Dissertations / Theses on the topic 'Chemical and biological'

Up to date, sludge filterability has been characterized by the Ruth&rsquo
s classical filtration theory and quantified by the well-known parameter specific cake resistance (SCR). However, the complexity of the actual phenomenon is clearly underestimated by the classical filtration theory and SCR is often not satisfactory in describing filterability. Although many scientific studies were conducted for a better analysis and understanding of the filtration theory, still a practically applicable solution to replace the classical theory for a better description of filterability has not been proposed yet. In the present study, blocking filtration laws proposed by Hermans and Bredé
e, dating back to 1936, which have been extensively used in the membrane literature for the analysis of fouling phenomenon and the multiphase filtration theory developed by Willis and Tosun (1980) highlighting the importance of the cake-septum interface in determining the overall filtration rate have been adopted for the analysis of filterability of sludge systems. Firstly, the inadequacy of the classical filtration theory in characterizing the filterability of real sludge systems and also the lack of the currently used methodology in simulating filtration operation was highlighted. Secondly, to better understand the effect of slurry characteristics and operational conditions on filtration, model slurries of spherical and incompressible Meliodent particles were formed. Finally, a methodology was developed with the gathered filtration data to assess the filterability of the sludge systems by both theories. The results clearly show that both approaches were superior to the classical approach in terms of characterizing the filterability of sludge systems. While blocking laws yielded a slurry specific characterization parameter to replace the commonly used SCR, the multiphase theory provided a better understanding of the physical reality of the overall process.

Digenetic trematodes are a common pest problem in aquaculture where their unappetizing appearance often reduces the marketability of food fish. Aquatic snails are intermediate hosts in the trematode lifecycle and are commonly targeted with control measures to prevent the crop fish from becoming infected. I evaluated several chemical and biological snail control strategies as alternatives to the potentially invasive black carp. Copper sulfate, hydrated lime slurry, and several fish and decapod species were tested for effectiveness against physid (Physa spp.) and planorbid (Helisoma spp.) snails in laboratory aquaria trials. Hydrated lime demonstrated effectiveness with the least potential to be toxic to cultured fish in regional application. Hybrid sunfish (redear × green sunfish) consumed large quantities of both snails in ad libitum feedings. The most effective biological (redear × green sunfish) and chemical (hydrated lime) control methods identified in the laboratory were evaluated further in research ponds. Hydrated lime applications of 9.07 kg over 9.14 m2 were found to be effective against Helisoma spp. confined to enclosures along the pond shoreline; average survival was 2%. When stocked in aquaculture ponds, hybrid redear sunfish did not significantly influence snail capture rates; however ponds stocked with redear sunfish experienced a gradual decrease in snail populations throughout the 2008 growing season. Hydrated lime and a combination of redear sunfish and hybrid redear sunfish were evaluated separately and in tandem as a combined chemical/biological treatment in the 2009 growing season. Evaluation occurred under mock production conditions in which hybrid striped bass were raised in the research ponds to determine snail treatment effects on trematode abundance. Ponds stocked with sunfish at 494 fish/ha had snail densities significantly (P ≤ 0.05) lower than control ponds after two months. Ponds treated with hydrated lime at 31.7 kg/31.5 m of shoreline in a 1 m swath experienced 99% estimated reductions in snail densities following application, but snail populations rebounded to previous levels within two months. The mean snail density in ponds treated with both hydrated lime and sunfish was significantly lower than control one month post treatment; this mean rebounded slightly by the conclusion of the trial, but not as much as in the chemical treatment group. Hybrid striped bass examined thoroughly for trematodes revealed a positive relationship between trematode abundance in fish and increasing Helisoma densities. This relationship was most apparent when estimates of snail density from only the beginning of the trial were used. Based on these results, it appears that a nearly complete reduction of Helisoma, particularly at the time of stocking fingerlings, is necessary to avoid a high abundance of trematodes in cultured fish. To this end, an early-season application of molluscicides followed closely by stocking of predator sunfish has potential to achieve a uniformly low density of snails throughout the growing season.

Many biological and non-biological materials in the form of microscopic particles (or microparticles) are used to produce functional products for a wide range of industrial sectors including pharmaceutical and medical, chemical, agrochemical, food and feed, personal and household care. Understanding their mechanical properties is essential for predicting their behaviour in manufacturing and processing, and for maximising their performance in end-use applications. However, it had not been possible to determine the mechanical properties of single microparticles until the author, as the main contributor, developed a novel micromanipulation technique at the University of Birmingham. The technique is capable of determining the mechanical properties of both biological and non-biological particles as small as 400 nm in diameter, and can be used for obtaining force-displacement data of single microparticles at large deformations, including those corresponding to rupture. The technique was enhanced by mathematical modelling and finite element analysis in order to allow intrinsic material properties to be determined, for example, the particle (or particle wall) elastic modulus, viscoelastic and plastic properties, and stress/strain at rupture. For biological materials, applications of this technique include understanding mechanical damage to animal cells in suspension cultures, yeast and bacterial disruption in downstream processing equipment, biomechanics of chondrocytes and chondrons for tissue engineering, and adhesion and cohesion of biofilms and food fouling deposits. For non-biological materials, applications include understanding and controlling particle breakage in processing equipment, and the formulation of microcapsules with optimum mechanical strength to achieve controlled release and targeted delivery of functional active ingredients. The research on micromanipulation has been sponsored by BBSRC, EPSRC, DEFRA, DTI, EU, the Royal Society K C Wong Fellowships and 19 national and international companies, and has resulted in more than one hundred academic publications. The knowledge generated has also assisted these companies to commercialise particulate functional products.

Since its discovery, nitric oxide (NO) has been identified to influence a large number of physiological processes. This project examines S-nitrosothiols (RSNO) as pro-drugs of NO. The overall aim of this project was to improve our present understanding of the chemical and biological properties of RSNOs. This project has demonstrated that under physiological conditions the stability of RSNOs varies with structure. Results have shown that S-nitrosocysteine and S-nitroso-L-cysteinylgylcine were the least stable of the RSNOs investigated, whereas S-nitroso-N-acetyl-L-cysteine, S-nitroso-3-mercaptopropionic acid and S-nitroso-2-mercapto-ethane sulphonic acid were the most stable. The decomposition of certain RSNOs is catalysed by trace amounts of copper. This phenomenon was particularly evident with the RSNOs, S-nitrosocysteine and S-nitroso-L-cysteinylglycine. Copper catalysed decomposition appears to occur more readily with RSNOs that allow the formation of a stable ring structure, in which Cu+ is bound to the nitrogen of the NO group and another electron-rich atom such as the nitrogen of an amino group. Copper catalysed the decomposition of S-nitrosoglutathione and S-nitroso-L--glutamyl-L-cysteine, but to a lesser extent. Investigations have shown that the decomposition of a stable RSNO is more rapid in the presence of a thiol which gives rise to an unstable RSNO via a transnitrosation reaction. In contrast, decomposition of an unstable RSNO is slower in the presence of a thiol which leads to the formation of a stable RSNO. All RSNOs studied inhibited platelet aggregation and relaxed vascular smooth muscle in a dose dependent manner. In addition, all the RSNOs exhibited a dose-dependent inhibition of growth of A549 cells. Generally no real correlation between the chemical and biological properties of RSNOs was observed. It is clear that there are many factors controlling the release of NO from RSNOs which may have implications regarding the biological activity of these compounds.

This thesis is concerned with the loading of transferrin with manganese and some of its chemical and biological properties. Manganese is bound to transferrin as Mn(III) with a characteristic ligand (Tyr) to metal (Mn(III) charge-transfer band at a wavelength of 430 nm. Caeruloplasmin is shown to enhance the uptake of manganese from MnC1₂ by apo-hTf. However binding is often incomplete and slow. A novel method of loading hTf with Mn using KMnO₄ is reported. This method leads to rapid uptake and inductively coupled plasma atomic emission spectroscopy (ICP-AES) determinants confirmed the binding of at least two Mn per hTf molecule. The possible oxidising effects of MnO₄^- on protein amino acid side chains was considered. In model systems MnO₄^- oxidises methionine to methionine sulfoxide and methionine sulfone. Evidence of structural changes in apo-hTf induced by Mn(III) binding was obtained by studies using [e-¹³C]Met-hTf. Preliminary work suggests that Mn(III), like several other metals studied, preferentially binds to the C-lobe first, although this may result in an open domain conformation. Fe(III) as Fe(NTA)₂ was found to displace Mn(III) from hhTf but displacement was slower when hTf had been loaded using KMnO₄ rather than MnCl₂. KMnO₄ was not able to displace Fe(III) from Fe₂-hTf. Attempts to crystallise Mn-hTf to characterise these structural changes proved difficult. Crystals grew but were of poor quality and did not diffract. Many large crystals were obtained from solutions of Fe₂-hTf. The crystals were red/orange and ellipsoidal in shape. Of the Fe₂-hTf crystals grown, one diffracted to 3.3 Å with the data being complete to 90%, but not enough information was gained for adequate molecular replacement and structural solution.

