Erratum to: Spatial and Temporal Heavy Metal Concentration (Cu,Pb, Zn,Hg, Fe,Mn, Ni) in Sediments of the Mar Piccolo in Taranto (Ionian Sea,Italy)

Water, Air, &; Soil Pollution -     

Nanopore sequencing for the detection and identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

Xylella fastidiosa (Xf) is a gram-negative bacterial plant pathogen that can infect over 500 plant species. While it is endemic in America, X. fastidiosa subsp. pauca was reported for the first time in Europe in 2013 on olive trees in southern Italy. The availability of fast, sensitive, and reliable diagnostic tools is indispensable for managing current and future outbreaks of Xf. In this paper, we use the OXford Nanopore Technologies (ONT) MinION platform for detecting and identifying Xf at species, subspecies, and sequence type (ST) level. Two workflows were developed: the first one provided a “shotgun” strategy, that is, exploring the possibility of detecting Xf within DNA extracted from plant samples. This allowed detection of Xf by direct DNA sequencing and identifying the subspecies only in samples with high bacterial levels. Nanopore amplicon sequencing was pursued as a second workflow. This consists of PCR amplification of a set of seven multilocus sequence typing (MLST) fragments, officially adopted for identifying Xf at type strain level, followed by Nanopore-sequencing of the amplicons and an ad hoc pipeline to generate MLST consensus calls. This combined approach, which takes only a few hours, allowed the detection and identification of Xf at ST level in plant material with low bacterial infection.     

Effects of different cooking methods on nutritional and physicochemical characteristics of selected vegetables

The objective of the present study was to evaluate the effect of three common cooking practices (i.e., boiling, steaming, and frying) on phytochemical contents (i.e., polyphenols, carotenoids, glucosinolates, and ascorbic acid), total antioxidant capacities (TAC), as measured by three different analytical assays [Trolox equivalent antioxidant capacity (TEAC), total radical-trapping antioxidant parameter (TRAP), ferric reducing antioxidant power (FRAP)] and physicochemical parameters of three vegetables (carrots, courgettes, and broccoli). Water-cooking treatments better preserved the antioxidant compounds, particularly carotenoids, in all vegetables analyzed and ascorbic acid in carrots and courgettes. Steamed vegetables maintained a better texture quality than boiled ones, whereas boiled vegetables showed limited discoloration. Fried vegetables showed the lowest degree of softening, even though antioxidant compounds were less retained. An overall increase of TEAC, FRAP, and TRAP values was observed in all cooked vegetables, probably because of matrix softening and increased extractability of compounds, which could be partially converted into more antioxidant chemical species. Our findings defy the notion that processed vegetables offer lower nutritional quality and also suggest that for each vegetable a cooking method would be preferred to preserve the nutritional and physicochemical qualities.     

Studies on proofing of yeasted bread dough using near- and mid-infrared spectroscopy

Dough proofing is the resting period after mixing during which fermentation commences. Optimum dough proofing is important for production of high quality bread. Near- and mid-infrared spectroscopies have been used with some success to investigate macromolecular changes during dough mixing. In this work, both techniques were applied to a preliminary study of flour doughs during proofing. Spectra were collected contemporaneously by NIR (750-1100 nm) and MIR (4000-600 cm(-1)) instruments using a fiberoptic surface interactance probe and horizontal ATR cell, respectively. Studies were performed on flours of differing baking quality; these included strong baker's flour, retail flour, and gluten-free flour. Following principal component analysis, changes in the recorded spectral signals could be followed over time. It is apparent from the results that both vibrational spectroscopic techniques can identify changes in flour doughs during proofing and that it is possible to suggest which macromolecular species are involved.     

Sourdough bread: Starch digestibility and postprandial glycemic response

To evaluate the influence of sourdough fermentation on starch digestibility in bread, four experimental breads were obtained, prepared from two different wheat flours (whole or white) by two different leavening techniques (sourdough and with Saccharomyces cerevisiae). Products were analyzed for their starch, fiber and resistant starch (RS) content and then submitted to in vitro hydrolysis with porcine alpha-amylase. On the same breads, postprandial blood glucose was evaluated in healthy human subjects. Both sourdough fermented breads gave glycaemic responses significantly lower (p < 0.001) than the corresponding products leavened with S. cerevisiae. On the contrary, the presence of fiber did not influence the glycaemic potential of breads. RS levels were higher in the sourdough products, whereas no differences were observed either in the rate of starch hydrolysis or in the degree of polymerization of the starch residues after the in vitro hydrolysis. We may conclude that sourdough fermentation is a technique able to reduce the glycaemic response to bread and that the mechanism does not seem related to the rate of starch hydrolysis.     

