Identification of a novel ligand binding motif in the transthyretin channel

The design of therapeutic compounds targeting transthyretin (TTR) is challenging due to the low specificity of interaction in the hormone binding site. Such feature is highlighted by the interactions of TTR with diclofenac, a compound with high affinity for TTR, in two dissimilar modes, as evidenced by crystal structure of the complex. We report here structural analysis of the interactions of TTR with two small molecules, 1-amino-5-naphthalene sulfonate (1,5-AmNS) and 1-anilino-8-naphthalene sulfonate (1,8-ANS). Crystal structure of TTR: 1,8-ANS complex reveals a peculiar interaction, through the stacking of the naphthalene ring between the side-chain of Lys15 and Leu17. The sulfonate moiety provides additional interaction with Lys15` and a water-mediated hydrogen bond with Thr119`. The uniqueness of this mode of ligand recognition is corroborated by the crystal structure of TTR in complex with the weak analogue 1,5-AmNS, the binding of which is driven mainly by hydrophobic partition and one electrostatic interaction between the sulfonate group and the Lys15. The ligand binding motif unraveled by 1,8-ANS may open new possibilities to treat TTR amyloid diseases by the elucidation of novel candidates for a more specific pharmacophoric pattern. (C) 2009 Published by Elsevier Ltd.

Sample stacking in CZE using dynamic thermal junctions I. Analytes with low dpK(a)/dT crossing a single thermally induced pH junction in a BGE with high dpH/dT

The possibility to compress analyte bands at the beginning of CE runs has many advantages. Analytes at low concentration can be analyzed with high signal-to-noise ratios by using the so-called sample stacking methods. Moreover, sample injections with very narrow initial band widths (small initial standard deviations) are sometimes useful, especially if high resolutions among the bands are required in the shortest run time. In the present work, a method of sample stacking is proposed and demonstrated. It is based on BGEs with high thermal sensitive pHs (high dpH/dT) and analytes with low dpK(a)/dT. High thermal sensitivity means that the working pK(a) of the BGE has a high dpK(a)/dT in modulus. For instance, Tris and Ethanolamine have dpH/dT = -0.028/degrees C and -0.029/degrees C, respectively, whereas carboxylic acids have low dpK(a)/dT values, i.e. in the -0.002/degrees C to+0.002/degrees C range. The action of cooling and heating sections along the capillary during the runs affects also the local viscosity, conductivity, and electric field strength. The effect of these variables on electrophoretic velocity and band compression is theoretically calculated using a simple model. Finally, this stacking method was demonstrated for amino acids derivatized with naphthalene-2,3-dicarboxaldehyde and fluorescamine using a temperature difference of 70 degrees C between two neighbor sections and Tris as separation buffer. In this case, the BGE has a high pH thermal coefficient whereas the carboxylic groups of the analytes have low pK(a) thermal coefficients. The application of these dynamic thermal gradients increased peak height by a factor of two (and decreased the standard deviations of peaks by a factor of two) of aspartic acid and glutamic acid derivatized with naphthalene-2,3-dicarboxaldehyde and serine derivatized with fluorescamine. The effect of thermal compression of bands was not observed when runs were accomplished using phosphate buffer at pH 7 (negative control). Phosphate has a low dpH/dT in this pH range, similar to the dK(a)/dT of analytes. It is shown that vertical bar dK(a)/dT-dpH/dT vertical bar >> 0 is one determinant factor to have significant stacking produced by dynamic thermal junctions.

Sample stacking in CZE using dynamic thermal junctions II: Analytes with high dpK(a)/dT crossing a single thermal junction in a BGE with low dpH/dT