As depicted in Chapter I, 2-oxoglutarate- (2OG) dependent oxygenases are ubiquitous in living systems and display a wide range of cellular functions, spanning metabolism, transcription, and translation. Although functionally diverse, the 2OG oxygenases share a high degree of structural similarities between their catalytic sites. From a medicinal chemistry point of view, the combination of biological diversity and structural similarity presents a rather challenging task for the development of selective small molecules for functional studies in vivo. The non-selective metal chelator 8-hydroxyquinoline (8HQ) was used as a template for the generation of tool compound I for the KDM4 subfamily of histone demethylases via application of the Betti reaction. Structural analogue II was used as the corresponding negative control (Figure A). These compounds were characterised in vitro against a range of 2OG oxygenases and subsequently used for studies in cells. I displays selectivity for KDM4 and increases the level of the H3K9me3 histone mark in cells. It has an effect on the post-translational modification pattern of histone H3, but not other histones, and reduces the viability of lung cancer cells, but not normal lung cells, derived from the same patient. I also stabilises hypoxia-inducable factor HIF in cells via a mechanism which seems to be independent from prolyl hydroxylase inhibition. This work is described in Chapters II and III. The chemical biology research in epigenetics is complemented by qualitative analysis conducted in the social sciences at Said Business School. With a global view on how innovation occurs and may actively be fostered, Chapter IV focuses on the potential of epigenetics in drug discovery and how this process may actively be promoted within the framework of open innovation. Areas of focus include considerations of incremental and disruptive technology; how to claim, demarcate, and control the market; how knowledge brokering occurs; and insights about process, management, organisation, and culture of open innovation. In contrast to the open-skies approach adopted for the development of a tool compound in Chapters II and III, a focused-library approach was taken for the generation of a tool compound for the OGFOD1 ribosomal prolyl hydroxylase. The development of a suitable in vitro activity assay for OGFOD1 in Chapter V enabled the development of lead compound III in Chapter VI. III is selective for OGFOD1 against the structurally closely related prolyl hydroxylase PHD2.

Natural products (NPs) are commonly defined as the secondary metabolites derived from plants, microorganisms, fungi, insects, and marine invertebrates, as the result of adaptation to the environment or as defense mechanisms against predators. Throughout history, the use of NPs has been described in the form of traditional medicines in different cultures for the treatment of ailments. Apart from their role in medicinal applications, the structures of NPs can also act as lead molecules to inspire the design of new drugs. Of the 1562 new approved drugs by U.S. Food and Drug Administration (FDA) from 1981–2014, 791 (51%) were NPs, NP derivatives or NP-inspired drugs. Since the development of SCUBA in the mid-twentieth century, the marine environment, which contains an incredible diversity of organisms, has been described as the most desired source of NPs for drug discovery research. To date, approximately 35,147 marine natural products (MNPs) had been identified from various organisms, such as marine invertebrates (e.g. sponges, crinoids and ascidians), microorganisms and algae. Many of these MNPs have been found to exhibit a wide variety of pharmaceutically relevant bioactivities, such as anticancer, antimicrobial, antiviral, and anti-inflammatory activities. There are currently 12 marine-derived compounds that have been approved as therapeutic drugs for the treatment of cancer, viral infections, hypertriglyceridemia, and analgesia; while 27 drug candidates are currently in phase I, II, or III clinical trials. While numerous marine invertebrates have been well explored for bioactive MNPs in the last seven decades, crinoids belong to the phylum Echinodermata remained under investigated for their chemistry. Crinoids are the most primitive group of presentday echinoderms. They are known to produce diverse polyketide-derived pigments, which are not only responsible for their colourful appearance, but also have demonstrated significant activity in a range of biomedical assays. There are approximately 700 crinoid species that have been identified worldwide, however, only 36 species have been chemically investigated and only 91 new compounds have been reported to date. Owing to our continuing research interest on crinoid chemistry, the main aim of this PhD project was to identify new chemistry from crinoids sourced from Australian waters and subsequently screen the isolated compounds in a variety of biological assays. The first crinoid project of this thesis focused on the chemistry of the feather star Capillaster multiradiatus since no studies had been undertaken on this Australian species. Capillasterin A, a novel pyrano[2,3-f]chromene, together with seven known naphthopyrones including comaparvin, TMC-256C1, 6-methoxycomaparvin 5-methyl ether, 5,8-dihydroxy-6-methoxy-2-propyl-4H-naphtho[2,3-b]pyran-4-one, 5,8- dihydroxy-6,10-dimethoxy-2-propyl-4H-naphtho[2,3-b]pyran-4-one, TMC-256A1 and 6-methoxycomaparvin were isolated from an EtOH/H2O extract of C. multiradiatus collected by collaborators from the Queensland Museum. The structures of all the compounds were determined by detailed spectroscopic (1D/2D NMR and MS) data analysis. As previous studies demonstrated that HIV gene expression is dependent on the host transcription factor complex NF-B and naphthopyrones were reported to inhibit NF-B signalling pathway, the six known naphthopyrones isolated from this crinoid, together with capillasterin A were screened in an anti-HIV assay. Five known naphthopyrones were observed to display moderate inhibition of in vitro HIV-1 replication in a T cell line with EC50 values ranging from 7.5 to 25.5 μM without concomitant cytotoxicity. The three most abundant compounds, capillasterin A, 6- methoxycomaparvin 5-methyl ether, and TMC-256A1 were also tested for their ability to stimulate the proliferation of GFP-expressing immortalised mouse olfactory ensheathing cells (mOEC) using a cell proliferation assay; none of the compounds showed a significant increase in mOEC viability at 10 μM after 24 hours of treatment. The AIMS Bioresources Library, which consisted of over 3000 marine samples, has recently been transferred to the NatureBank biota repository, which presented us with the opportunity to explore several new crinoid samples from a chemical perspective. Hence, the second PhD project, two AIMS-derived Australian crinoid Comatula rotalaria specimens collected from different locations on the Great Barrier Reef were selected for potential new chemistry, since preliminary UHPLC analysis of these crinoid extracts suggested the presence of new anthraquinone chemistry; only four acyl derivatives of anthraquinones had been identified from this species prior to our studies. Five new taurine-conjugated anthraquinones, named comatulins A−E, together with 11 known metabolites, rhodocomatulin 7-methyl ether, 12-desethylrhodocomatulin 7-methyl ether, rhodocomatulin 5,7-dimethyl ether, 12-desethylrhodocomatulin 5,7-dimethyl ether, rhodocomatulin, rhodolamprometrin, 6-methoxyrhodocomatulin 7-methyl ether, rheoemodin, 6-methoxycomaparvin, 6-methoxycomaparvin 5-methyl ether, and 5,8- dihydroxy-6,10-dimethoxy-2-methyl-4H-benzo[h]chromen-4-one were identified. The structures of all the compounds were elucidated by detailed spectroscopic and spectrometric data analysis. The first X-ray crystal structure of a crinoid-derived acyl anthraquinone, rhodocomatulin 5,7-dimethyl ether, was also obtained. Ten compounds together with two additional naphthopyrone derivatives (comaparvin and 6- methoxycomaparvin 5,8-dimethyl ether) were evaluated for their ability to inhibit HIV-1 replication in vitro; none of the compounds were active at 100 μM. Furthermore, a subset of compounds was tested for their nematocidal activity against Haemonchus contortus, which is a highly pathogenic parasite of small ruminants. The semi-synthetic compound, 6-methoxycomaparvin 5,8-dimethyl ether, showed an inhibitory effect on larval motility (IC50 = 30 μM) and development (IC50 = 31 μM) and induced the eviscerated (Evi) phenotype. In Chapter 4, since none of the crinoid-derived polyketides identified during this PhD had been evaluated for their ability to increase phagocytic activity of human OECs (hOEC), six naphthopyrones and eight anthraquinones were screened using an hOEC phagocytosis assay that has recently been developed by the Clem Jones Centre for Neurobiology and Stem Cell Research group. In addition, microthecaline A and its acetylated, methylated and pivaloylated derivatives, together with antimalarial drug amodiaquine obtained from the in-house Davis compound library, were incorporated into the screening. Results from the primary screening demonstrated that four compounds including 6-methoxycomaparvin 5-methyl ether, 5,8-dihydroxy-6,10-dimethoxy-2- methyl-4H-benzo[h]chromen-4-one, comatulin A, and amodiaquine were found to significantly increase the phagocytic activity and the phagocytic efficiency of hOECs. These findings warrant further investigations in the near future to further expand the preliminary biology results and gain insights in compound specificity and potency. Encouraged by our findings in Chapter 3, we developed a dereplication method using UHPLC-MS for the identification of new sulphur-containing metabolites from Australian crinoids, the details of which are described in Chapter 5. The n-BuOH soluble material of 16 crinoids, including the two C. rotalaria samples described in Chapter 3, were subjected to UHPLC-MS profiling using an optimised method. These crinoids were all sourced from Griffith University’s NatureBank biota repository. The generated UHPLC-MS data were analysed based on the characteristic fragment ions of sulphated compounds in conjunction with scientific database mining; SciFinder Scholar and MarinLit databases were used in this particular study. These investigations led to the large-scale extraction and isolation work on the prioritised crinoid Dichrometra flagellata, which resulted in the isolation of a previously undescribed sulphated compound, which we have tentatively assigned as 5,10-dihydroxy-6–methoxy-8- sulphate-2-propyl-4H-naphtho[2,3-b]pyran-4-one. In summary, this thesis describes the isolation of seven new polyketide constituents and 17 known compounds from four crinoids collected from Australian waters. The chemical structures of all compounds were determined by detailed spectroscopic and spectrometric data analysis. Among all the tested crinoid metabolites, comaparvin was the most active compound in an anti-HIV replication assay, with an IC50 of 7.5 ± 1.7 μM; 6-methoxycomaparvin 5,8-dimethyl ether displayed an inhibitory effect on larval motility (IC50 = 30 μM) and development (IC50 = 31 μM), and induced the Evi phenotype in an anthelmintic assay; 6-methoxycomaparvin 5-methyl ether, 5,8- dihydroxy-6,10-dimethoxy-2-methyl-4H-benzo[h]chromen-4-one, and comatulin A significantly increased the phagocytic activity and the phagocytic efficiency of hOECs. All compounds isolated during this PhD project will be deposited into the Davis Open- Access Compound Library, which is located at Compounds Australia, Griffith University. Compounds Australia makes this academic library available for biological evaluations by both local and international researchers. In addition, the UHPLC-MS methodology developed during these studies enabled the rapid identification of new sulphur-containing compounds from n-BuOH soluble material derived from 16 crinoids, which resulted in the isolation of a new sulphated compound from the prioritised crinoid Dichrometra flagellata; this is the first report of NP chemistry from this crinoid genus. These findings further highlight the importance of UHPLC-MS as a dereplication tool in NP research.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
Full Text

