Interactions of prion proteins with soil

Prions, are proteinaceous particles recognized as the agents of a class of neurodegenerative disorders, called transmissible spongiform encephalopathies (TSE), or prion diseases. Epidemiological data suggest that TSE-contaminated environments may serve as source of infectivity, but there is no information about adsorption of prions onto soil. We carried out experiments by mixing, healthy, or scrapie-infected hamster brains homogenates with three types of soil suspended in different buffers: (i) two saline buffers, i.e., phosphate buffer solution (PBS) and CaCl₂ solution; (ii) a mix of nondenaturing detergents, i.e., Triton X-100 and sodium deoxycholate (DOC) solution; (iii) a non-ionic detergent, i.e., lauryl maltoside; (iv) two anionic detergents, i.e., Sarkosyl or sodium dodecyl sulphate (SDS); and (v) a chaotropic agent, i.e., urea. The unbound prion proteins were detected in the supernatants (after centrifugation of soil suspension) by Western blotting. Results clearly demonstrate that both the no infectious (PrP^C) and infectious (PrP^Sc) forms are adsorbed by all soils. Only 1% sodium dodecylsulphate (SDS) partially impeded the association of PrP^C, but not that of PrP^Sc with the sandy loam soil. Agents with different interacting properties towards hydrophilic and/or hydrophobic domains failed to extract PrP^Sc from sediments of soil-brain homogenate mixtures. The strong interaction of PrP^Sc with soil favors the accumulation of prions in soils, especially if amended with prion-containing organic fertilizers and/or whenever TSE-affected animal carcasses, placenta, and excreta in general are buried or laid at the soil surface.     

Genome-wide analysis of plastome sequence variation and development of plastidial CAPS markers in common potato and related <Emphasis Type="Italic">Solanum</Emphasis> species

The plastome sequence of the European cultivated potato, Solanum tuberosum subsp. tuberosum (tbr, GenBank accession no. DQ386163), was compared with that of S. bulbocastanum, a wild potato relative (blb, GenBank accession no. DQ347958), in order to characterize the degree and type of variability in different genomic regions, and develop molecular markers relevant to genetics, breeding and biotechnology of potato. One hundred forty-two and 251 PICs (Potentially Informative Characters) were found in coding and non-coding sequences (NCSs), respectively. Further, while variation in coding regions was almost exclusively due to nucleotide substitutions, 25% of PICs in NCSs of tbr and blb were due to indels, most of them mononucleotide or longer tandem repeats (micro and minisatellites). Four intergenic regions were selected for further analyses in other 16 tuber-bearing Solanum species. The rps16-trnQ ^UUG gene spacer was found to be the most variable, forty-six PICs in this region distinguishing 18 haplotypes. Analysis of haplotype relationships, based on variability in the four intergenic regions, confirmed that the most primitive species from Central America were the most distant to S. tuberosum. Finally, polymorphic sites in the same regions were used to develop a set of CAPS (Cleaved Amplified Polymorphic Sequences) markers for species/cytoplasm identification in Solanum spp.     

Isolation and biochemical characterization of a basic myrosinase from ripe Crambe abyssinica seeds,highly specific for epi-progoitrin

On the basis of previous studies on the mechanism-based inhibition, activation, and active site structure of myrosinase(s) isolated from Sinapis alba and other cruciferous seeds, crambe myrosinase shows uncommon properties and behavior. For this reason homogeneous crambe myrosinase was isolated and investigated to establish the most important physicochemical features, including kinetic properties determined with the epimers progoitrin (R) and epi-progoitrin (S) as substrates, with and without ascorbate as an activator. The results of this study demonstrate that crambe myrosinase is highly specific for epi-progoitrin due to a better stabilization of the enzyme-substrate complex. This stabilization is caused by additional hydrogen bonding that only epi-progoitrin can set up between its hydroxyl group and a suitable residue in the hydrophobic pocket where the "docking" of the glucosinolates side chain takes place.     

Effects of water content and N addition on potential greenhouse gas production from two differently textured soils under laboratory conditions

GHGs production and emission may vary depending on soil physical properties, water management and fertilization. Two paddy soils characterized by different texture were incubated to evaluate the impact of flooding (permanent or intermittent) and N addition on potential N₂O, CH₄ and CO₂ production and release into atmosphere and soil solution. Relationships with volumetric water content (VWC) and water filled pore space (WFPS) were evaluated. Overall, the finer clayey soil (CL) produced 58% more CH₄ than the coarser sandy soil (SA) and showed an earlier sink to source transition; the difference was lower with N addition. Permanent flooding favoured the amount of dissolved CH₄. SA produced more N₂O emissions than CL under permanent flooding (31.0 vs. 3.7%); an opposite pattern was observed for dissolved N₂O (16.4 vs. 52.7%). Fertilization increased N₂O emissions under dry conditions in CL and under flooding in SA.