In a previous work [M. Mandaji, et al., this issue] a sample stacking method was theoretically modeled and experimentally demonstrated for analytes with low dpK(a)/dT (analytes carrying carboxylic groups) and BGEs with high dpH/dT (high pH-temperature-coefficients). In that work, buffer pH was modulated with temperature, inducing electrophoretic mobility changes in the analytes. In the present work, the opposite conditions are studied and tested, i.e. analytes with high dpK(a)/dT and BGEs that exhibit low dpH/dT. It is well known that organic bases such as amines, imidazoles, and benzimidazoles exhibit high dpK(a)/dT. Temperature variations induce instantaneous changes on the basicity of these and other basic groups. Therefore, the electrophoretic velocity of some analytes changes abruptly when temperature variations are applied along the capillary. This is true only if BGE pH remains constant or if it changes in the opposite direction of pK(a) of the analyte. The presence of hot and cold sections along the capillary also affects local viscosity, conductivity, and electric field strength. The effect of these variables on electrophoretic velocity and band stacking efficacy was also taken into account in the theoretical model presented. Finally, this stacking method is demonstrated for lysine partially derivatized with naphthalene-2,3-dicarboxaldehyde. In this case, the amino group of the lateral chain was left underivatized and only the alpha amino group was derivatized. Therefore, the basicity of the lateral amino group, and consequently the electrophoretic mobility, was modulated with temperature while the pH of the buffer used remained unchanged.

Dichlorvos exposure impedes extraction and amplification of DNA from insects in museum collections

Background: The insecticides dichlorvos, paradichlorobenzene and naphthalene have been commonly used to eradicate pest insects from natural history collections. However, it is not known how these chemicals affect the DNA of the specimens in the collections. We thus tested the effect of dichlorvos, paradichlorobenzene and naphthalene on DNA of insects (Musca domestica) by extracting and amplifying DNA from specimens exposed to insecticides in two different concentrations over increasing time intervals. Results: The results clearly show that dichlorvos impedes both extraction and amplification of mitochondrial and nuclear DNA after relatively short time, whereas paradichlorobenzene and naphthalene do not. Conclusion: Collections treated with paradichlorobenzene and naphthalene, are better preserved concerning DNA, than those treated with dichlorvos. Non toxic pest control methods should, however, be preferred due to physical damage of specimens and putative health risks by chemicals.

Investigation of urinary volatile organic metabolites as potential cancer biomarkers by solid-phase microextraction in combination with gas chromatography-mass spectrometry

BACKGROUND: Non-invasive diagnostic strategies aimed at identifying biomarkers of cancer are of great interest for early cancer detection. Urine is potentially a rich source of volatile organic metabolites (VOMs) that can be used as potential cancer biomarkers. Our aim was to develop a generally reliable, rapid, sensitive, and robust analytical method for screening large numbers of urine samples, resulting in a broad spectrum of native VOMs, as a tool to evaluate the potential of these metabolites in the early diagnosis of cancer. METHODS: To investigate urinary volatile metabolites as potential cancer biomarkers, urine samples from 33 cancer patients (oncological group: 14 leukaemia, 12 colorectal and 7 lymphoma) and 21 healthy (control group, cancer-free) individuals were qualitatively and quantitatively analysed. Dynamic solid-phase microextraction in headspace mode (dHS-SPME) using a carboxenpolydimethylsiloxane (CAR/PDMS) sorbent in combination with GC-qMS-based metabolomics was applied to isolate and identify the volatile metabolites. This method provides a potential non-invasive method for early cancer diagnosis as a first approach. To fulfil this objective, three important dHS-SPME experimental parameters that influence extraction efficiency (fibre coating, extraction time and temperature of sampling) were optimised using a univariate optimisation design. The highest extraction efficiency was obtained when sampling was performed at 501C for 60min using samples with high ionic strengths (17% sodium chloride, wv 1) and under agitation. RESULTS: A total of 82 volatile metabolites belonging to distinct chemical classes were identified in the control and oncological groups. Benzene derivatives, terpenoids and phenols were the most common classes for the oncological group, whereas ketones and sulphur compounds were the main classes that were isolated from the urine headspace of healthy subjects. The results demonstrate that compound concentrations were dramatically different between cancer patients and healthy volunteers. The positive rates of 16 patients among the 82 identified were found to be statistically different (Po0.05). A significant increase in the peak area of 2-methyl3-phenyl-2-propenal, p-cymene, anisole, 4-methyl-phenol and 1,2-dihydro-1,1,6-trimethyl-naphthalene in cancer patients was observed. On average, statistically significant lower abundances of dimethyl disulphide were found in cancer patients. CONCLUSIONS: Gas chromatographic peak areas were submitted to multivariate analysis (principal component analysis and supervised linear discriminant analysis) to visualise clusters within cases and to detect the volatile metabolites that are able to differentiate cancer patients from healthy individuals. Very good discrimination within cancer groups and between cancer and control groups was achieved.

