Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice

The plant PTR/NRT1 (peptide transporter/nitrate transporter 1) gene family comprises di/tripeptide and low-affinity nitrate transporters; some members also recognize other substrates such as carboxylates, phytohormones (auxin and abscisic acid), or defence compounds (glucosinolates). Little is known about the members of this gene family in rice (Oryza sativa L.). Here, we report the influence of altered OsPTR9 expression on nitrogen utilization efficiency, growth, and grain yield. OsPTR9 expression is regulated by exogenous nitrogen and by the day-night cycle. Elevated expression of OsPTR9 in transgenic rice plants resulted in enhanced ammonium uptake, promotion of lateral root formation and increased grain yield. On the other hand, down-regulation of OsPTR9 in a T-DNA insertion line (osptr9) and in OsPTR9-RNAi rice plants had the opposite effect. These results suggest that OsPTR9 might hold potential for improving nitrogen utilization efficiency and grain yield in rice breeding.

The anticoagulant activation of antithrombin by heparin

Antithrombin, a plasma serpin, is relatively inactive as an inhibitor of the coagulation proteases until it binds to the heparan side chains that line the microvasculature. The binding specifically occurs to a core pentasaccharide present both in the heparans and in their therapeutic derivative heparin. The accompanying conformational change of antithrombin is revealed in a 2.9-Å structure of a dimer of latent and active antithrombins, each in complex with the high-affinity pentasaccharide. Inhibitory activation results from a shift in the main sheet of the molecule from a partially six-stranded to a five-stranded form, with extrusion of the reactive center loop to give a more exposed orientation. There is a tilting and elongation of helix D with the formation of a 2-turn helix P between the C and D helices. Concomitant conformational changes at the heparin binding site explain both the initial tight binding of antithrombin to the heparans and the subsequent release of the antithrombin–protease complex into the circulation. The pentasaccharide binds by hydrogen bonding of its sulfates and carboxylates to Arg-129 and Lys-125 in the D-helix, to Arg-46 and Arg-47 in the A-helix, to Lys-114 and Glu-113 in the P-helix, and to Lys-11 and Arg-13 in a cleft formed by the amino terminus. This clear definition of the binding site will provide a structural basis for developing heparin analogues that are more specific toward their intended target antithrombin and therefore less likely to exhibit side effects.

Protonation dynamics of the extracellular and cytoplasmic surface of bacteriorhodopsin in the purple membrane.

The dynamics of proton binding to the extracellular and the cytoplasmic surfaces of the purple membrane were measured by laser-induced proton pulses. Purple membranes, selectively labeled by fluorescein at Lys-129 of bacteriorhodopsin, were pulsed by protons released in the aqueous bulk from excited pyranine (8-hydroxy-1,3,6-pyrenetrisulfonate) and the reaction of protons with the indicators was measured. Kinetic analysis of the data imply that the two faces of the membrane differ in their buffer capacities and in their rates of interaction with bulk protons. The extracellular surface of the purple membrane contains one anionic proton binding site per protein molecule with pK = 5.1. This site is within a Coulomb cage radius (approximately 15 A) from Lys-129. The cytoplasmic surface of the purple membrane bears 4-5 protonable moieties (pK = 5.1) that, due to close proximity, function as a common proton binding site. The reaction of the proton with this cluster is at a very fast rate (3.10(10) M-1.s-1). The proximity between the elements is sufficiently high that even in 100 mM NaCl they still function as a cluster. Extraction of the chromophore retinal from the protein has a marked effect on the carboxylates of the cytoplasmic surface, and two to three of them assume positions that almost bar their reaction with bulk protons. The protonation dynamics determined at the surface of the purple membrane is of relevance both for the vectorial proton transport mechanism of bacteriorhodopsin and for energy coupling, not only in halobacteria, but also in complex chemiosmotic systems such as mitochondrial and thylakoid membranes.

Location of the active site of allosteric chorismate mutase from Saccharomyces cerevisiae, and comments on the catalytic and regulatory mechanisms.