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005.
Includes bibliographical references.
This thesis research focused on biological applications of ultra-thin weak polyelectrolyte multilayers with specific emphasis on cell patterning, drug delivery, and antibacterial coatings. All of these very different applications were studied using three different polymers - polyacrylic acid (PAA), poly(allylamine hydrochloride) (PAH), polyacrylamide (PAAm). The first part of this thesis focuses on patterning polyelectrolyte multilayers found to resist mammalian cell adhesion, with ligands that promote specific interactions for adhesion. It was found that by patterning PAH on polyelectrolyte multilayers, the patterned functional group density and thickness could be tuned through ink pH adjustment. By changing the surface density of amine groups in the PAH patterns, the ligand density could also be altered using specific chemistry to attach peptides containing the tri-peptide sequence, RGD, which is known to promote cell adhesion in a number of cell types. The RGD density in the patterned regions determined the number of cells attached and the amount of cytoskeletal protein organization. The second part is an evaluation of porous polyelectrolyte multilayers as a delivery system for controlled release of small molecule drugs. The loading and releasing properties of porous PAH/PAA multilayers were investigated using the two drugs, ketoprofen and cytochalasin D. It was determined that the amount of drug released was proportional to the number of porous layers. Nanoporous films showed zero-order release, whereas microporous films displayed Fickian diffusion. The efficacy of the released drugs was checked by monitoring the effect of released cytochalasin D on fibroblasts' division.
(cont.) In the final part of this thesis, the antibacterial properties of both silver-loaded polyelectrolyte multilayers and superhydrophobic multilayers are examined. It was found that silver loaded multilayers killed bacteria to an extent greater than 99.99% for both airborne and waterborne models. Superhydrophobic films showed excellent anti-fouling properties for proteins, mammalian cells, and bacteria.
by Michael C. Berg.
Ph.D.

Two open wet oxidation methods are described for the digestion of selected seafoods prior to total mercury determination using a cold vapour atomic absorption spectrophotometric technique. The first employs two acids (i.e. HNO3 and H2SO4) and two oxidants (i.e. KMnO4 and K2S2O8), and is suitable for use with a Perkin-Elmer Mercury Analysis System (MAS) and a Perkin-Elmer Mercury Analyzer 50A (MA). Excellent recoveries were obtained for mussel samples spiked with various quantities of inorganic mercury [Hg(N03)2]. For the optimum part of the calibration curve of the MAS (0.1–0.7 μg/ml Hg), the percentage recovery (%R) fluctuated between 98.26 and 101.98. The limit of detection (LOD) was calculated to be 18.7 ng of mercury per sample analysed and sensitivity of 0.011 μg of mercury was obtained. Results for fish samples determined with both units showed excellent agreement and precision (RSD = 3.23 -4.25). However, the MA was found inadequate for the determination of the low mercury levels encountered with the mussel samples. It was shown that a desiccant assembly must be installed whenever samples with low mercury content are analysed, i.e. less than 0.5 μg per sample digested.

This dissertation is about treatment of the nonbiodegradable organic content of landfill leachate by chemical oxidation combined with biological treatment. It is divided into three parts. In the first part, ferrate was compared to Fenton's reagent for the purpose of removing non-biodegradable organic compounds from mature leachate. Oxidation conditions (time, pH, and dose) were optimized to yield maximum organic removal using two leachate samples from 20 and 12-year old solid waste cells. Results from this research demonstrated that ferrate and Fenton's reagent had similar optimum pH ranges (3-5), but different organic removal capacities, ranging from 54 to 79 % of initial leachate organic contents. An advantage of ferrate was that it was relatively effective over a wide pH range (Fenton's reagent lost its reactivity outside optimum pH range). Advantages associated with Fenton's reagent include a higher organic removal capacity, production of more oxidized organic compounds (measured as chemical oxygen demand/dissolved organic carbon), and production of more biodegradable byproducts (measured as 5-day biochemical oxygen demand/chemical oxygen demand). Finally, both treatments were found to oxidize larger molecules (>1000 dalton) and produce smaller molecules, as indicated by an increase in smaller molecule contribution to organic carbon. In part two, effects of Fenton's reagent treatment on biodegradability of three landfill leachates collected from a Florida landfill were evaluated using biochemical oxygen demand (BOD), biochemical methane potential (BMP), and tertamethylammonium hydroxide (TMAH) thermochemolysis gas chromatography/mass spectrometry (GC/MS). The hypothesis was that Fenton's reagent will remove refractory compounds that inhibit biodegradation and will produce smaller, more biodegradable organic molecules which will result in an increase in BOD and BMP values. Both BOD and BMP results demonstrated that Fenton's reagent treatment did not convert mature leachate to biodegradable leachate, as indicated by a low BOD5 expressed as C /dissolved organic carbon (DOC) ratio of almost 0.15 in treated samples and a low net methane production / theoretical methane potential (less than 0.15). Ultimate BOD only slightly increased. However the first-order BOD reaction rate increased by more than five fold, suggesting that Fenton's reagent removed refractory and inhibitory compounds. BMP results demonstrated that the ratio of CO2/CH4 produced during anaerobic biodegradation did not increase in treated leachate (compared to untreated), indicating that small biodegradable organic acids produced by oxidation were removed by coagulation promoted by Fenton's reagent. Finally, the TMAH thermochemolysis results showed that several of the refractory and inhibitory compounds were detected fewer times in treated samples and that carboxylic acids did not appear in treated samples. In the third part of this dissertation the application of flushing/Fenton's reagent oxidation to produce sustainable solid waste cells was evaluated. A treatment similar to pump and treat process utilizing Fenton's reagent on-site treated leachate combined with in-situ aeration was proposed. Treated leachate would be recycled to the landfill cell flushes releasable nonbiodegradable carbon from the cell and oxidizes it externally. This technique was demonstrated to have treatment cost and time benefits over other alternatives for producing completely stable solid waste cells such as anaerobic flushing and biological and/or mechanical pretreatment of solid waste (used in the EU).
Ph.D.
Department of Civil and Environmental Engineering
Engineering and Computer Science
Environmental Engineering