Caracterização funcional de dois cDNAs homólogos à ciclofilina e à proteína reprimida por auxina (ARP) identificados em bibliotecas subtrativas a para floração em tomateiro

Flowering is a fundamental process in the life cycle for plant. This process is marked by vegetative to reproductive apical meristem conversion, due to interactions between several factors, both internal and external to plant. Therefore, eight subtractive libraries were constructed using apical meristem induced or not induced for two contrasting species: Solanum lycopersicum cv. Micro-Tom and Solanum pimpinellifolium. Several cDNAs were identified and among these, were selected two cDNAs: one homologous cDNA to cyclophilin (LeCYP1) and the other to Auxin repressed protein (ARP). It has observed that LeCYP1 and ARP genes are important in the developmental process to plants. In silico analysis, were used several databases with the exclusion criterion E-value <1.0x10-15. As a result, conservation was observed for proteins analyzed by means of multiple alignments and the presence of functional domains. Then, overexpression cassettes were constructed for the ARP cDNA in sense and antisense orientations. For this step, it was used the CaMV35S promoter. The cDNA orientation (sense or antisense) in relation to the promoter was determined by restriction enzymes and sequencing. Then, this cassette was transferred to binary vector pZP211 and these cassettes were transferred into Agrobacterium tumefaciens LBA4404. S. lycopersicum cv. Micro-Tom (MT) and MT-Rg1 plants were transformed. In addition, seedlings were subjected to hormone treatments using a synthetic auxin (- naphthalene acetic acid) and cyclosporin A (cyclophilin inhibitor) treatments and it was found that the hormone treatment there were changes in development of lateral roots pattern, probably related to decreases in auxin signaling caused by reduction of LeCYP1 in MT-dgt plants while cyclosporin A treatments, there was a slight delay in flowering in cv. MT plants. Furthermore, assay with real-time PCR (RT-qPCR) were done for expression level analysis from LeCYP1 and ARP in order to functionally characterize these sequences in tomato plants.

Hidrocarbonetos policíclicos aromáticos em sedimentos de fundo do estuário do rio Potengi, região da grande Natal (RN): implicações ambientais

Estuaries are environments prone to the input of chemical pollutants of various kinds and origins, including polycyclic aromatic hydrocarbons (PAHs). Anthropogenic PAHs may have two possible sources: pyrolytic (with four or more aromatic rings and low degree of alkylation) and petrogenic (with two and three aromatic rings and high degree of alkylation). This study aimed to evaluate the levels, distribution and possible sources of polycyclic aromatic hydrocarbons in the estuary of the Potengi river, Natal, Brazil. Samples of bottom sediments were collected in the final 12 km of the estuary until its mouth to the sea, where the urbanization of the Great Natal is more concentrated. Sampling was performed on 12 cross sections, with three stations each, totaling 36 samples, identified as T1 to T36. The non alkylated and alkylated PAHs were analyzed by gas chromatography coupled to mass spectrometry (GC / MS). PAHs were detected in all 36 stations with total concentration on each varying 174-109407 ng g-1. These values are comparable to those of several estuarine regions worldwide with high anthropogenic influence, suggesting the record of diffuse contamination installed in the estuary. PAHs profiles were similar for most stations. In 32 of the 36 stations, low molecular weight PAHs (with 2 and 3 ring: naphthalene, phenanthrene and their alkylated homologues) prevailed, which ranged from 54% to 100% of the total PAH, indicating that leaks, spills and combustion fuels are the dominant source of PAH pollution in the estuary. The level of contamination by PAHs in most stations suggests that there is potential risk of occasional adverse biological effects, but in some stations adverse impacts on the biota may occur frequently. The diagnostic ratios could differentiate sources of PAHs in sediments of the estuary, which were divided into three groups: petrogenic, pyrolytic and mixing of sources. The urban concentration of the Great Natal and the various industrial activities associated with it can be blamed as potential sources of PAHs in bottom sediments of the estuary studied. The data presented highlight the need to control the causes of existing pollution in the estuary