The active site of the allosteric chorismate mutase (chorismate pyruvatemutase, EC 5.4.99.5) from yeast Saccharomyces cerevisiae (YCM) was located by comparison with the mutase domain (ECM) of chorismate mutase/prephenate dehydratase [prephenate hydro-lyase (decarboxylating), EC 4.2.1.51] (the P protein) from Escherichia coli. Active site domains of these two enzymes show very similar four-helix bundles, each of 94 residues which superimpose with a rms deviation of 1.06 A. Of the seven active site residues, four are conserved: the two arginines, which bind to the inhibitor's two carboxylates; the lysine, which binds to the ether oxygen; and the glutamate, which binds to the inhibitor's hydroxyl group in ECM and presumably in YCM. The other three residues in YCM (ECM) are Thr-242 (Ser-84), Asn-194 (Asp-48), and Glu-246 (Gln-88). This Glu-246, modeled close to the ether oxygen of chorismate in YCM, may function as a polarizing or ionizable group, which provides another facet to the catalytic mechanism.

Complexos de dirutênio com os fármacos ibuprofeno, ácido acetilsalicílico, naproxeno, indometacina, e com ácido y-linolêncio: Síntese, caracterização, avaliação da ação antiproliferativa sobre células tumorais e estudo da interação da unidade dimetálica com adenina e adenosina

Este trabalho tem como principal objetivo contribuir para o desenvolvimento de novos potenciais metalofármacos de rutênio. Nele são descritas a síntese, a caracterização e a avaliação da ação antiproliferativa de alguns complexos de dirutênio (II,III) com os fármacos antiinflamatórios não-esteróides (AINEs): ibuprofeno (ibp), ácido acetilsalicílico (aas), naproxeno (npx) e indometacina (ind) e também com o ácido γ-linolênico (lin), sobre células cancerígenas. Os compostos obtidos foram caracterizados por análise elementar, espectroscopia de absorção eletrônica, medidas de susceptibilidade magnética, espectroscopia vibracional FTIR e Raman, difratometria de raios X de pó, medidas de condutividade molar e análise térmica (TG, OTAe OSC). Todos os complexos sintetizados apresentam estrutura em gaiola, com os carboxilatos derivados dos fármacos AINEs coordenados à unidade dimetálica Ru2( (II,III), em ponte equatorial, estabilizando assim a ligação direta rutênio-rutênio. As posições axiais são ocupadas por íons cloreto, no caso dos complexos [Ru2(O2(CR)4(Cl] (O2(CR = ibp, aas, npx ou ind), ou por moléculas de água, nas espécies do tipo [Ru2(O2(CR)4(H2O)2]PF6(O2CR =npx e ind). Ensaios biológicos demonstraram que os compostos [Ru2(ibp) 4Cl]•½H2O e [Ru2(npx)4(H2O)2]PF6 apresentam ação antiproliferativa sobre células de glioma de rato C6 in vitro, dependendo do tempo de exposição do meio celular ao complexo. O complexo [Ru2 (lin)4Cl] também apresenta efeito sobre a proliferação de células C6; entretanto, nesse caso, efeitos significativos são observaçlos já nas primeiras 24 h de exposição. Estudos mostraram que as bases adenina e adenosina reagem com o complexo [Ru2(OAc)4(H2O)2]PF6 sem que ocorra quebra da estrutura em gaiola. As bases nitrogenadas substituem axialmente as moléculas de água, formando pontes axiais entre duas unidades de dirutênio (II,III) no estado sólido.

Historic records of organic compounds from a high Alpine glacier: influences of biomass burning, anthropogenic emissions, and dust transport

Historic records of α-dicarbonyls (glyoxal, methylglyoxal), carboxylic acids (C6–C12 dicarboxylic acids, pinic acid, p-hydroxybenzoic acid, phthalic acid, 4-methylphthalic acid), and ions (oxalate, formate, calcium) were determined with annual resolution in an ice core from Grenzgletscher in the southern Swiss Alps, covering the time period from 1942 to 1993. Chemical analysis of the organic compounds was conducted using ultra-high-performance liquid chromatography (UHPLC) coupled to electrospray ionization high-resolution mass spectrometry (ESI-HRMS) for dicarbonyls and long-chain carboxylic acids and ion chromatography for short-chain carboxylates. Long-term records of the carboxylic acids and dicarbonyls, as well as their source apportionment, are reported for western Europe. This is the first study comprising long-term trends of dicarbonyls and long-chain dicarboxylic acids (C6–C12) in Alpine precipitation. Source assignment of the organic species present in the ice core was performed using principal component analysis. Our results suggest biomass burning, anthropogenic emissions, and transport of mineral dust to be the main parameters influencing the concentration of organic compounds. Ice core records of several highly correlated compounds (e.g., p-hydroxybenzoic acid, pinic acid, pimelic, and suberic acids) can be related to the forest fire history in southern Switzerland. P-hydroxybenzoic acid was found to be the best organic fire tracer in the study area, revealing the highest correlation with the burned area from fires. Historical records of methylglyoxal, phthalic acid, and dicarboxylic acids adipic acid, sebacic acid, and dodecanedioic acid are comparable with that of anthropogenic emissions of volatile organic compounds (VOCs). The small organic acids, oxalic acid and formic acid, are both highly correlated with calcium, suggesting their records to be affected by changing mineral dust transport to the drilling site.

