Novel Primate-Specific Genes, RMEL 1, 2 and 3, with Highly Restricted Expression in Melanoma, Assessed by New Data Mining Tool

Melanoma is a highly aggressive and therapy resistant tumor for which the identification of specific markers and therapeutic targets is highly desirable. We describe here the development and use of a bioinformatic pipeline tool, made publicly available under the name of EST2TSE, for the in silico detection of candidate genes with tissue-specific expression. Using this tool we mined the human EST (Expressed Sequence Tag) database for sequences derived exclusively from melanoma. We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression. Using a diverse panel of human tissues and cell lines, we validated the expression of a subset of three previously uncharacterized genes (clusters Hs.295012, Hs.518391, and Hs.559350) to be highly restricted to melanoma/melanocytes and named them RMEL1, 2 and 3, respectively. Expression analysis in nevi, primary melanomas, and metastatic melanomas revealed RMEL1 as a novel melanocytic lineage-specific gene up-regulated during melanoma development. RMEL2 expression was restricted to melanoma tissues and glioblastoma. RMEL3 showed strong up-regulation in nevi and was lost in metastatic tumors. Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes. The three genes are composed of multiple exons and map to 2q12.2, 1q25.3, and 5q11.2, respectively. They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found. Hairpin RNA secondary structures were also predicted. Concluding, this work offers new melanoma-specific genes for future validation as prognostic markers or as targets for the development of therapeutic strategies to treat melanoma.

Evaluation of grinding methods for pellets preparation aiming at the analysis of plant materials by laser induced breakdown spectrometry

It has been demonstrated that laser induced breakdown spectrometry (LIBS) can be used as an alternative method for the determination of macro (P, K. Ca, Mg) and micronutrients (B, Fe, Cu, Mn, Zn) in pellets of plant materials. However, information is required regarding the sample preparation for plant analysis by LIBS. In this work, methods involving cryogenic grinding and planetary ball milling were evaluated for leaves comminution before pellets preparation. The particle sizes were associated to chemical sample properties such as fiber and cellulose contents, as well as to pellets porosity and density. The pellets were ablated at 30 different sites by applying 25 laser pulses per site (Nd:YAG@1064 nm, 5 ns, 10 Hz, 25J cm(-2)). The plasma emission collected by lenses was directed through an optical fiber towards a high resolution echelle spectrometer equipped with an ICCD. Delay time and integration time gate were fixed at 2.0 and 4.5 mu s, respectively. Experiments carried out with pellets of sugarcane, orange tree and soy leaves showed a significant effect of the plant species for choosing the most appropriate grinding conditions. By using ball milling with agate materials, 20 min grinding for orange tree and soy, and 60 min for sugarcane leaves led to particle size distributions generally lower than 75 mu m. Cryogenic grinding yielded similar particle size distributions after 10 min for orange tree, 20 min for soy and 30 min for sugarcane leaves. There was up to 50% emission signal enhancement on LIBS measurements for most elements by improving particle size distribution and consequently the pellet porosity. (C) 2011 Elsevier B.V. All rights reserved.

Comparison of univariate and multivariate calibration for the determination of micronutrients in pellets of plant materials by laser induced breakdown spectrometry

The application of laser induced breakdown spectrometry (LIBS) aiming the direct analysis of plant materials is a great challenge that still needs efforts for its development and validation. In this way, a series of experimental approaches has been carried out in order to show that LIBS can be used as an alternative method to wet acid digestions based methods for analysis of agricultural and environmental samples. The large amount of information provided by LIBS spectra for these complex samples increases the difficulties for selecting the most appropriated wavelengths for each analyte. Some applications have suggested that improvements in both accuracy and precision can be achieved by the application of multivariate calibration in LIBS data when compared to the univariate regression developed with line emission intensities. In the present work, the performance of univariate and multivariate calibration, based on partial least squares regression (PLSR), was compared for analysis of pellets of plant materials made from an appropriate mixture of cryogenically ground samples with cellulose as the binding agent. The development of a specific PLSR model for each analyte and the selection of spectral regions containing only lines of the analyte of interest were the best conditions for the analysis. In this particular application, these models showed a similar performance. but PLSR seemed to be more robust due to a lower occurrence of outliers in comparison to the univariate method. Data suggests that efforts dealing with sample presentation and fitness of standards for LIBS analysis must be done in order to fulfill the boundary conditions for matrix independent development and validation. (C) 2009 Elsevier B.V. All rights reserved.