Avaliação de HPA e BTEX no solo e água subterrânea, em postos de revenda de combustíveis: estudo de caso na cidade de Natal -RN

The retail fuel stations are partially or potentially polluters and generators of environmental accidents, potentially causing contamination of underground and surface water bodies, soil and air. Leaks in fuel retail stations´ underground storage systems are often detected in Brazil and around the world. Monoaromatic hydrocarbons, BTEX (benzene, toluene, ethylbenzene and xylenes) and polycyclic aromatic hydrocarbons (PAHs) are an indication of the presence of contamination due to its high toxicity. This paper presents a case study of contamination in a Fuel Retail Station by petroleum derivative products in the city of Natal. For identification and quantification of the hydrocarbons, EPA analytical methods were used. The values of benzene quantified by EPA method 8021b CG-PID/FID, ranged from 1.164 to 4.503 mg.Kg-1 in soil samples, and from 12.10 to 27,639 μg.L-1 in underground water samples. Among the PAHs, naphthalene and anthracene showed the most significant results in soil samples, 0.420 to 15.46 mg.Kg-1 and 0.110 to 0,970 mg.Kg-1, respectively. In underground water samples, the results for Naphthalene varied between 0.759 and 614.7 μg.L-1. PAHs were quantified by EPA Method 8270 for GCMS. All of the results for the chemical analysis were compared with the values for the CONAMA 420/2009 resolution. The results for benzene (27,639 μg.L-1) showed levels highly above the recommended by the CONAMA 420 resolution, wherein the maximum permissible for underground water is 5 μg.L-1. This is a worrying factor, since underground water makes up 70% of the city of Natal´s water supply

Induction of somatic embryogenesis in soybean: physicochemical factors influencing the development of somatic embryos

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Avaliação do processo oxidativo avançado por permanganato de potássio no tratamento de solos contaminados com idrocarbonetos poliaromáticos

The soil contamination with petroleum is one of the major concern of industries operating in the field and also of environmental agencies. The petroleum consists mainly of alkanes and aromatic hydrocarbons. The most common examples of hydrocarbons polyaromatic are: naphthalene, anthracene, phenanthrene, benzopyrene and their various isomers. These substances cause adverse effects on human and the environment. Thus, the main objective of this work is to study the advanced oxidation process using the oxidant potassium permanganate (KMnO4) for remediation of soils contaminated with two polyaromatic hydrocarbons (PAHs): anthracene and phenanthrene. This study was conducted at bench scale, where the first stage was at batch experiment, using the variables: the time and oxidant dosage in the soil. The second stage was the remediation conducted in continous by a fix column, to this stage, the only variable was remediation time. The concentration of oxidant in this stage was based on the best result obtained in the tests at batch, 2,464 mg / L. The results of degradation these contaminants were satisfactory, at the following dosages and time: (a) 5g of oxidant per kg soil for 48 hours, it was obtained residual contaminants 28 mg phenanthrene and 1.25 mg anthracene per kg of soil and (b) for 7g of oxidant per kg soil in 48 hours remaining 24 mg phenanthrene and anthracene 0.77 mg per kg soil, and therefore below the intervention limit residential and industrial proposed by the State Company of Environmental Sao Paulo (CETESB)

Tratamento eletroquímico de água produzida sintética para remoção de hidrocarbonetos policíclicos aromáticos