Boric acid catalyzed chemoselective esterification of alpha-hydroxycarboxylic acids

Boric acid catalyzes the selective esterification of alpha-hydroxycarboxylic acids without causing significant esterification to occur with other carboxylic acids. The procedure is simple, high-yielding, and applicable to the esterification of alpha-hydroxy carboxylates in the presence of other carboxylic acids including beta-hydroxyacids within the same molecule.

Intra- vs intermolecular photoinduced electron transfer reactions of a macrocyclic donor-acceptor dyad

The synthesis, structural characterization, and photophysical behavior of a 14-membered tetraazamacrocycle with pendant 4-dimethylaminobenzyl (DMAB) and 9-anthracenylmethyl groups is reported (L-3, 6-((9-anthracenylmethyl)amino)-trans-6,13-dimethyl-13-((4-dimethylaminobenzyl)amino)-1,4,8,11-tetraaza-cyclotetradecane). In its free base form, this compound displays rapid intramolecular photoinduced electron transfer (PET) quenching of the anthracene emission, with both the secondary amines and the DMAB group capable of acting as electron donors. When complexed with Zn(II), the characteristic fluorescence of the anthracene chromophore is restored as the former of these pathways is deactivated by coordination. Importantly, it is shown that the DMAB group, which remains uncoordinated and PET active, acts only very weakly to quench emission, by comparison to the behavior of a model Zn complex lacking the pendant DMAB group, [ZnL2](2+) (Chart 1). By contrast, Stern-Volmer analysis of intermolecular quenching of [ZnL2](2+) by N,N-dimethylaniline (DMA) has shown that this reaction is diffusion limited. Hence, the pivotal role of the bridge in influencing intramolecular PET is highlighted.

Spectroscopic characterization of copper(II) binding to the immunosuppressive drug mycophenolic acid

Mycophenolic acid (MPA) is a drug that has found widespread use as an immunosuppressive agent which limits rejection of transplanted organs. Optimal use of this drug is hampered by gastrointestinal side effects which can range in severity. One mechanism by which MPA causes gastropathy may involve a direct interaction between the drug and gastric phospholipids. To combat this interaction we have investigated the potential of MPA to coordinate Cu(II), a metal which has been used to inhibit gastropathy associated with use of the NSAID indomethacin. Using a range of spectroscopic techniques we show that Cu(II) is coordinated to two MPA molecules via carboxylates and, at low pH, water ligands. The copper complex formed is stable in solution as assessed by mass spectrometry and H-1 NMR diffusion experiments. Competition studies with glycine and albumin indicate that the copper-MPA complex will release Cu(II) to amino acids and proteins thereby allowing free MPA to be transported to its site of action. Transfer to serum albumin proceeds via a Cu(MPA)(albumin) ternary complex. These results raise the possibility that copper complexes of MPA may be useful in a therapeutic situation.

Studies in organobismuth chemistry

Perturbations in the bismuth market resulted in Mining and Chemical Products Ltd., seeking further outlets in the market. Together with Manchem Ltd. they were anxious to evaluate the possibility of using bismuth compounds as a replacement for lead/calcium soaps in paint driers. A range of new organobismuth compounds were synthesised of the type RBiX2 and R3BiX2 (X= halogen, OOCR, dithiocarbamate). A variety of synthetic techniques were explored, including the use of mathematical reactions, phase-transfer catalysis and microwave energy. The preparation of a range of trivalent and pentavalent organobismuth carboxylates is reported and their infra-red , 13C, lH nmr spectra. The compounds were evaluated as paint driers and in cases found to enhance paint drying to a greater degree than the standard driers, to which they were being compared. The drying times of paint films containing the organobismuth compounds are reported, together with a comparison of the drying times with the addition of bismuth tris-diethyldithiocarbamate, which may promote the cross-linking reaction that occur in paint films during the drying process. Examples are reported to illustrate the great reductions in reaction times possible when using microwave energy. Reactions such as metallation of aromatic rings, ligand redistribution and synthesis were carried out in PTFE containers in a conventional domestic microwave oven. An X-ray diffraction study of (phenylazophenyl-C,N')mercury(II) chloride has shown it to be dimeric via long Hg-Cl bridging interactions of 3.367A. Its crystal structure is reported, together with its 13C nmr spectra and mass spectrum. The Lewis acidity of compounds of the type RBiX2 was investigated. The donor group being anchored to the organo group (R). The dithiocarbamates bis- (diethyldithiobarbamato)phenylbismuth(Ill) and [2-2-pyridyl)phenylbismuth(III) were synthesised, and their crystal structures, 14N, 13C nmr ar1d infra-red spectra are reported. Both compounds are pseudo-pentagonal bipyramidal in geometry, with two long Bi-S bonds and two short Bi-S bonds. The reaction of RBiBr2 (R= 2-(pyridyl) with various ligands is reported. The infra-red evidence suggesting that the coordination of extra ligands is accompanied by a reduction of the strength of the Bi-interaction.