Evaluation of laser induced breakdown spectrometry for the determination of macro and micronutrients in pharmaceutical tablets

The aim of this work is to demonstrate the feasibility of laser induced breakdown spectrometry (LIBS) for the determination of macro and micronutrients in multielement tablets. The experimental setup was designed by using a laser Q-switch (Nd:YAG, 10 Hz, lambda = 1064 nm) and the emission signals were collected by lenses into an optical fiber coupled to an echelle spectrometer equipped with a high-resolution intensified charge coupled device (ICCD). Tablets were cryogenically ground and thereafter pelletized before LIBS analysis. Calibration curves were made by employing samples and mixtures of commercial multielement tablets with binders at different ratios. Best results were achieved by using the following experimental conditions: 29 J cm(-2) laser fluence, 165 mm lens to sample distance (f = 200 mm), 2.0 mu s delay time, 5.0 mu s integration time and 5 accumulated laser pulses. In general, the results obtained by the proposed LIBS procedure were in agreement with those obtained by ICP OES from the corresponding acid digests and coefficients variation of LIBS measurements varied from 2 to 16%. The metrological figures of merit indicate that LIBS fits for the intended purposes, and can be recommended for the analysis of multielement tablets and similar matrices aiming the determination of Ca, Cu, Fe, Mg, Mn, P and Zn.

Evaluation of laser induced breakdown spectroscopy for cadmium determination in soils

Cadmium is known to be a toxic agent that accumulates in the living organisms and present high toxicity potential over lifetime. Efforts towards the development of methods for microanalysis of environmental samples, including the determination of this element by graphite furnace atomic absorption spectrometry (GFAAS). inductively coupled plasma optical emission spectrometry (ICP OES), and inductively coupled plasma-mass spectrometry (ICP-MS) techniques, have been increasing. Laser induced breakdown spectroscopy (UBS) is an emerging technique dedicated to microanalysis and there is a lack of information dealing with the determination of cadmium. The aim of this work is to demonstrate the feasibility of LIBS for cadmium detection in soils. The experimental setup was designed using a laser Q-switched (Nd:YAG, 10 Hz, lambda = 1064 nm) and the emission signals were collimated by lenses into an optical fiber Coupled to a high-resolution intensified charge-coupled device (ICCD)-echelle spectrometer. Samples were cryogenically ground and thereafter pelletized before LIBS analysis. Best results were achieved by exploring a test portion (i.e. sampling spots) with larger surface area, which contributes to diminish the uncertainty due to element specific microheterogeneity. Calibration curves for cadmium determination were achieved using certified reference materials. The metrological figures of merit indicate that LIBS can be recommended for screening of cadmium contamination in soils. (C) 2009 Elsevier B.V. All rights reserved.

Simultaneous optimization by neuro-genetic approach for analysis of plant materials by laser induced breakdown spectroscopy

A simultaneous optimization strategy based on a neuro-genetic approach is proposed for selection of laser induced breakdown spectroscopy operational conditions for the simultaneous determination of macronutrients (Ca, Mg and P), micro-nutrients (B, Cu, Fe, Mn and Zn), Al and Si in plant samples. A laser induced breakdown spectroscopy system equipped with a 10 Hz Q-switched Nd:YAG laser (12 ns, 532 nm, 140 mJ) and an Echelle spectrometer with intensified coupled-charge device was used. Integration time gate, delay time, amplification gain and number of pulses were optimized. Pellets of spinach leaves (NIST 1570a) were employed as laboratory samples. In order to find a model that could correlate laser induced breakdown spectroscopy operational conditions with compromised high peak areas of all elements simultaneously, a Bayesian Regularized Artificial Neural Network approach was employed. Subsequently, a genetic algorithm was applied to find optimal conditions for the neural network model, in an approach called neuro-genetic, A single laser induced breakdown spectroscopy working condition that maximizes peak areas of all elements simultaneously, was obtained with the following optimized parameters: 9.0 mu s integration time gate, 1.1 mu s delay time, 225 (a.u.) amplification gain and 30 accumulated laser pulses. The proposed approach is a useful and a suitable tool for the optimization process of such a complex analytical problem. (C) 2009 Elsevier B.V. All rights reserved.

