Degradation of commercial glyphosate-based herbicide via advanced oxidative processes in aqueous media and phytotoxicity evaluation using maize seeds.

Glyphosate is a herbicide that acts as a broad-spectrum, non-selective, post-emergence systemic pest controller. Its continuing, increasing, and excessive use in many countries in recent years poses a significant threat to the environment and human health due to the prevalence of this herbicide in water bodies and its impact on non-target organisms. In this context, it is essential to develop processes aimed at the non-selective degradation of glyphosate and its by-products. In this study, various advanced oxidative processes were applied: Fenton, electro-Fenton, photoelectro-oxidation, and photoelectro-Fenton, with the objective of oxidizing glyphosate in the commercial product Roundup®. The resultant oxidation products and the phytotoxicological effect on maize seed germination were also analyzed. Following each treatment, chemical oxygen demand (COD), total organic carbon (TOC), glyphosate degradation, and oxidation by-product formation were analyzed. The treated solutions were used to germinate maize seeds for 7 days in a germination chamber applying a photoperiod of 12 h at 24 °C. The % of germination, protein and hydrogen peroxide (H2O2) content, lipid peroxidation extent (MDA), and superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities were determined. The photoelectro-Fenton treatment was the most effective in degrading glyphosate, operating synergistically to break glyphosate bonds, thereby generating non-toxic short-chain molecules. Maize seed germination was satisfactory (> 50 %), but the persistent formation of reactive oxygen species (ROS) led to increased antioxidant activities of SOD, CAT, and POD enzymes acting in a compensatory manner against ROS, thus sustaining the photosynthetic apparatus. Hormesis, a stimulatory effect of glyphosate, was also observed in the presence of low concentrations of glyphosate.

Combined OPLS-DA and decision tree as a strategy to identify antimicrobial biomarkers of volatile oils analyzed by gas chromatography-mass spectrometry

ABSTRACT Bioguided isolation to discriminate antimicrobial compounds from volatile oils is a time- and money-consuming process. Considering the limitations of the classical methods, it would be a great improvement to use chemometric techniques to identify putative biomarkers from volatile oils. For this purpose, antimicrobial assays of volatile oils extracted from different plant species were carried out against Streptococcus mutans. Eight volatile oils that showed different antimicrobial effects (inactive, weakly active, moderately active and very active) were selected in this work. The volatile oils' composition was determined by GC-MS-based metabolomic analysis. Orthogonal projection to latent structures discriminant analysis and decision tree were carried out to access the metabolites that were highly correlated with a good antimicrobial activity. Initially, the GC-MS metabolomic data were pretreated by different methods such as centering, autoscaling, Pareto scaling, level scaling and power transformation. The level scaling was selected by orthogonal projection to latent structures discriminant analysis as the best pretreatment according to the validation results. Based on this data, decision tree was also carried out using the same pretreatment. Both techniques (orthogonal projection to latent structures discriminant analysis and decision tree) pointed palmitic acid as a discriminant biomarker for the antimicrobial activity of the volatile oils against S. mutans. Additionally, orthogonal projection to latent structures discriminant analysis and decision tree predicted as "very active" the antimicrobial activity of volatile oils, which did not belong to the training group. This predicted result is in agreement with our experimental result (MIC = 31.25 µg ml−1). The present study can contribute to the development of useful strategies to help identifying antimicrobial constituents of complex oils.

GFAAS determination of mercury in muscle samples of fish from Amazon, Brazil.

In the present study, a simple, rapid and sensitive method was developed for the determination of mercury concentrations in the muscle tissue of fish from the Brazilian Amazon using graphite furnace atomic absorption spectrometry (GFAAS) following acid mineralization of the samples in an ultrasonic cold water bath. Using copper nitrate as a chemical modifier in solution and sodium tungstate as permanent modifier, we were able to attain thermal stabilization of the mercury up to the atomisation temperature of 1600 °C in the GFAAS assay. The calculated limits of detection (LOD) and quantification (LOQ) were 0.014 and 0.047 mg kg(-1), respectively.

A preliminary and qualitative metallomics study of mercury in the muscle of fish from Amazonas, Brazil.

This paper presents preliminary findings for a metallomics study of mercury in the muscle of the fish species from Amazonas, Brazil, after protein separation by two-dimensional polyacrylamide gel electrophoresis and subsequent evaluation of mercury by synchrotron radiation X-ray fluorescence. The fluorescence spectra revealed mercury in two protein spots. The mercury-containing protein spots showed molecular weights of 20.8 ± 0.7 and 19.8 ± 0.5 kDa and isoelectric points of 5.6 ± 0.2 and 7.5 ± 0.3, respectively.

Levels of copper in Nile tilapia from Brazil.