Formulation of immunomodulatory agents

Reversed-phase high-performance liquid chromatography procedures were developed for the analysis of pyrimidine-based drugs bropirimine and its derivatives (2-N-acetyl- and 2-N-propanoyl-) and for pyrimethamine and its 2/4- substituted derivatives (2, N-propanoyl and 2,4-N, N-dipropanoyl-) and its 6- substituted (methyl-, ethyl-, propyl- and isopropyl- carboxylates) analogues. Stability studies indicated that these derivatives were not sufficiently labile to act as potential prodrugs. Solubility-pH profiles were constructed from which the dissociation constants were calculated. The physicochemical properties of these compounds were studied and attempts were made to increase the poor aqueous solubility of bropirimine (35μg/mL) by prodrug synthesis, solvate formation (acetic acid, N, N-dimethylformamide and N-methylformamide) and the use of co-solvents and additives. The first two methods proved to be fruitless whereas the latter method resulted in an intravenous formulation incorporating 32mg/mL of bropirimine. An in-vitro method for the detection of precipitation was developed and the results suggested that by using low injection rates (< 0.24mL/min) and high mobile phase flow rates (> 500mL/hr) precipitation could be minimised. Differential scanning calorimetry showed that bropirimine debrominates in the presence of a number of additives commonly used in formulation work but the temperature at which this occurred were usually > 200oC. In-vitro work gave encouraging results for the possibility of rectal delivery of bropirimine but in-vivo work on rabbits showed considerable variations in the resulting plasma levels and pharmacokinetic parameters.

Remoção de metais utilizando o hexadecanoato de sódio

Industrial activities like mining, electroplating and the oil extraction process, are increasing the levels of heavy metals such as Cu, Fe, Mg and Cd in aquatic ecosystems. This increase is related to the discharge of effluents containing trace of this elements above the maximum allowed by law. Methods such as ion exchange, membrane filtration and chemical precipitation have been studied as a means of treatment of these metals contamination. The precipitation of metals using anionic surfactants derived from carboxylic acids emerged as an alternative for the removal of metals from industrial effluents. The reaction between bivalent ions and these types of surfactants in aqueous solution leads to the formation of metal carboxylates, which can precipitate in the form of flakes and are subsequently removed by a process of decantation or simple filtration. In this work the metals extraction is performed by using the surfactant sodium hexadecanoate as extracting agent. The main purpose was to study the effect of temperature, solution pH, and concentration of surfactant in the metal removal process. The statistical design of the process showed that the process is directly dependent to changes in pH and concentration of surfactant, but inversely proportional and somewhat dependent to temperature variation, with the latter effect being considered negligible in most cases. The individual study of the effect of temperature showed a strong dependence of the process with the Kraft point, both for the surfactant used as extracting agent, as for the surfactant obtained after the reaction of this surfactant with the metal. From data of temperatures and concentrations of the surfactant was possible to calculate the equilibrium constant for the reaction between sodium hexadecanoate and copper ions. Later, thermodynamic parameters were determined, showing that the process is exothermic and spontaneous.