Propolis or bee glue, is collected by bees and contains secondary metabolites largely derived from trees or shrubs; it has been used traditionally as a natural remedy with a wide range of biological activities. Its chemical composition is highly complex and variable, and it has been studied in detail worldwide except in Africa. This study investigated the chemical composition and activity of African propolis against blood stream form of Trypanosoma brucei, the causative agent for sleeping sickness that threatens a large population of both humans and animals in sub-Saharan Africa. Extracts of propolis samples (n=12) collected from different regions in Nigeria and one sample collected from South Africa were chemically profiled by using various analytical techniques. These included high performance liquid chromatography (HPLC), coupled with different detection systems including evaporative light scattering detection (ELSD), ultraviolet detection (UV), and high resolution mass spectrometry (HRMS), along with gas chromatography- mass spectrometry (GC-MS) and proton-nuclear magnetic resonance (1H-NMR).Principal components analysis (PCA) of the processed LC-MS data collected was used in order to characterize samples according to their chemical composition. PCA demonstrated the uniqueness in chemical composition of some samples that were also active against Trypanosoma brucei. Therefore, the study proceeded to investigate in detail four samples collected mainly from the southern part of Nigeria. An optimized medium pressure chromatographic technique was used to isolate some of the component(s) responsible for the anti-trypanosomal activity. Two samples collected from Rivers State Nigeria had a different appearance from the rest of the propolis samples, being red in colour and had the highest trypanocidal activity (EC50=4.2 and 6.9 μg/mL) respectively. Their chemical composition was comparable to that of Brazilian red propolis. Fractionation work led to the isolation of ten phenolic compounds including calycosin, liquiritigenen, pinocembrin, vestitol, medicarpin, 8-prenylnaringenin, 6-prenylnaringenin, propolin D, macarangin and a new benzofuran. All compounds structurally elucidated by 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy and LC-MSn. Some compounds showed strong inhibitory activity against trypanosomes such as medicarpin (MIC=11.5 μM) and propolin D (MIC=7.4 μM), macarangin (EC50 =18.5 μM), 8-prenylnaringenin (EC50= 17.9 μM), and vestitol (EC50= 30.5 μM). The new benzofuran was moderately active with (EC50=58.01 μM). Fractionation of the propolis sample collected from the Ugelli/Delta sample led to isolation of three compounds 1,3,7-trihydroxy-2,8-di-(3-methylbut-2-enyl) xanthone, 1,3,7-trihydroxy-4,8-di-(3-methylbut-2-enyl) xanthone and a new xanthone. These compounds were tested against T. brucei and presented high activities of EC50= 3.9, 11.04, 14.7 μM respectively. Triterpenes were the main fingerprint compounds in a sample collected from Ijebu-Ode/Ogun; three compounds were isolated and elucidated as ambonic acid, mangiferonic acid and α-amyrin. These compounds had EC50 values against T. brucei of 39.5, 25.5 and 20.9 μM respectively. Finally, sample D46SA from South Africa was found to contain mainly flavonols and diterpenic acids; three compounds pinocembrin, acetylimbricatolic acid and (-)-pimara-8 (14), 15-dien-19-oic acid were isolated and tested. All were moderately active against T. brucei.with MIC ranging from 41.4-137.3 μMIn conclusion, this work has proved the variabiliy of propolis collected even from the same region and the widespread activity of propolis against (blood stream form) T. brucei. It is likely that some of the propolis samples contain compounds with even higher activity that have not yet been isolated.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2009.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 101-109).
In this thesis I designed, fabricated and characterized two types of sensors: chemical sensors based on organic thin film transistors, and a miniaturized surface plasmon resonance biosensors for biotechnology and medical diagnostics applications. During completion of my research projects I designed and optimized several device architectures using numerical simulations and fundamental physical evaluation of sensing mechanism and performance. Fabricated devices were tested in custom built experimental setups in microfluidic testing chambers using automatic data measurement. Surface functionalization of device surface using self assembled monolayer techniques was employed for experiments that required specificity towards analyzed biological species.
by Mihail Bora.
Ph.D.

The aim of modern cancer chemotherapy is to develop targeted drugs designed to exploit pharmacological differences between tumour cells and healthy tissues. One focus of this effort has been the identification of protein kinases that are expressed at elevated levels or in mutated forms, indicating a reliance of the tumour on specific kinase function. Nek2 is a human serine/threonine protein kinase related to the fungal protein NIMA, a critical mediator of mitosis. Interestingly, Nek2 is found to be upregulated in a variety of tumour cell lines derived from breast, cervical and prostate carcinomas, as well as lymphomas. Human Nek2 is implicated in the regulation of the centrosome and formation of a bipolar spindle, a framework that is vital for correct separation of sister chromatids during mitosis. It is proposed that Nek2 may complex with, and phosphorylate, proteins accumulated at the centrosome, possibly playing a role in intercentriolar linker cleavage during the centrosome cycle. Abnormalities in centrosome number and function are common in many cancers, indicating that loss of centrosome cycle regulation may be a major contributing factor in tumour progression. Overexpression of Nek2 may result in premature centrosome disjunction, and deregulation of this tightly controlled mitotic machinery leads to chromatid segregation errors, aneuploidy and chromosomal instability, common genetic abnormalities observed in tumour cells. This indicates a role for abnormal Nek2 function in tumourigenesis, and Nek2 depletion in a number of tumour cell lines has been shown to cause growth suppression and apoptosis. Nek2 is thus a potentially attractive cancer therapeutic target for small-molecule kinase inhibitors. Previous studies identified substituted purine derivatives as modest inhibitors of Nek2, leading to the discovery of two distinct inhibitor classes, exhibiting ATP-competitive and irreversible inhibition of the kinase, respectively. Purine-based compounds bearing substituents at the 8-position have emerged as modest competitive inhibitors of Nek2 that occupy the kinase ATP-domain through an unusual binding orientation (45; IC = 51.8 M). Additional possible interactions within the ATP- 50 binding site available to inhibitors of this class were explored, with the objective of developing tight-binding type II reversible inhibitors of Nek2. Structure-activity relationship studies resulted in a 10-fold improvement in activity over the initial hit compounds and a substantial improvement in drug-like properties (e.g. 129; IC = 5.1 M)). However, all 50 efforts to improve the potency of this series were unsuccessful. 6-Ethynylpurines have been identified as irreversible inhibitors of Nek2 through covalent modification of an active-site cysteine residue. The initial hit compound (147; IC = 0.14 50 M) was found to be a potent and selective inhibitor of the kinase in vitro, but with poor cellular activity attributed to limited permeability. Extensive structural modification of the 2- arylamino side-chain of this series afforded cell permeable analogues with improved potency, both in vitro and in vivo (e.g. 177; IC = 0.062 ± 0.01 M). 50 Biochemical studies using 177 suggested that inhibition of Nek2 resulted in an increase in mitotic abnormalities and a delay in mitotic progression, despite poor cellular growth inhibition being observed in initial tumour cell lines. Further cellular growth inhibition and cytotoxicity studies with selected compounds identified several sensitive tumour cell lines. However, kinase-inactive control compounds essentially devoid of Nek-inhibitory activity (e.g. 425; IC > 100 M) retained growth-inhibitory activity, indicating an alternative locus 50 of activity for the 6-ethynylpurine chemotype.

FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico
Margaritopsis carrascoana is a small shrub belonging to the Rubiaceae family and endemic from northeastern of Brazil flora growing in the sandy soils of the region of Ibiapaba and Araripe plateaus â Cearà state. The absence of reports of phytochemical studies related to this species, combined with occurrence of bioactive alkaloids in the genus, motivated us to perform chemical study. The plant specimen was collected in Araripe plateu, in MoreilÃndia-PE county. The phytochemical investigation of the ethanolic extract from the stems yielded the alkaloids calycosidine, hodgkinsine, N-8â-formyl-calycosidine and N-8â-methyl-N-1â-desmethylisocalycosidine, besides neolignan dihydrodehydrodiconiferyl alcohol 4-O-β-D-glucopyranoside, the flavonol luteolin 7-O-α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranosyl, the triterpenes lupeol and ursolic acid, and the mixture of β-sitosterol and stigmasterol steroids, as aglycones and glycosylated. From the ethanolic extract of the leaves were isolated the flavonoid luteolin 7-O-[β-D-apiofuranosyl-(1→6)]-β-D-glucopyranoside, chrysoeriol 7-O-[β-D-apiofuranosyl-(1→6)]-β-D-glucopyranoside, luteolin 7-O-{β-D-apiofuranosyl-(1→6)-[β-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyl} and luteolin 7-O-{α-L-rhamnopyranosyl-(1→6)-[β-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyl}. The alkaloids N-8"-formyl-calycosidine, N-8â-methyl-N-1â-desmethylisocalycosidine, luteolin 7-O-{β-D-apiofuranosyl-(1→6)-[β-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyl} and luteolin 7-O-{α-L-rhamnopyranosyl-(1→6)-[β-L-rhamnopyranosyl-(1→2)]-β-D-glucopyra-nosyl}, are being reported for the first time in the literature, and the other secondary metabolites are unprecedented in the genus Margaritopsis. The secondary metabolites were isolated using classical chromatography techniques; including adsorption chromatography on silica gel, exclusion chromatography on Sephadex LH-20, reverse phase chromatography (C-18), and high performance liquid chromatography (HPLC). For structural characterization were used infrared spectroscopy, mass spectrometry and nuclear magnetic resonance techniques including uni (1H NMR and 13C NMR and DEPT 135) and two-dimensional experiments (HMBC, HSQC, COSY and NOESY), and comparison with the literature data. In addition, the flavonoids flavonol luteolin 7-O-α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranosyl, luteolin 7-O-[β-D-apiofuranosyl-(1→6)]-β-D-glucopyranoside, luteolin 7-O-{β-D-apiofuranosyl-(1→6)-[β-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyl} and luteolin 7-O-{α-L-rhamnopyranosyl-(1→6)-[β-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyl, sho-wed antioxidant activity greater than the BHT and quercetin standards, while ethanol extracts of stems and leaves showed inhibitory activity on the acetylcholinesterase enzyme. On the other hand, hodgkinsine showed potent cytotoxic activity against ovary, glioblastoma and colon cancer cells lines. The ethanol extract of the leaves and its alkaloidal fraction were submitted to nociception test and yielded good results. The ethanolic extract of the leaves was subjected to gastric antiulcer activity test, leading to a significant reduction in gastric lesions induced by ethanol in mice.
Margaritopsis carrascoana à um pequeno arbusto pertencente à famÃlia Rubiaceae e endÃmico da flora do Nordeste brasileiro, que cresce em solos arenosos do planalto da Ibiapaba e serra do Araripe - CearÃ. A ausÃncia de relatos acerca de estudos fitoquÃmicos relacionados à espÃcie, aliada a ocorrÃncia de alcalÃides bioativos no gÃnero, nos motivou ao seu estudo quÃmico. Desta forma, o espÃcimen vegetal foi coletado na chapada do Araripe, municÃpio de MoreilÃndia-PE. A investigaÃÃo fitoquÃmica do extrato etanÃlico dos talos resultou no isolamento dos alcalÃides calicosidina, hodgkinsina, N-8â-formilcalicosidina e N-8â-metil-N-1â-desmetilisocalicosidina, da neolignana Ãlcool 4-O-β-D-glicopiranosil-di-hidro-desidrodiconiferÃlico, do flavonÃide 7-O-[α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil luteolina, dos triterpenos lupeol e o Ãcido ursÃlico, e da mistura de esterÃides β-sitosterol e estigmasterol, como agliconas e nas formas glicosiladas. A partir do estudo do extrato etanÃlico das folhas foram isolados os flavonÃides 7-O-[β-D-glicopiranosil-(1→6)-β-D-apiofuranosil] luteolina, 7-O-[β-D-glicopiranosil-(1→6)-β-D-apiofuranosil] crisoeriol, 7-O-{β-D-apiofuranosil-(1→6)-[α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil} luteolina e 7-O-{α-L-ramnopiranosil - (1→6) - [α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil} luteolina. Os alcalÃides N-8â-formilcalicosidina e N-8â-metil-N-1â-desmetilisocalicosidina, e os flavonÃides 7-O-{β-D-apiofuranosil-(1→6)-[α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil} luteolina e 7-O-{α-L-ramnopiranosil-(1→6)-[α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil} luteolina, estÃo sendo relatados pela primeira vez na literatura, enquanto todas as demais substÃncias possuem carÃter inÃdito no gÃnero Margaritopsis. O isolamento dos metabÃlitos secundÃrios foi conduzido atravÃs de tÃcnicas cromatogrÃficas clÃssicas, incluindo cromatografia de adsorÃÃo em gel de sÃlica, cromatografia por exclusÃo molecular em Sephadex LH-20, cromatografia de fase reversa (C-18) e cromatografia lÃquida de alta eficiÃncia (CLAE). Para a caracterizaÃÃo estrutural foram utilizadas tÃcnicas espectroscÃpicas utilizando infravermelho, espectrometria de massas e ressonÃncia magnÃtica nuclear, incluindo tÃcnicas uni (RMN 1H e RMN 13C e DEPT 135) e bidimensionais (HMBC, HSQC, COSY e NOESY), alÃm de comparaÃÃo com dados descritos na literatura. Em adiÃÃo, os flavonÃides 7-O-[α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil luteolina, 7-O-[β-D-glicopiranosil-(1→6)-β-D-apiofuranosil] luteolina, 7-O-{β-D-apiofuranosil-(1→6)-[α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil} luteolina e 7-O-{α-L-ramnopiranosil-(1→6) - [α-L-ramnopiranosil-(1→2)-β-D-glicopiranosil} luteolina apresentaram atividade antioxidante maior que os padrÃes BHT e quercetina, enquanto os extratos etanÃlicos dos talos e folhas apresentaram atividade inibidora da enzima acetilcolinesterase. Por outro lado, o alcaloide hodgkinsina apresentou potencial citotÃxico frente Ãs cÃlulas de ovÃrio, glioblastoma e colon. No teste de nocicepÃÃo, realizado com o extrato etanÃlico das folhas e a fraÃÃo alcalÃidica, foram observados resultados positivos para ambas as fraÃÃes. O extrato etanÃlico das folhas foi submetido a teste de atividade antiÃlcera gÃstrica, levando a uma reduÃÃo significativa da Ãrea de lesÃo gÃstrica induzida pelo etanol em camundongos.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico
This present work reports the chemical and biological analysis of the stem and leaves from Bauhinia pulchella. In this study, the ethanol extract from stems was obtained by maceration, subjected to chromatographic fractionation, leading to isolation of three flavonoids: (+)-3â,4â-dihydroxyphenyl-chroman-7-ol (BP-2), (-)-fisetinidol (BP-3) and (+)-epicatechin (BP-4); a mixture of triterpenes taraxerone and β-amyrenone (BP-1); a mixture of steroids sitosterol and stigmasterol (BP-5); and a bibenzyl named 2-hydroxy-3â,5â-dimethoxybibenzyl (BP-6). It is notewhorthy to mention that BP-1 and BP-4 substances are unprecedented in the genus, while BP-2 is unpublished. Chemical structures of secondary metabolites obtained were elucidated by 1H and 13C NMR; IR and MS associated with comparison of data described in the literature. Chemical composition of the essential oil from leaves of B. pulchella, obtained by hydrodistillation, was determined and quantified by gas chromatography-mass spectroscopy (GC/MS) and gas chromatography-flame ionization detector (GC/FID), which identified 95,68% of all constituents. α-pinene (23.89%); caryophyllene oxide (22.43%) and β-pinene (12.19%) were the major components. The essential oil was tested against Aedes aegypti larvae and showed LC50 value of 105.93 Â 1.48 μg/mL. The cytotoxic activity of essential oil was evaluated on human tumor cell lines (HL-60; MCF-7; NCI-H292 and HEP-2) was evaluated, showing IC50 values with confidence intervals of 9.941 (8.238 to 12.00), 53.05 (41.39 to 67.99), 48.98 (44.22 to 54.25) and 50.42 (42.47 to 59.87) μg/mL, respectively and the cell line HL-60 the most sensitive among the cells tested. This is the first report of the chemical study of Bauhinia pulchella, as well the investigation of larvicidal activity and cytotoxicity of the essential oil from its leaves.
O presente trabalho relata o estudo quÃmico e biolÃgico do caule e das folhas de Bauhinia pulchella. Nesse estudo, o extrato etanÃlico do caule, obtido por maceraÃÃo, foi submetido a fracionamento cromatogrÃfico levando ao isolamento de trÃs flavonoides (+)-3â-4âdiidroxifenil-cromano-7-ol (BP-2), (-)-fisetinidol (BP-3) e (+)-epicatequina (BP-4); da mistura de triterpenos taraxerona e β-amirenona (BP-1); da mistura de esteroides sitosterol e estigmasterol (BP-5) e de um bibenzil denominado 2-hidrÃxi-3â-5â-dimetoxibibenzila (BP-6). Cabe ressaltar que as substÃncias BP-1 e BP-4 sÃo inÃditas no gÃnero, enquanto BP-2 à inÃdita na literatura. As estruturas dos metabÃlitos secundÃrios isolados foram elucidadas por RMN 1H e 13C; IV e EM, juntamente com a comparaÃÃo com os dados descritos na literatura. A composiÃÃo quÃmica do Ãleo essencial das folhas de B. pulchella, obtido por hidrodestilaÃÃo, foi determinada e quantificada por cromatografia gasosa acoplada à espectrometria de massas (CG-EM) e detector de ionizaÃÃo por chama (CG-DIC), sendo, portanto, identificados 95,68% dos seus constituintes: α-pineno (23,89%), Ãxido de cariofileno (22,43%) e β-pineno (12,19%) foram os constituintes majoritÃrios. O Ãleo essencial teve sua atividade larvicida sobre Aedes aegypti avaliada, sendo obtido um valor de CL50 igual a 105,93  1,48 μg/mL. O poder citotÃxico do Ãleo essencial foi avaliado sobre as linhagens tumorais humanas HL-60, MCF-7, NCI-H292 e HEP-2, sendo obtidos valores de CI50 e intervalos de confianÃa iguais a 9,941 (8,238 a 12,00); 53,05 (41,39 a 67,99); 48,98 (44,22 a 54,25) e 50,42 (42,47 a 59,87) μg/mL, respectivamente, sendo a linhagem celular HL-60 a mais sensÃvel dentre as cÃlulas testadas. Este à o primeiro relato do estudo quÃmico de Bauhinia pulchella, bem como da investigaÃÃo da atividade larvicida e citotÃxica do Ãleo essencial de suas folhas.

