iogurte com potencial efeito benéfico para a saúde

O desenvolvimento de alimentos funcionais evoluiu consideravelmente ao longo dos anos e a capacidade tecnológica para produzir um alimento com compostos fisiologicamente ativos tem crescido significativamente. O presente trabalho teve como objetivo criar um novo alimento, utilizando um subproduto proveniente da indústria agroalimentar. O alimento seleccionado foi o iogurte natural, o qual foi enriquecido com um extrato de bagaço de maçã. O bagaço de maçã contém compostos fenólicos e fibra, mostrando atividade antioxidante significativa e por conseguinte apresenta um potencial efeito positivo na saúde. Avaliaram-se características químicas do bagaço de maçã e das farinhas obtidas a partir deste subproduto, designadamente: acidez, teor em açúcares totais e redutores, cinza, matéria gorda, humidade, proteína bruta, fibra dietética insolúvel e solúvel. O extrato aquoso obtido a partir do subproduto foi também caracterizado quanto ao seu conteúdo fenólico e atividade antioxidante. O iogurte produzido com incorporação do extrato de bagaço de maçã foi estudado do ponto de vista de parâmetros químicos tais como acidez, açúcares totais, cinza, humidade, proteína bruta, pH e fibra bruta, conteúdo em fenólicos totais e atividade antioxidante. O subproduto, os extratos e o iogurte foram também avaliados quanto à sua carga microbiológica. Na caracterização química do bagaço foram obtidos os seguintes valores, expressos em base seca: 2,0±0,01% de acidez (expressa em equivalentes de ácido málico); 15,96±1,53% de açúcares totais; 13,35±1,91% de açúcares redutores; 1,88±0,07% de cinza, 2,49±0,5% de matéria gorda, 81,17±1,98% de humidade e 5,01±0,01% de proteína bruta. Quanto ao seu conteúdo em fibra dietética, o bagaço contém na sua composição 65,80% de fibra dietética insolúvel e 4,90% de fibra dietética solúvel. A farinha obtida após secagem a 60 °C do bagaço de maçã apresentou, na base seca, 1,9±0,04% de acidez, 10,57±1,31% de açúcares totais; 8,50±1,00% de açúcares redutores; 2,22±0,04%de cinza, 4,73±0,11% de matéria gorda, 6,34±0,62% de humidade e 5,40±0,26% de proteína. A atividade antioxidante do extrato aquoso, (AQ_6X10) obtido do bagaço de maçã, utilizado para incorporação no iogurte, determinada através do método ABTS foi de 5,00±1,28µmol TE/g amostra e apresentou um teor em compostos fenólicos de 221,42±0,734 mg EAG/ 100g de extrato, na base seca. Ao nível microbiológico o extrato revelou parâmetros aceitáveis, de acordo com a tabela 13 (anexos 3), para utilização como ingrediente alimentar. Os iogurtes produzidos foram analisados quimicamente. O iogurte, com extrato aquoso de bagaço de maçã incorporado, apresentou 89,64±0,00% de humidade, 0,93±0,00% de acidez (expressa em equivalentes de ácido láctico); 6,42±0,26% de açúcares totais; 0,74%±0,00% de cinza, 3,83±0,00% de proteína bruta e 0,2±0,00% de fibra bruta. O seu conteúdo em compostos fenólicos foi de 12,41±1,69mg EAG/ 100g de iogurte, e a sua atividade antioxidante foi 54,84±4,40 µmol TE/g iogurte. Avaliou-se ainda o iogurte no que diz respeito ao crescimento de bactérias lácticas e constatou-se, por comparação com o iogurte de controlo, que estas se desenvolveram normalmente ao longo do processo de fabrico. A análise microbiológica revelou ainda que o iogurte é seguro do ponto de vista alimentar de acordo com a Tabela 15 (anexos 3). A análise sensorial realizada aos iogurtes demonstrou que o iogurte fortificado apresentou uma aceitação muito boa pelo painel de provadores. O presente estudo demonstrou que o bagaço de maçã, um subproduto das indústrias agroalimentares, é seguro do ponto de vista microbiológico, podendo ser utilizado na preparação de ingredientes alimentares para serem incorporados, por exemplo em iogurte, conferindo-lhe características que se destacam pelo maior teor em fibra e atividade antioxidante em relação ao iogurte não enriquecido, e atributos sensoriais apelativos em termos de textura e sabor.