Nucleophilic addition of Nitrones to Electron deficient acetylenes and related studies

Nitrones or azomethine-N-oxides are important precursors for the synthesis of several heterocyclic systems. They belong to the allyl anion type 1,3-dipoles and possess unique structural features which make them extraordinarily useful synthons. They behave as 1,3-dipoles in 1,3-dipolar cycloaddition reactions and as electrophiles in reactions with organometallic reagents. These are the two basic reactions given by nitrones. Nitrones also act as ‘spin traps’ in which they react with short-lived radicals to furnish stable nitroxide radicals which can be detected and identified by electron paramagnetic resonance (EPR) spectroscopy. Recently SmI2 catalysed reductive cross-coupling reactions of nitrones have gained significant interest in which the reactions are initiated by single electron transfer (SET) to nitrones. Apart from these reactions, nitrones are also known to participate in reactions which are initiated by the nucleophilic attack of nitrone-oxygen. In our group, we have also explored the nucleophilic character of nitrones through various reactions. The results obtained enabled us to develop a novel two-step one-pot strategy for quinolines and indoles - the heterocycles renowned for their pharmacological applications, from nitrones and electron deficient acetylenes. Using dibenzoylacetylene and phenylbenzoylacetylene as dipolarophiles, we could introduce a desired functional group at a predetermined position of the quinolines or indoles to be synthesised. In this context, the thesis entitled “NUCLEOPHILIC ADDITION OF NITRONES TO ELECTRON DEFICIENT ACETYLENES AND RELATED STUDIES” portrays our attempt to expand the scope of our x novel synthetic protocol using ester functionalised acetylenes: dimethyl acetylenedicarboxylate (DMAD) and methyl propiolate. The thesis is organised in to five chapters. The first chapter briefly describes the different classes of reactions that nitrone functionality can tolerate. The research problem is defined at the end of this chapter. The second chapter describes the synthesis of different nitrones used for the present study. The optimisation and expansion of scope of the novel strategy towards quinoline synthesis is discussed in the third chapter. The fourth chapter portrays the synthesis of indole-3-carboxylates using the novel strategy. In the fifth chapter, the reaction of N-(2,6-dimethylphenyl) and N-(2,4,6-trimethylphenyl)nitrones are discussed. Here we also discuss the mechanistic reinvestigation of Baldwin’s proposal in the isoxazoline-oxazoline rearrangement. The major outcome of the work is given at the end of the thesis. The structural formulae, schemes, tables and figures are numbered chapter-wise since each chapter of the thesis is organized as an independent unit. All new compounds (except two compounds reported in fourth chapter) are fully characterised on the basis of spectral and analytical data and single crystal X-ray analysis on representative examples. Relevant references are included at the end of individual chapters.

Applications of Photoinduced Electron Transfer Chemistry: Photoremovable Protecting Groups and Carbon Dioxide Conversion

Traditional organic chemistry has long been dominated by ground state thermal reactions. The alternative to this is excited state chemistry, which uses light to drive chemical transformations. There is considerable interest in using this clean renewable energy source due to concerns surrounding the combustion byproducts associated with the consumption of fossil fuels. The work presented in this text will focus on the use of light (both ultraviolet and visible) for the following quantitative chemical transformations: (1) the release of compounds containing carboxylic acid and alcohol functional groups and (2) the conversion of carbon dioxide into other useable chemicals. Chapters 1-3 will introduce and explore the use of photoremovable protecting groups (PPGs) for the spatiotemporal control of molecular concentrations. Two new PPGs are discussed, the 2,2,2-tribromoethoxy group for the protection of carboxylic acids and the 9-phenyl-9-tritylone group for the protection of alcohols. Fundamental interest in the factors that affect C–X bond breaking has driven the work presented in this text for the release of carboxylic acid substrates. Product analysis from the UV photolysis of 2,2,2-tribromoethyl-(2′-phenylacetate) in various solvents results in the formation of H–atom abstraction products as well as the release of phenylacetic acid. The deprotection of alcohols is realized through the use of UV or visible light photolysis of 9-phenyl-9-tritylone ethers. Central to this study is the use of photoinduced electron transfer chemistry for the generation of ion diradicals capable of undergoing bond-breaking chemistry leading to the release of the alcohol substrates. Chapters 4 and 5 will explore the use of N-heterocyclic carbenes (NHCs) as a catalyst for the photochemical reduction of carbon dioxide. Previous experiments have demonstrated that NHCs can add to CO2 to form stable zwitterionic species known as N-heterocylic-2-carboxylates (NHC–CO2). Work presented in this text illustrate that the stability of these species is highly dependent on solvent polarity, consistent with a lengthening of the imidazolium to carbon dioxide bond (CNHC–CCO2). Furthermore, these adducts interact with excited state electron donors resulting in the generation of ion diradicals capable of converting carbon dioxide into formic acid.

Estudo da polimerização térmica de óleos e gorduras

Dissertação (mestrado)—Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2011.