The red propolis originally from the state of Alagoas has a chemical composition rich in isoflavones and has been used as traditional popular medicine presented as an antioxidant and antiviral properties. Its relevance to this study is mainly due to the same present several biological properties, among them: antimicrobial, anti-cancer, cytotoxic and anti-tumor. In this work it was performed the study of the fixed compounds present in hexane fraction of propolis, which presented three esters: the methyl hexadecanoate (15,20%), the methyl tetracosanoate (10,40%) and the methyl octadecanoate (2,39%). Four isoflavanes were isolated from the thanolic extract (2'-hydroxy-4',7-dimethoxyisoflavane [PV-1], 2',7-dihydroxy-4'-methoxyisoflavane [PV-3],4',7-dihydroxy-2'-methoxyisoflavane [PV-4] and 2',4'-ihydroxy-7-methoxyisoflavane [PV-5]), one chalcone (2',4 ',4-trihydroxychalcone [PV-6]) and a triterpene (lup-20(29)-en-3-ol [PV-2]), known in red propolis. The structural determination of substances were performed by spectroscopic methods IR, 1H NMR, 13C-BB NMR,13C NMR DEPT-135Â, COSY, HSQC, HMBC and GC-MS. It was performed the determination of total phenols, using a spectrophotometer, in the ethanolic extract (EEPV), which presented a phenolic content of 133.3 Â 4.35 mg GAE / g sample, a result lower than those reported in the literature. Another test was performed on the antioxidant activity, the scavenging method using DPPH radical, both ethanolic extract and the hexane, dichloromethane, ethyl acetate and metanol fractions, with satisfactory results and higher than standart Vitamin C. Besides the antioxidant test, if was performed the inhibition of acetylcholinesterase assay by colorimetric method, of the ethanolic extract and hexane, dichloromethane, ethyl acetate and metanol fractions, that yielded positive results in almost all, regarding standart Eserine salt.
A prÃpolis vermelha oriunda do Estado de Alagoas possui uma composiÃÃo quÃmica rica em isoflavonoides e tem sido usada como remÃdio tradicional na medicina popular por apresentar propriedades antioxidante e antiviral. Sua relevÃncia decorre, principalmente, por apresentar diversas propriedades biolÃgicas, dentre elas: antimicrobiana, anti-cancerÃgena, citotÃxica e antitumoral. Neste trabalho foi realizado o estudo dos compostos fixos presentes na fraÃÃo hexÃnica da prÃpolis, o qual apresentou trÃs Ãsteres: o hexadecanoato de metila (15,20%), o tetracosanoato de metila (10,40%) e o octadecanoato de metila (2,39%). Foram isoladas do extrato etanÃlico quatro isoflavanas (2â-hidroxi-4â,7-dimetoxiisoflavana [PV-1], 2â,7-dihidroxi-4â-metoxiisoflavana [PV-3], 4â,7-dihidroxi-2â-metoxiisoflavana [PV-4] e 2â,4â-dihidroxi-7-metoxiisoflavana [PV-5]), uma chalcona (2â,4â,4-trihidroxichalcona [PV-6]), e um triterpeno (lup-20(29)-en-3-ol [PV-2]), jà conhecidos na prÃpolis vermelha. A determinaÃÃo estrutural das substÃncias foi realizada atravÃs de mÃtodos espectroscÃpicos de IV, RMN de 1H, RMN de 13C-BB, RMN de 13C-DEPT 135Â, COSY, HSQC, HMBC e CG-EM. Realizou-se a determinaÃÃo de fenÃis totais, usando espectofotÃmetro, no extrato etanÃlico (EEPV), o qual apresentou um teor de compostos fenÃlicos de 133,3  4,35 mg de EAG/ g de amostra, resultado inferior aos relatados na literatura. Outro teste realizado foi o de atividade antioxidante, usando o mÃtodo de sequestro do radical DPPH, tanto no extrato etanÃlico, quanto nas fraÃÃes hexÃnica, diclorometano, acetato de etila e metanÃlica, apresentando resultados satisfatÃrios e superiores ao do padrÃo Vitamina C. AlÃm deste, foi realizado o ensaio de inibiÃÃo da enzima acetilcolinesterase, atravÃs de mÃtodo colorimÃtrico, no extrato etanÃlico e nas fraÃÃes hexÃnica, diclorometano, acetato de etila e metanÃlica, quase todos apresentando resultados positivos em relaÃÃo ao padrÃo sal de Eserina.

A simple and widely applicable method for the synthesis of technetium nitrosyl complexes containing either [99Tc] or [99mTc] has been developed using hydroxylamine as a reducing agent. A number of readily available complexes such as [TcO4]- or [TcX6]2- (X = Cl, Br, I) may be employed as the starting material.

Mestrado em Biotecnologia - Biotecnologia Alimentar
Atualmente, existe um elevado interesse na valorização de recursos naturais como fontes de compostos bioativos com potenciais efeitos benéficos para a saúde. A salicórnia é uma planta halófita que tem sido usada na alimentação e na medicina tradicional e mais recentemente no desenvolvimento de novos produtos alimentares, ilustrando o interesse da sua caracterização e avaliação. Esta planta encontra-se dispersa mundialmente, estando presente em algumas regiões em Portugal, nomeadamente na Ria de Aveiro e na Ria da Formosa, no Algarve. Esta planta cresce espontaneamente em ambientes salinos, estando inserida num ambiente de elevado stress. O género Salicornia compreende cerca de 25-30 espécies sendo a Salicornia ramosissima uma das menos estudadas atendendo à sua composição química. Alguns compostos bioativos são reportados nesta espécie, nomeadamente ácidos gordos, esteróis e compostos fenólicos, no entanto a informação encontra-se muito dispersa atendendo aos seus efeitos biológicos e composição. Neste sentido, o conhecimento da composição química e dos potenciais efeitos biológicos da S. ramosissima é extremamente importante para introduzir novas aplicações. Assim, o objetivo principal desta tese foi a caracterização química e avaliação in vitro da atividade antioxidante e anti-inflamatória extratos da S. ramosissima, recolhida na ria de Aveiro. Foram recolhidas quatro amostras, no estado de frutificação, em três locais da ria de Aveiro, estas amostras foram tratadas e armazenadas para posterior caracterização. Inicialmente foi estudado a fração lipofílica (extratos de diclorometano) da planta por GC-qMS, seguida do estudo da fração polar (extratos de metanol seguidos de extração com éter de petróleo/água) por LC-QqQ-MS. Posteriormente foram analisados minerais essenciais por ICP-OES e componentes potencialmente tóxicos por ICP-MS. Na fase final foi avaliada ainda a atividade antioxidante e anti-inflamatória dos extratos da fração polar da planta. De um total de 35 compostos da fração lipofílica, o ácido linolénico, o ácido linoleico, o stigmasterol, o β-sitosterol e o ácido palmítico foram os compostos maioritários. O conteúdo total de lipofílicos variou entre 541 e 5412 mg/100g peso seco. Na fração polar, o conteúdo em fenóis totais variou entre 1391 e 3398 mg de equivalentes de ácido gálico por 100g. A amostra vermelha da Marinha dos peixinhos (MPR) apresentou o maior conteúdo de fenóis. Da análise detalhada dos compostos fenólicos, foram identificados 32, sendo que 22 são reportados pela primeira vez nesta espécie. Isorhamnetina é composto maioritário presente nesta espécie. MPR apresentou um maior número de compostos identificados assim como um maior conteúdo estimado (1676.6 μg/g de extrato peso seco). O estudo dos minerais revelou que o sódio é o mineral mais abundante em todas as amostras, no entanto o consumo de 5g desta planta fresca numa salada corresponde apenas a 6.0-7.1% da dose diária recomendada (DDR) para este mineral. Relativamente ao selénio, magnésio e potássio pode contribuir para a DDR dos mesmos com 1.9-2.6%, 1.3-2.1% e 0.2-0.3%, respetivamente. Os estudos in vitro da atividade antioxidante foram expressos em valores de EC50. Os diferentes estudos permitiram avaliar o potencial da S. ramosissima como fonte de antioxidantes, estando os compostos fenólicos relacionados com esta atividade (r2>0.77). A atividade anti-inflamatória foi avaliada através da inibição da produção de dois metabolitos do metabolismo do ácido araquidónico (TXA2 e PGE2). Apesar de nenhum dos extratos inibir a produção de PGE2, o extrato da Marinha dos Peixinhos (MP) e o extrato do Rio Boco (BC) inibiram a produção de TXA2 em 33.2% e 18.1%. A aspirina, conhecida pelos seus efeitos em processos anti-inflamatórios foi usada na mesma metodologia, inibindo o PGE2 e o TXA2 em 18% e 69.3%, respetivamente. Sendo que algumas reações neste metabolismo envolvem radicais, os compostos previamente identificados nos extratos podem ser fundamentais para a atividade reportada. Além disso sendo que a aspirina inibe preferencialmente TXA2, pode-se inferir que os extratos de S. ramosissima apresentam um comportamento similar. Em conclusão os resultados obtidos permitiram a caracterização química sumária da S. ramosissima da Ria de Aveiro, com especial destaque para os compostos lipofílicos e fenólicos e ainda a presença de minerais essenciais. A presença de compostos com potenciais efeitos benéficos para a saúde humana (flavonoides, fitoesteróis e ácidos gordos ω-3 e ω-6) pode ser um fator determinante para a valorização desta planta assim como a presença de baixo teor de sal, podendo ser usado como coadjuvante na dieta de forma a diminuir o risco de doenças cardiovasculares. O efeito anti-inflamatório dos extratos da S. ramosissima revelou o seu potencial impacto na produção de TXA2.
Relativamente ao selénio, magnésio e potássio pode contribuir para a DDR dos mesmos com 1.9-2.6%, 1.3-2.1% e 0.2-0.3%, respetivamente. Os estudos in vitro da atividade antioxidante foram expressos em valores de EC50. Os diferentes estudos permitiram avaliar o potencial da S. ramosissima como fonte de antioxidantes, estando os compostos fenólicos relacionados com esta atividade (r2>0.77). A atividade anti-inflamatória foi avaliada através da inibição da produção de dois metabolitos do metabolismo do ácido araquidónico (TXA2 e PGE2). Apesar de nenhum dos extratos inibir a produção de PGE2, o extrato da Marinha dos Peixinhos (MP) e o extrato do Rio Boco (BC) inibiram a produção de TXA2 em 33.2% e 18.1%. A aspirina, conhecida pelos seus efeitos em processos anti-inflamatórios foi usada na mesma metodologia, inibindo o PGE2 e o TXA2 em 18% e 69.3%, respetivamente. Sendo que algumas reações neste metabolismo envolvem radicais, os compostos previamente identificados nos extratos podem ser fundamentais para a atividade reportada. Além disso sendo que a aspirina inibe preferencialmente TXA2, pode-se inferir que os extratos de S. ramosissima apresentam um comportamento similar. Em conclusão os resultados obtidos permitiram a caracterização química sumária da S. ramosissima da Ria de Aveiro, com especial destaque para os compostos lipofílicos e fenólicos e ainda a presença de minerais essenciais. A presença de compostos com potenciais efeitos benéficos para a saúde humana (flavonoides, fitoesteróis e ácidos gordos ω-3 e ω-6) pode ser um fator determinante para a valorização desta planta assim como a presença de baixo teor de sal, podendo ser usado como coadjuvante na dieta de forma a diminuir o risco de doenças cardiovasculares. O efeito anti-inflamatório dos extratos da S. ramosissima revelou o seu potencial impacto na produção de TXA2.