Preliminary studies of laser-induced breakdown spectrometry for the determination of Ba, Cd, Cr and Pb in toys

The performance of laser-induced breakdown spectrometry (LIBS) for the determination of Ba, Cd, Cr and Pb in toys has been evaluated by using a Nd:YAG laser operating at 1064 nm and an Echelle spectrometer with intensified charge-coupled device detector. Samples were purchased in different cities of Sao Paulo State market and analyzed directly without sample preparation. Laser-induced breakdown spectrometry experimental conditions (number of pulses, delay time. integration time gate and pulse energy) were optimized by using a Doehlert design. Laser-induced breakdown spectrometry signals correlated reasonably well with inductively coupled plasma optical emission spectrometry (ICP OES) concentrations after microwave-assisted acid digestion of selected samples. Thermal analysis was used for polymer identification and scanning electron microscopy to Visualize differences in crater geometry of different polymers employed for toy fabrication. Results indicate that laser-induced breakdown spectrometry can be proposed as a rapid screening method for investigation of potentially toxic elements in toys. The unique application of laser-induced breakdown spectrometry for identification of contaminants in successive layers of ink and polymer is also demonstrated. (C) 2009 Elsevier B.V. All rights reserved.

Evaluation of laser induced breakdown spectroscopy for the determination of micronutrients in plant materials

Laser induced breakdown spectroscopy (LIBS) has been evaluated for the determination of micronutrients (B, Cu, Fe, Mn and Zn) in pellets of plant materials, using NIST, BCR and GBW biological certified reference materials for analytical calibration. Pellets of approximately 2 mm thick and 15 mm diameter were prepared by transferring 0.5 g of powdered material to a 15 mm die set and applying 8.0 tons cm(-2). An experimental setup was designed by using a Nd:YAG laser operating at 1064 nm (200 mJ per pulse, 10 Hz) and an Echelle spectrometer with ICCD detector. Repeatability precision varied from 4 to 30% from measurements obtained in 10 different positions (8 laser shots per test portion) in the same sample pellet. Limits of detection were appropriate for routine analysis of plant materials and were 2.2 mg kg(-1) B, 3.0 mg kg(-1) Cu, 3.6 mg kg(-1) Fe, 1.8 mg kg(-1) Mn and 1.2 mg kg(-1) Zn. Analysis of different plant samples were carried out by LIBS and results were compared with those obtained by ICP OES after wet acid decomposition. (C) 2009 Elsevier B.V. All rights reserved.

Evaluation of laser induced breakdown spectroscopy for the determination of macronutrients in plant materials

Laser induced breakdown spectroscopy (LIBS) has become an analytical tool for the direct analysis of a large variety of materials in order to provide qualitative and/or quantitative information. However, there is a lack of information for LIBS analysis of agricultural and environmental samples. In this work a LIBS system has been evaluated for the determination of macronutrients (P, K, Ca, Mg) in pellets of vegetal reference materials. An experimental setup was designed by using a Nd:YAG laser operating at 1064 nm and an Echelle spectrometer with ICCD detector. The plasma temperature was estimated by Boltzmann plots and instrumental paragmeters such as delay time, lens-to-sample distance and pulse energy were evaluated. Certified reference materials as well as reference materials were used for analytical calibrations of P, K, Ca, and Mg. Most results of the direct analysis of plant samples by LIBS were in reasonable agreement with those obtained by ICP OES after wet acid decomposition. (C) 2008 Elsevier B.V. All rights reserved.

Total carbon measurement in whole tropical soil sample

Soils are an important component in the biogeochemical cycle of carbon, storing about four times more carbon than biomass plants and nearly three times more than the atmosphere. Moreover, the carbon content is directly related on the capacity of water retention, fertility. among other properties. Thus, soil carbon quantification in field conditions is an important challenge related to carbon cycle and global climatic changes. Nowadays. Laser Induced Breakdown Spectroscopy (LIBS) can be used for qualitative elemental analyses without previous treatment of samples and the results are obtained quickly. New optical technologies made possible the portable LIBS systems and now, the great expectation is the development of methods that make possible quantitative measurements with LIBS. The goal of this work is to calibrate a portable LIBS system to carry out quantitative measures of carbon in whole tropical soil sample. For this, six samples from the Brazilian Cerrado region (Argisoil) were used. Tropical soils have large amounts of iron in their compositions, so the carbon line at 247.86 nm presents strong interference of this element (iron lines at 247.86 and 247.95). For this reason, in this work the carbon line at 193.03 nm was used. Using methods of statistical analysis as a simple linear regression, multivariate linear regression and cross-validation were possible to obtain correlation coefficients higher than 0.91. These results show the great potential of using portable LIBS systems for quantitative carbon measurements in tropical soils. (C) 2008 Elsevier B.V. All rights reserved.