The broad spectrum of bioactive properties of phenolic extracts: a prospective study in three different plants

Natural resources like plants are currently used all over developed and under developed countries of the world as traditional home remedies and are promising agents for drug discovery as they play crucial role in traditional medicine. The use of plants for medicinal purpose usually varies from country to country and region to region because their use depends on the history, culture, philosophy and personal attitudes of the users (Ahmad et al., 2015). The use of plants and plant products as drugs predates the written human history (Hayta et al., 2014). Plants are a very important resource for traditional drugs and around 80% of the population of the planet use plants for the treatment of many diseases and traditional herbal medicine accounts for 30-50% of the total medicinal consumption in China. In North America, Europe and other well-developed regions over 50% of the population have used traditional preparations at least once (Dos Santos Reinaldo et al., 2015). Medicinal plants have been used over years for multiple purposes, and have increasingly attract the interest of researchers in order to evaluate their contribution to health maintenance and disease’s prevention (Murray, 2004). Recently between 50,000 and 70,000 species of plants are known and are being used in the development of modern drugs. Plants were the main therapeutic agents used by humans from the 19th century, and their role in medicine is always topical (Hayta et al., 2014). The studies of medicinal plants are rapidly increasing due to the search for new active molecules, and to improve the production of plants or bioactive molecules for the pharmaceutical industries (Rates, 2001). Several studies have been reported, but numerous active compounds directly responsible for the observed bioactive properties remain unknown, while in other cases the mechanism of action is not fully understood. According to the WHO 25% of all modern medicines including both western and traditional medicine have been extracted from plants, while 75% of new drugs against infective diseases that have arrived between 1981 and 2002 originated from natural sources, it was reported that the world market for herbal medicines stood at over US $60 billion per year and is growing steadily (Bedoya et al., 2009). Traditional medicine has an important economic impact in the 21st century as it is used worldwide, taking advantage on the low cost, accessibility, flexibility and diversity of medicinal plants (Balunas & Kinghorn, 2005).

Efeitos do extrato de Rhynchelytrum Repens em modelo murino de obesidade e hiperglicemia induzidas por dieta hiperlipídica

Dissertação (mestrado)—Universidade de Brasília, Programa de Pós-Graduação em Ciências da Saúde, 2015.

Dispositifs optoélectroniques à base de semi-conducteurs organiques en couches minces

Les petites molécules de type p à bandes interdites étroites sont de plus en plus perçues comme des remplaçantes possibles aux polymères semi-conducteurs actuellement utilisés conjointement avec des dérivés de fullerènes de type n, dans les cellules photovoltaïques organiques (OPV). Par contre, ces petites molécules tendent à cristalliser facilement lors de leur application en couches minces et forment difficilement des films homogènes appropriés. Des dispositifs OPV de type hétérojonction de masse ont été réalisés en ajoutant différentes espèces de polymères semi-conducteurs ou isolants, agissant comme matrices permettant de rectifier les inhomogénéités des films actifs et d’augmenter les performances des cellules photovoltaïques. Des polymères aux masses molaires spécifiques ont été synthétisés par réaction de Wittig en contrôlant précisément les ratios molaires des monomères et de la base utilisée. L’effet de la variation des masses molaires en fonction des morphologies de films minces obtenus et des performances des diodes organiques électroluminescentes reliées, a également été étudié. La microscopie électronique en transmission (MET) ou à balayage (MEB) a été employée en complément de la microscopie à force atomique (AFM) pour suivre l’évolution de la morphologie des films organiques minces. Une nouvelle méthode rapide de préparation des films pour l’imagerie MET sur substrats de silicium est également présentée et comparée à d’autres méthodes d’extraction. Motivé par le prix élevé et la rareté des métaux utilisés dans les substrats d’oxyde d’indium dopé à l’étain (ITO), le développement d’une nouvelle méthode de recyclage eco-responsable des substrats utilisés dans ces études est également présenté.

Development of an organocatalytic method for the enantioselective synthesis of rivastigmine

The focus of this thesis was the study of a recently developed class of picolinamide cinchona alkaloid derivatives for the synthesis of Rivastigmine, a biologically active compound used for the treatment of Alzheimer’s disease. Six 9-picolinamide-cinchona alkaloid derivatives were successfully synthesized through simple and effective methods. These catalysts were then applied in the enantioselective reduction of O-protected ketimines (intermediates of Rivastigmine). The hydrosilylation of the N-phenyl ketimines afforded good results with excellent yields and high enantioselectivities, while much lower values, in terms of both enantioselectivity and yield, were obtained in the reduction of N-benzyl ketimines. Preliminary studies on the immobilization of these organocatalysts to different solid supports were conducted, with the purpose of applying them in continuous flow systems, which to date has never been reported; RESUMO: No âmbito deste trabalho, foi estudada a síntese de um composto biologicamente ativo usado para o tratamento da doença de Alzheimer, Rivastigmina, usando uma classe de picolinamidas derivadas de alcaloides de cinchona recentemente desenvolvida. Seis 9-picolinamida derivados de alcaloides de cinchona foram preparados com êxito através de metodologias simples e eficazes. Os organocatalisadores foram posteriormente aplicados na redução enantiosseletiva de cetiminas O-protegidas (intermediários de Rivastigmina). Foram obtidos bons resultados na hidrossililação de N-fenilo cetiminas, com rendimentos excelentes e elevadas enantiosseletividades, enquanto a redução de N-benzilo cetiminas proporcionou valores muito mais baixos, tanto em termos de rendimento como de enantiosseletividade. Com o objetivo de serem aplicados em sistemas de fluxo contínuo, realizaram-se estudos preliminares sobre a imobilização destes organocatalisadores em diferentes suportes sólidos, a qual, ate à data, ainda não foi descrita na literatura.