Thesis (Ph.D.)--George Mason University, 2008.
Vita: p. 232. Thesis director: Andrew Loerch. Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biodefense. Title from PDF t.p. (viewed July 7, 2008). Includes bibliographical references (p. 226-231). Also issued in print.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (p. 345-363).
Elevated levels of nitric oxide (NO) in vivo are associated with a variety of cellular modifications thought to be mutagenic or carcinogenic. These processes are likely mediated by reactive nitrogen species (RNS) such as nitrogen dioxide (NO2) and peroxynitrite formed from the respective reactions of NO with oxygen and superoxide anion. Controlled delivery of these RNS at levels expected to occur in vivo is desirable in studying these processes and their role in the etiology of various diseases. Two delivery systems were developed that provide novel capabilities for steady, quantitative exposure of biological targets to RNS over periods from hours to days. Quantitative models are presented that accurately describe the behavior of both systems. The first system achieves NO concentrations of 0.6-3.0 [mu]M in a stirred, liquid-filled vessel by diffusion from a gas stream through a porous poly(tetrafluoroethylene) membrane. Oxygen, consumed by reaction with NO or by other processes, is supplied by diffusion from a separate gas stream through a loop of poly(dimethylsiloxane) tubing. The adventitious chemistry observed in a prior device for NO delivery [Wang C. Ann Biomed Eng (2003) 31:65-79] is eliminated in the present design, as evidenced by the close match to model predictions of the accumulation rate of nitrite, the stable end product of NO oxidation. The second system delivers NO2 by direct contacting of a stirred liquid with an NO2- containing gas mixture. Accumulation rates of products in the presence and absence of the NO2-reactive substrate 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) matched model predictions within 15% for all conditions studied. The predicted steady NO2 concentration in the liquid is on the order of 400 pM, similar to what is expected to be present in extracellular fluids in the presence of 1 [mu]M NO. This system appears to be the first reported with the capability for sustained, quantitative NO2 delivery to suspended cell cultures. Results from initial efforts to test a novel mixing model for bolus delivery of peroxynitrite to agitated solutions imply that the proposed model might accurately describe mixing in bolus delivery experiments with agitation by vortex mixing, but further work is required to validate the model.
by Brian Thomas Skinn.
Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2007.
Includes bibliographical references (p. 437-458).
Sequential motif discovery, the ability to identify conserved patterns in ordered datasets without a priori knowledge of exactly what those patterns will be, is a frequently encountered and difficult problem in computational biology and biochemical engineering. The most prevalent example of such a problem is finding conserved DNA sequences in the upstream regions of genes that are believed to be coregulated. Other examples are as diverse as identifying conserved secondary structure in proteins and interpreting time-series data. This thesis creates a unified, generic approach to addressing these (and other) problems in sequential motif discovery and demonstrates the utility of that approach on a number of applications. A generic motif discovery algorithm was created for the purpose of finding conserved patterns in arbitrary data types. This approach and implementation, name Gemoda, decouples three key steps in the motif discovery process: comparison, clustering, and convolution. Since it decouples these steps, Gemoda is a modular algorithm; that is, any comparison metric can be used with any clustering algorithm and any convolution scheme. The comparison metric is a data-specific function that transforms the motif discovery problem into a solvable graph-theoretic problem that still adequately represents the important similarities in the data.
(cont.) This thesis presents the development of Gemoda as well as applications of this approach in a number of different contexts. One application is an exhaustive solution of an abstraction of the transcription factor binding site discovery problem in DNA. A similar application is to the analysis of upstream regions of regulons in microbial DNA. Another application is the identification of protein sequence homologies in a set of related proteins in the presence of significant noise. A quite different application is the discovery of extended local secondary structure homology between a protein and a protein complex known to be in the same structural family. The final application is to the analysis of metabolomic datasets. The diversity of these sample applications, which range from the analysis of strings (like DNA and amino acid sequences) to real-valued data (like protein structures and metabolomic datasets) demonstrates that our generic approach is successful and useful for solving established and novel problems alike. The last application, of analyzing metabolomic datasets, is of particular interest. Using Gemoda, an appropriate comparison function, and appropriate data handling, a novel and useful approach to the interpretation of metabolite profiling datasets obtained from gas chromatography coupled to mass spectrometry is developed.
(cont.) The use of a motif discovery approach allows for the expansion of the scope of metabolites that can be tracked and analyzed in an untargeted metabolite profiling (or metabolomic) experiment. This new approach, named SpectConnect, is presented herein along with examples that verify its efficacy and utility in some validation experiments. The beginning of a broader application of SpectConnect's potential is presented as well. The success of SpectConnect, a novel application of Gemoda, validates the utility of a truly generic approach to motif discovery. By not getting bogged down in the specifics of a type of data and a problem unique to that type of data, a broader class of problems can be addressed that otherwise would have been extremely difficult to handle.
by Mark Philip-Walter Styczynski.
Ph.D.

Acanthodactylus boskianus is a common lizard species frequently occurring in different habitats throughout Egypt. Both males and females have well developed epidermal femoral glands. This species is territorial and males acquire dominance hierarchies in captivity. The current work included three different techniques to study the importance of femoral gland secretions in communication and signal evolution of A. boskianus. These are behaviour, chemical and DNA analyses techniques. Behavioural bioassays in different experiments showed that the femoral gland secretions are used in communication between the lizards. Communication includes possible roles in mate choice, agonistic behaviour between potential competitor males, and chemical trailing of scent pheromones. These behavioural results reflect the chemical results which showed the chemical variability between male ages, sexes, and allopatric populations. Chemical analysis of the secretions resulted in the identification of natural compounds not previously reported in reptiles, glycerolmonoethers and monoglycerides. The secretions seem to be used as scent pheromones, which are involved in signal evolution processes resulting in divergence of the chemical fingerprints of the gland secretion between allopatric populations.