The purpose of this work was to determine the concentration of copper in samples of farmed Nile tilapia (Oreochromis niloticus L.) fillets purchased in the city of Botucatu (São Paulo, Brazil) and in fillet and liver samples of Tilapia fed diets supplemented with different concentrations of Cu from the Laboratory of Aquatic Organism Nutrition/FMVZ-UNESP (Botucatu, Brazil). The fillet samples were prepared by lyophilisation and cryogenic grinding into particles smaller than 60 µm, and copper was extracted ultrasonically using 0.10 mol l(-1) HCl as extraction solution. Copper determination was performed by graphite furnace atomic absorption spectrometry (GFAAS) with optimised temperatures of drying, pyrolysis, atomisation and cleaning. Palladium nitrate was injected into the samples as a chemical modifier and tungsten as a permanent modifier. Copper concentrations of 0.70-1.60 mg kg(-1) were found, which are in line with Brazilian regulations. The accuracy and precision of the copper concentrations determined in this study were evaluated using certified standard Lake Michigan fish tissue (NIST SRM 1947).

Analytical approach to the metallomic of Nile tilapia (Oreochromis niloticus) liver tissue by SRXRF and FAAS after 2D-PAGE separation: Preliminary results.

An investigation was made into calcium, iron and zinc in protein spots in samples of Nile tilapia (Oreochromis niloticus) liver tissue obtained after protein separation by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and subsequent qualitative and quantitative evaluation by synchrotron radiation X-ray fluorescence (SRXRF) and Flame Atomic Absorption Spectrometry (FAAS). An analysis of the fluorescence spectra indicated the presence of calcium, iron and zinc in 12, 6 and 8 liver protein spots, respectively. The metal ions found were distributed mainly in proteins with a molar mass of less than 40.00 kDa and more than 12.00 kDa, with pI in the range of 4.70-9.40. The only exception was a spot presenting protein with a molar mass of 10.10 kDa. In addition to calcium, iron and zinc, sulfur and phosphorus - which are non-metals that may be part of the protein structure, were also detected. After microwave-assisted acid mineralization of the proteins spots, a FAAS estimation of the concentration of calcium, iron and zinc ions bound to these proteins indicated a range of 1.08-5.80 mg g(-1), 2.02-8.03 mg g(-1) and 1.60-8.55 mg g(-1), respectively.

An integrated BAC and genome sequence physical map of Phytophthora sojae.

Phytophthora spp. are serious pathogens that threaten numerous cultivated crops, trees, and natural vegetation worldwide. The soybean pathogen P. sojae has been developed as a model oomycete. Here, we report a bacterial artificial chromosome (BAC)-based, integrated physical map of the P. sojae genome. We constructed two BAC libraries, digested 8,681 BACs with seven restriction enzymes, end labeled the digested fragments with four dyes, and analyzed them with capillary electrophoresis. Fifteen data sets were constructed from the fingerprints, using individual dyes and all possible combinations, and were evaluated for contig assembly. In all, 257 contigs were assembled from the XhoI data set, collectively spanning approximately 132 Mb in physical length. The BAC contigs were integrated with the draft genome sequence of P. sojae by end sequencing a total of 1,440 BACs that formed a minimal tiling path. This enabled the 257 contigs of the BAC map to be merged with 207 sequence scaffolds to form an integrated map consisting of 79 superscaffolds. The map represents the first genome-wide physical map of a Phytophthora sp. and provides a valuable resource for genomics and molecular biology research in P. sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes.

Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum.

Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1x coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40-70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP-dROX, we assembled a physical map for P.chrysogenum, with 2-3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes.

A BAC- and BIBAC-based physical map of the soybean genome.

Genome-wide physical maps are crucial to many aspects of advanced genome research. We report a genome-wide, bacterial artificial chromosome (BAC) and plant-transformation-competent binary large-insert plasmid clone (hereafter BIBAC)-based physical map of the soybean genome. The map was constructed from 78001 clones from five soybean BAC and BIBAC libraries representing 9.6 haploid genomes and three cultivars, and consisted of 2905 BAC/BIBAC contigs, estimated to span 1408 Mb in physical length. We evaluated the reliability of the map contigs using different contig assembly strategies, independent contig building methods, DNA marker hybridization, and different fingerprinting methods, and the results showed that the contigs were assembled properly. Furthermore, we tested the feasibility of integrating the physical map with the existing soybean composite genetic map using 388 DNA markers. The results further confirmed the nature of the ancient tetraploid origin of soybean and indicated that it is feasible to integrate the physical map with the linkage map even though greater efforts are needed. This map represents the first genome-wide, BAC/BIBAC-based physical map of the soybean genome and would provide a platform for advanced genome research of soybean and other legume species. The inclusion of BIBACs in the map would streamline the utility of the map for positional cloning of genes and QTLs, and functional analysis of soybean genomic sequences.