Structure-function relationship of new crotamine isoform from the Crotalus durissus cascavella

In this work we isolated a novel crotamine like protein from the Crotalus durissus cascavella venom by combination of molecular exclusion and analytical reverse phase HPLC. Its primary structure was:YKRCHKKGGHCFPKEKICLPPSSDLGKMDCRWKRK-CCKKGS GK. This protein showed a molecular mass of 4892.89 da that was determined by Matrix Assisted Laser Desorption Ionization Time-of-flight (MALDI-TOF) mass spectrometry. The approximately pI value of this protein was determined in 9.9 by two-dimensional electrophoresis. This crotamine-like protein isolated here and that named as Cro 2 produced skeletal muscle spasm and spastic paralysis in mice similarly to other crotamines like proteins. Cro 2 did not modify the insulin secretion at low glucose concentration (2.8 and 5.6 mM), but at high glucose concentration (16.7 mM) we observed an insulin secretion increasing of 2.7-3.0-fold than to control. The Na+ channel antagonist tetrodoxin (6 mM) decreased glucose and Cro 2-induced insulin secretion. These results suggested that Na+ channel are involved in the insulin secretion. In this article, we also purified some peptide fragment from the treatment of reduced and carboxymethylated Cro 2 (RC-Cro 2) with cyanogen bromide and protease V8 from Staphylococcus aureus. The isolated pancreatic beta-cells were then treated with peptides only at high glucose concentration (16.7 mM), in this condition only two peptides induced insulin secretion. The amino acid sequence homology analysis of the whole crotamine as well as the biologically-active peptide allowed determining the consensus region of the biologically-active crotamine responsible for insulin secretion was KGGHCFPKE and DCRWKWKCCKKGSG.

Purification and characterization of the biological effects of phospholipase A(2) from sea anemone Bunodosoma caissarum

Sea anemones contain a variety of biologically active substances. Bunodosoma caissarum is a sea anemone from the Cnidaria phylum, found only in Brazilian coastal waters. The aim of the present work was to study the biological effects of PLA(2) isolated from the sea anemone B. caissarum on the isolated perfused kidney, the arteriolar mesenteric bed and on insulin secretion. Specimens of B. caissarum were collected from the Sao Vicente Channel on the southern coast of the State of São Paulo, Brazil. Reverse phase HPLC analysis of the crude extract of B. caissarum detected three PLA(2) proteins (named BcPLA(2)1, BCPLA(2)2 and BcPLA(2)3) found to be active in B. caissarum extracts. MALDI-TOF mass spectrometry of BcPLA(2)1 showed one main peak at 14.7 kDa. The N-terminal amino acid sequence of BcPLA(2)1 showed high amino acid sequence identity with PLA(2) group III protein isolated from the Mexican lizard (PA23 HELSU, HELSU, PA22 HELSU) and with the honey bee Apis mellifera (PLA(2) and 1POC_A). In addition, BcPLA(2)1 also showed significant overall homology to bee PLA(2). The enzymatic activity induced by native BCPLA(2)1 (20 mu g/well) was reduced by chemical treatment with p-bromophenacyl bromide (p-BPB) and with morin. BcPLA(2)1 strongly induced insulin secretion in presence of high glucose concentration. In isolated kidney, the PLA(2) from B. caissarum increased the perfusion pressure, renal vascular resistance, urinary flow, glomerular filtration rate, and sodium, potassium and chloride levels of excretion. BcPLA(2)1, however, did not increase the perfusion pressure on the mesenteric vascular bed. In conclusion, PLA(2), a group III phospholipase isolated from the sea anemone B. caissarum, exerted effects on renal function and induced insulin secretion in conditions of high glucose concentration. (C) 2009 Elsevier Ltd. All rights reserved.