The aim of this work is the treatment of produced water from oil by using electrochemical technology. Produced water is a major waste generated during the process of exploration and production in the oil industry. Several approaches are being studied aiming at the treatment of this effluent; among them can be cited the biological process and chemical treatments such as advanced oxidation process and electrochemical treatments (electrooxidation, electroflotation, electrocoagulation, electrocoagulation). This work studies the application of electrochemical technology in the treatment of the synthetic produced water effluent through the action of the electron, in order to remove or transform the toxic and harmful substances from the environment by redox reactions in less toxic substances. For this reason, we used a synthetic wastewater, containing a mixture H2SO4 0,5M and 16 HPAs, which are: naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, pyrene, benzo (a) anthracene, chrysene, benzo(b)fluoranthene, benzo(k) fluoranthene, benzo(a)pyrene, indeno(1,2,3-cd)pyrene, dibenzo(a, h)anthracene, benzo(g, h, i)perylene. Bulk electrochemical oxidation experiments were performed using a batch electrochemical reactor containing a pair of parallel electrodes, coupled with a power supply using a magnetic stirrer for favoring the transfer mass control. As anodic material was used, a Dimensionally Stable Anode (DSA) of Ti/Pt, while as cathode was used a Ti electrode. Several samples were collected at specific times and after that, the analysis of these samples were carried out by using Gas Chromatography Coupled to Mass Spectrometry (GC - MS) in order to determine the percentage of removal. The results showed that it was possible to achieve the removal of HPAs about 80% (in some cases, more than 80%). In addition, as an indicator of the economic feasibility of electrochemical treatment the energy consumption was analyzed for each hour of electrolysis, and based on the value kWh charged by ANEEL, the costs were estimated. Thus, the treatment costs of this research were quite attractive

Enraizamento de estacas de Trichilia catigua A. Juss (catigua) em diferentes estações do ano

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Active-site properties of Phrixotrix railroad worm green and red bioluminescence-eliciting luciferases

The luciferases of the railroad worm Phrixotrix (Coleoptera: Phengodidae) are the only beetle luciferases that naturally produce true red bioluminescence. Previously, we cloned the green- (PxGR) and red-emitting (PxRE) luciferases of railroad worms Phrixotrix viviani and P. hirtus[OLE1]. These luciferases were expressed and purified, and their active-site properties were determined. The red-emitting PxRE luciferase displays flash-like kinetics, whereas PxGR luciferase displays slow-type kinetics. The substrate affinities and catalytic efficiency of PxRE luciferase are also higher than those of PxGR luciferase. Fluorescence studies with 8-anilino-1-naphthalene sulfonic acid and 6-p-toluidino-2-naphthalene sulfonic acid showed that the PxRE luciferase luciferin-binding site is more polar than that of PxGR luciferase, and it is sensitive to guanidine. Alutagenesis and modelling studies suggest that several invariant residues in the putative luciferin-binding site of PxRE luciferase cannot interact with excited oxyluciferin. These results suggest that one portion of the luciferin-binding site of the red-emitting luciferase is tighter than that of PxGR luciferase, whereas the other portion could be more open and polar.

Optimization of photo-polymerized sol gel monolithic stationary phases prepared in polyacrylate-coated fused-silica capillaries for capillary electrochromatography

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Reguladores vegetais e o desbaste químico de frutos de tangor murcote

O tangor 'Murcote' apresenta necessidade de desbaste de frutos devido a alternância de produção, caracterizado por anos de excessiva produção intercalado com anos de baixa produção, evitando assim, a diminuição da qualidade dos frutos. O presente trabalho teve por objetivo avaliar a eficiência de reguladores vegetais, a auxina ANA (ácido naftalenacético) e ethephon (etileno) no desbaste químico de frutos de tangor 'Murcote' aplicado 40 dias após o pleno florescimento. O experimento foi conduzido em Pratânia, SP, onde plantas de 5 anos de idade, enxertadas sobre o limoeiro 'Cravo', foram pulverizadas com ANA a 0, 100, 200, 300 e 400 mg L-1 e com ethephon a 200, 300 e 400 mg L-1, ambos em solução aquosa juntamente com adjuvante não iônico a 0,05%. A contagem dos frutos foi realizada previamente aos tratamentos em 2 ramos marcados por planta. O ANA não interferiu significativamente no desbaste de frutos, com porcentagens de queda variando entre 7 a 14%, enquanto que as pulverizações com ethephon mostraram maior eficiência no desbaste de frutos, principalmente na dose de 400 mg L-1, promovendo 66,6% de queda de frutos, sem contudo induzir a abscisão foliar. As doses inferiores de ethephon também promoveram desbaste de frutos da ordem de 40%. As porcentagens de queda de frutos foram pequenas, para plantas pulverizadas com ANA, enquanto que a aplicação de ethephon promoveu maior eficiência no desbaste de frutos.