One of the main problems with the use of synthetic polymers as biomaterials is the invasion of micro-organisms causing infection. A study of the properties of polymeric antibacterial agents, in particular polyhexamethylene biguanide, has revealed that the essential components for the design of a novel polymeric antibacterial are a balance between hydrophilicity and hydrophobicity coupled with sites of cationicity. The effect of cation incorporation on the physical properties of hydrogels has been investigated. Hydrogel systems copolymerised with either N-vinyl imidazole or dimethylaminoethyl methacrylate have been characterised in terms of their water binding, mechanical and surface properties. It has been concluded that the incorporation of these monomers does not adversely affect the properties of such hydrogels and that these materials are potential candidates for further development for use in biomedical applications. It has been reported that hydro gels with ionic character may increase the deposition of biological material onto the hydrogel surface when it is in contact with body fluids. An investigation into the deposition characteristics of hydrogels containing the potentially cationic monomers has been carried out, using specific protein adsorption and in vitro spoilation techniques. The results suggest that at low levels of cationicity, the deposition of positively charged proteins is reduced without adversely affecting the uptake of the other proteins. The gross deposition characteristics were found to be comparable to some commercially available contact lens materials. A preliminary investigation into the development of novel antibacterial polymers has been completed and some novel methods of bacterial inhibition discussed. These methods include development of an hydrogel whose potential application is as a catheter coating.

Thermal desorption (TD) remediates hydrocarbon-contaminated soil by heating the soil (200 to 500 ?C) to volatilize the hydrocarbons, effectively removing the contaminant from the soil. If the soil is then used for agricultural production, reclamation success can be determined by quantifying aspects of soil health. Cation exchange capacity (CEC), cation selectivity and Gibbs free energy (?Gex) of TD-treated and untreated soil were compared. Although CEC and ?Gex differed, cation selectivities were not altered suggesting that alternative fertility management to retain previous soil productivity may not be needed. From field plots, N-transforming genes were lowered in contaminated and TD-treated soils as compared to non-contaminated soil, but the addition of surface soil (1:1 blends) increased N-cycling genes to levels reported in the literature. Thermal desorption may not alter soil chemical as much as biological metrics, but blending treated or contaminated soils with native surface soils can enhance soil function and, ultimately, productivity.
Tesoro Logistics Operations, LLC

This thesis presents three different topics in phosphorus-containing heterocycles. The first topic is about novel phosphorus-containing flame-retardants to be used in poly-urethane foams. The background and importance of flame-retardants is discussed as well as the synthesis and testing data of compounds that were expected to have good flame-retardant properties. More importantly, these compounds represent a class of flame-retardants that can be chemically incorporated into the polymer, which will overcome current negative aspects such as leaching and fogging. The test results show that the tested compounds perform about as well as commercially available materials and that there are indications that they are chemically incorporated into the polymer. The second topic is about the cytotoxic effects of aziridines. The phosphate moiety of a DNA-chain can act as a nucleophile that ring-opens an aziridine. This reaction results in the formation of a phosphate triester with a potential nucleophile, namely an amino group, in a beta-position. These two factors make the hydrolysis of the DNA chain at this particular point much more likely. A model study was designed to investigate the likelihood of DNA-chain cleavage by aziridines as these form an important class of anti-tumour agents. From this model study it can be concluded that the cytotoxic effects of aziridines have to be contributed to alkylation of other nucleophilic sites at DNA than to strand cleavage preceded by alkylation of the phosphate backbone. The last topic covers a stereochemical investigation of the metal catalysed hydrolysis of a cyclic nucleotide. It presents the first stereochemical assignment of the metal catalysed hydrolysis of a phosphate ester. In line with most enzyme catalysed hydrolyses of phosphate esters the reaction investigated here was assigned to go with inversion of configuration.

The preparation of a novel complex, ferric bromopyruvate, is described. In solutions from which most of the carbonate has been removed, ferric bromopyruvate can be used both as an iron and pyruvate source for the full iron saturation of apotransferrin. Using ferric bromopyruvate as an iron donor, iron incorporation into human apotransferrin is biphasic; the N-terminal domain is saturated three times faster than its homologous C-terminal iron binding site. Following the reaction of apotransferrin with ferric bromopyruvate, 4 moles of pyruvate per mole of transferrin are covalently bound. Based on the effect of acetylation on pyruvate and iron binding, it is suggested that lysyl residues could be the target of pyruvate bonding. However, the reaction of pyruvate with other positively charged amino acid residues cannot be excluded. The possible sites of pyruvate binding within the N-terminal domain of human serum transferrin are discussed. Covalent attachment of pyruvate to cationic amino acid residues decreased both in vitro and in vivo iron release, preferentially from the N-terminal domain of transferrin. The decreased rate of iron incorporation from iron-pyruvate-transferrin complexes by rabbit reticulocytes caused a lower iron incorporation into heme. It is suggested that an impairment of iron release from transferrin may decrease the rate of heme synthesis in reticulocytes. In vitro studies on the iron removal from iron-pyruvate-transferrin complexes showed that pyrophosphate can remove iron from this complex at an acid pH to a similar extent to the cellular mediated iron release from this complex. Based on this data, a model for the intravesicular iron release from transferrin is proposed.

Magnetic fields of different strengths can be applied to chemical and biological systems to study processes involving radicals or radical pairs. This work uses two such techniques, electron paramagnetic resonance (EPR) spectroscopy (≥ 150 mT) in addition to time resolved EPR spectroscopy and time resolved infrared (TRIR) spectroscopy (≤ 37 mT). The former are used to monitor metalloproteins, and the photochemistry of phosphorus oxides, while TRIR spectroscopy is used to record the magnetic field effects on the reaction kinetics of neutral radical pairs. The thesis begins with an introduction and an overview of the experimental techniques and developments. This is followed by an EPR study of the Fe(III) binding proteins, transferrin and lactoferrin and the effect thereon of catecholamine stress hormones. Catecholamines mediate bacterial growth by sequestering iron from the iron binding proteins. The mechanism of iron capture is unknown, however, the current work reveals Fe(III) binding by the catecholamine and supports subsequent reduction as the most likely route. Since catecholamines are also administered therapeutically, the validity of EPR as a diagnostic technique is examined and iron loss from human serum transferrin is observed. Also within this work, experiments are presented in which TRIR spectroscopy is used to investigate factors that affect the development of magnetic field effects for radical pairs in different solutions. This initially involves studies on acylphosphine oxides. In addition to the reported photoprocesses, alternative chemistry is uncovered, which occurs when bisacylphosphine oxide is in solutions where the solvent is sufficiently nucleophilic. The photochemistry is investigated using time resolved EPR and density functional theory calculations to suggest three possible structures that are responsible for the additional radicals observed. Furthermore, encapsulated organic radical pairs in reverse micelles are studied. These experiments, in combination with dynamic light scattering measurements provide insight into the magnitude of the observed magnetic field effects and the differing kinetics of the radical pair in the reverse micelles.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.
Cataloged from PDF version of thesis. Page 199 blank.
Includes bibliographical references (pages 173-198).
Graphene exhibits a unique combination of properties making it particularly promising for sensing applications. This thesis builds new graphene chemical and biological sensing technologies from the ground up by developing device models, systems, and applications. On the modeling side, this thesis develops a DC model for graphene electrolyte-gated field-effect transistors (EGFETs). It also presents a novel frequency-dependent (AC) small-signal model for graphene EGFETs and demonstrates the ability of these devices to operate as functional amplifiers for the first time. Graphene sensors are transitioned to the system level by developing a new sensor array architecture in conjunction with a compact and easy-to-use custom data acquisition system. The system allows for simultaneous characterization of hundreds of sensors and provides insight into graphene EGFET performance variations. The system is adapted to develop solution-phase ionized calcium sensors using a graphene EGFET array that has been functionalized using a polyvinyl chloride (PVC) membrane containing a neutral calcium ionophore. Sensors are shown to accurately quantify ionized calcium over several orders of magnitude while exhibiting excellent selectivity, reversibility, response time, and a virtually ideal Nernstian response of 30.1 mV/decade. A new variation-insensitive distribution matching technique is also developed to enable faster readout. Finally, the sensor system is employed to develop gas-phase chemiresistive ammonia sensors that have been functionalized using cobalt porphyrin. Sensors provide enhanced sensitivity over pristine graphene while providing selectivity over interfering compounds such as water and common organic solvents. Sensor responses exhibit high correlation coefficients indicating consistent sensor response and reproducibility of the cobalt porphyrin functionalization. Variations in sensitivity follow a Gaussian distribution and are shown to stem from variations in the underlying sensor source-drain currents. A detailed kinetic model is developed describing sensor response profiles that incorporates two ammonia adsorption mechanisms--one reversible and one irreversible.
by Charles Mackin.
Ph. D.