Laser-induced breakdown spectroscopy and chemometrics for classification of toys relying on toxic elements

Quality control of toys for avoiding children exposure to potentially toxic elements is of utmost relevance and it is a common requirement in national and/or international norms for health and safety reasons. Laser-induced breakdown spectroscopy (LIBS) was recently evaluated at authors` laboratory for direct analysis of plastic toys and one of the main difficulties for the determination of Cd. Cr and Pb was the variety of mixtures and types of polymers. As most norms rely on migration (lixiviation) protocols, chemometric classification models from LIBS spectra were tested for sampling toys that present potential risk of Cd, Cr and Pb contamination. The classification models were generated from the emission spectra of 51 polymeric toys and by using Partial Least Squares - Discriminant Analysis (PLS-DA), Soft Independent Modeling of Class Analogy (SIMCA) and K-Nearest Neighbor (KNN). The classification models and validations were carried out with 40 and 11 test samples, respectively. Best results were obtained when KNN was used, with corrected predictions varying from 95% for Cd to 100% for Cr and Pb. (C) 2011 Elsevier B.V. All rights reserved.

PERMEABILITY MEASUREMENTS OF BRAZILIAN PINUS ELLIOTTII

The liquid and gas phase permeability, of Brazilian Pinus elliotii was studied with a custom built gas and liquid flow rate analysis chamber. The longitudinal gas phase permeability is shown to be six times greater than the radial permeability. There is no statistically significant difference between the longitudinal permeability of water versus wood preservative. Scanning Electron Microscopy (SEM) images confirm that the reported permeability properties arc due to the wood itself rather than to blocked pores or other artifacts of the sample cutting process. Wood composition analysis shows that the samples of Pinus elliotii grown in Brazil are similar to other species of Pinus grown in tropical climates. Specifically, the Pinus elliotti in this study is composed of 17% extractives, 0,27% ashes, 21% hemicellulose, 45% cellulose and 30% lignin. Results arc discussed in the context of the continued search for effective wood preservatives for use in tropical climates.

Analysis of genomic and functional RFLP derived markers associated with sucrose content, fiber and yield QTLs in a sugarcane (Saccharum spp.) commercial cross

Expressed sequence tags derived markers have a great potential to be used in functional map construction and QTL tagging. In the present work, sugarcane genomic probes and expressed sequence tags having homology to genes, mostly involved in carbohydrate metabolism were used in RFLP assays to identify putative QTLs as well as their epistatic interactions for fiber content, cane yield, pol and tones of sugar per hectare, at two crop cycles in a progeny derived from a bi-parental cross of sugarcane elite materials. A hundred and twenty marker trait associations were found, of which 26 at both crop cycle and 32 only at first ratoon cane. A sucrose synthase derived marker was associated with a putative QTL having a high negative effect on cane yield and also with a QTL having a positive effect on Pol at both crop cycles. Fifty digenic epistatic marker interactions were identified for the four traits evaluated. Of these, only two were observed at both crop cycles.

Characterization of new polymorphic functional markers for sugarcane

Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)[02/01167-1]

Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches` broom pathogen Moniliophthora perniciosa

Moniliophthora perniciosa is a hemibiotrophic fungus that causes witches` broom disease (WBD) in cacao. Marked dimorphism characterizes this fungus, showing a monokaryotic or biotrophic phase that causes disease symptoms and a later dikaryotic or saprotrophic phase. A combined strategy of DNA microarray, expressed sequence tag, and real-time reverse-transcriptase polymerase chain reaction analyses was employed to analyze differences between these two fungal stages in vitro. In all, 1,131 putative genes were hybridized with cDNA from different phases, resulting in 189 differentially expressed genes, and 4,595 reads were clusterized, producing 1,534 unigenes. The analysis of these genes, which represent approximately 21% of the total genes, indicates that the biotrophic-like phase undergoes carbon and nitrogen catabollite repression that correlates to the expression of phytopathogenicity genes. Moreover, downregulation of mitochondrial oxidative phosphorylation and the presence of a putative ngr1 of Saccharomyces cerevisiae could help explain its lower growth rate. In contrast, the saprotrophic mycelium expresses genes related to the metabolism of hexoses, ammonia, and oxidative phosphorylation, which could explain its faster growth. Antifungal toxins were upregulated and could prevent the colonization by competing fungi. This work significantly contributes to our understanding of the molecular mechanisms of WBD and, to our knowledge, is the first to analyze differential gene expression of the different phases of a hemibiotrophic fungus.