Evaluation of shelf-life of fresh-cut pineapple using FT-NIR and FT-IR spectroscopy

The aim of this work was to investigate the loss of freshness of fresh-cut pineapple samples stored at different temperatures using non-destructive spectroscopic methods. Three lots of fresh cut pineapples (Ananas comosus L. cv. Golden Ripe, from Costa Rica), packaged in PVC trays (250 g) were analyzed during storage at three different temperatures (5.3, 8.6 and 15.8 °C). Loss of quality of these fruit was evaluated by chemical and microbiological parameters and using NIR and MIR spectroscopy. The FT-NIR spectra were acquired in reflectance mode directly on the slice of fresh-cut pineapple, over the range 12,500–3900 cm⁻¹, while FT-IR spectra were collected over the range 4000–700 cm⁻¹ using an horizontal ATR cell. Some chemical and microbiological parameters were also measured. Principal component analysis (PCA) was applied to the second derivative of the spectra to uncover molecular modifications occurring over the storage time. A clear discrimination between “fresh” and “old” samples was obtained and a stability time corresponding to the time of the initial loss of freshness was defined at each temperature. The stability times revealed by NIR spectroscopy were in good accordance with those evaluated by MIR. At each temperature the stability times (i.e. the initial loss of freshness times) defined by spectroscopic techniques (4–5 d at 5.3 °C, 3–4 d at 8.6 °C and 1 d at 15.8 °C) were associated with a mesophilic bacteria count ranging between 10⁵ and 10⁶ CFU g⁻¹ and lower than the maximum limit for mesophilic bacteria (<5 × 10⁷ CFU g⁻¹) given by French hygienic regulations at consumption.These results show that NIR and MIR spectroscopy could support conventional techniques (chemical and microbiological analysis) in studying shelf-life of fresh-cut fruit. In particular these techniques define the initial loss of freshness time, indicating a product which rapidly will be no longer acceptable if stored beyond that time. The main advantage of using IR spectroscopic techniques is to rapidly draw a profile of the product related to its change in quality.     

Biosensor technology and surface plasmon resonance for real-time detection of genetically modified Roundup Ready soybean gene sequences

Biospecific interaction analysis (BIA) was performed using surface plasmon resonance (SPR) and biosensor technologies to detect genetically modified Roundup Ready soybean gene sequences. We first immobilized, on SA sensor chips, single-stranded biotinylated oligonucleotides containing soybean lectin and Roundup Ready gene sequences, and the efficiency of hybridization to oligonucleotide probes differing in length was determined. Second, we immobilized biotinylated PCR products from nontransgenic soybeans (genomes carrying only the lectin gene), as well as from genetically modified Roundup Ready soybean, and we injected the oligonucleotide probes. Furthermore, we used the sensor chips carrying either lectin and Roundup Ready soybean PCR products or 21-mer oligonucleotide as probes, and we injected both nonpurified and purified asymmetric PCR products. The results obtained show that 13 and 15 mer oligonucleotides are suitable probes to detect genetically modified Roundup Ready soybean gene sequences (either target oligonucleotides or PCR products) under standard BIA experimental conditions. By contrast, when 11 mer DNA probes were employed, no efficient hybridization was obtained. All the SPR-based formats were found to be useful for detection of Roundup Ready gene sequences, suggesting that these procedures are useful for the real-time monitoring of hybridization between target single-stranded PCR products, obtained by using as substrates DNA isolated from normal or transgenic soybeans, and oligonucleotide or PCR-generated probes, therefore enabling a one-step, nonradioactive protocol to perform detection.     

Surface Properties of Gluten Investigated by a Fluorescence Approach

The surface properties of glutens isolated from a durum wheat cultivar (Capeiti) and two bread wheats (Riband and Hereward) were investigated using intrinsic and extrinsic fluorescence. Intrinsic fluorescence decreased on increasing protein concentration and increased after urea addition. The extrinsic fluorescence was evaluated by a titration with 8‐anilino‐1‐naphthalene sulphonate (ANS), an hydrophobic probe. The saturating concentration for ANS and its dissociation constant (Kd) were determined. The hydrophobicity of durum and bread wheat gluten showed a different behavior increasing the protein concentration: Capeiti was not influenced, but there was a change on the gluten surface for Riband and Hereward. The significance in understanding gluten structure and the relevance of the surface properties are discussed.     

Chromatographic methods for metabolite profiling of virus- and phytoplasma-infected plants of Echinacea purpurea

This study was focused on the effects of virus and phytoplasma infections on the production of Echinacea purpurea (L.) Moench secondary metabolites, such as caffeic acid derivatives, alkamides, and essential oil. The identification of caffeic acid derivatives and alkamides was carried out by means of high-performance liquid chromatography-diode array detection (HPLC-DAD), HPLC-electrospray ionization-mass spectrometry (ESI-MS), and MS(2). Quantitative analysis of these compounds was carried out using HPLC-DAD. The results indicated that the presence of the two pathogens significantly decreases (P < 0.05) the content of cichoric acid, the main caffeic acid derivative. Regarding the main alkamide, dodeca-2E,4E,8Z,10E/Z-tetraenoic acid isobutylamide, a significant decrease (P < 0.05) in the content of this secondary metabolite was observed in virus-infected plants in comparison with healthy plants, while in the phytoplasma-infected sample the variation of this secondary metabolite was not appreciable. The % relative area of the E/Z isomers of this alkamide was also found to change in infected samples. The gas chromatography (GC) and GC-MS analysis of E. purpurea essential oil enabled the identification of 30 compounds. The main significant differences (P < 0.05) in the semiquantitative composition were observed for three components: limonene, cis-verbenol, and verbenone. The results indicate that the presence of virus and phytoplasma has an appreciable influence on the content of E. purpurea secondary metabolites, which is an important issue in defining the commercial quality, market value, and therapeutic efficacy of this herbal drug.