Our findings showed that i) VWC had a larger influence on N₂O and CH₄ emissions than WFPS, ii) soil type influenced the gas release into atmosphere or soil solution and the timing of sink to source transition in CH₄ emissions. Further investigation on timing of fertilization and drainage are needed to improve climate change mitigation strategies.     

Chemical and microbiological soil properties in organic and conventional management systems of Coffea arabica L.

The goal of this study was to evaluate the effect of organic (OS) and conventional (CS) farming of Arabica coffee on chemical and microbiological soil properties and to identify which attributes correlate and/or contribute to distinguishing these two management systems. We collected soil samples on a 100 × 100 m² grid in both, the OS and CS, in winter and summer and submitted chemical and microbiological properties to univariate and multivariate analyses (canonical discriminant analysis – CDA – and redundancy analysis – RDA). The best indicators to discriminate OS and CS were chemical and microbiological properties, as the elements calcium (Ca) and boron (B), besides microbial biomass carbon (MBC), metabolic quotient (qCO₂), acid phosphatase (ACP), and alkaline phosphatase (ALP). The RDA showed that, regardless of the season, MBC and ACP correlated with nitrogen (N), sulfur (S) and organic matter (OM), whereas basal respiration (C-CO₂) and ACP correlated with qCO₂ and with magnesium (Mg), calcium (Ca), phosphorus (P), potassium (K) and pH.     

The elusiveness of coffee aroma: new insights from a non-empirical approach

Aroma is central to a pleasurable eating/drinking experience but is one of the most labile components of food. Coffee is an outstanding example. Attempts to avoid or control aroma degradation are often frustrated by ignorance of the microscopic mechanisms that are responsible for it. One of the processes most frequently invoked is radical formation, yet the identity of the radicals and their involvement in aroma degradation are poorly understood at the molecular level. Here a step forward in the fundamental understanding of this complex problem is taken by identifying the most relevant radicals and their products using first-principles calculations. Over 100 radicals originating from key aroma compounds found in coffee and other foods have been studied and classified according to an unambiguous criterion: their thermodynamic stability relative to common radical sources. This classification scheme predicts that most aroma molecules are resistant to both peroxidation and attack from phenolic antioxidants but are unstable with respect to radicals such as .OH. Dimers--generated from radical reactions--were also considered, and the most volatile species, which may further contribute to coffee aroma degradation, were focused on. Those--which are very few indeed--that have this potential have been identified.     

Model studies on the photosensitized isomerization of bixin

The photosensitized isomerization reaction of the natural cis carotenoid bixin (methyl hydrogen 9'-cis-6, 6'-diapocarotene-6, 6'-dioate) with rose bengal or methylene blue as the sensitizer in acetonitrile/methanol (1:1) solution was studied using UV-vis spectroscopy, high-performance liquid chromatography (HPLC), and time-resolved spectroscopic techniques, such as laser-flash photolysis and singlet oxygen phosphorescence detection. In both N(2)- and air-saturated solutions, the main product formed was all-trans-bixin. The observed isomerization rate constants, k(obs), decreased in the presence of air or with increase in the bixin concentration, suggesting the participation of the excited triplet state of bixin, (3)Bix, as precursor of the cis--> trans process. On the other hand, bixin solutions in the absence of sensitizer and/or light did not degrade, indicating that the ground state of bixin is stable to thermal isomerization at room temperature. Time-resolved spectroscopic experiments confirmed the formation of the excited triplet state of bixin and its deactivation by ground state bixin and molecular oxygen quenching processes. The primary isomerization products only degraded in the presence of air and under prolonged illumination conditions, probably due to the formation of oxidation products by reaction with singlet molecular oxygen. An energy-transfer mechanism was used to explain the observed results for the bixin transformations, and the consequences for food color are discussed.     

Classification of cereal flours by chemometric analysis of MIR spectra

Different kinds of cereal flours submitted to various technological treatments were classified on the basis of their mid-infrared spectra by pattern recognition techniques. Classification in the wavelet domain was achieved by using the wavelet packet transform for efficient pattern recognition (WPTER) algorithm, which allowed singling out the most discriminant spectral regions. Principal component analysis (PCA) on the selected features showed an effective clustering of the analyzed flours. Satisfactory classification models were obtained both on training and test samples. Furthermore, mixtures of varying composition of the studied flours were distributed in the PCA space according to their composition.     

A chemometric approach to the comparison of different sample treatments for metals determination by atomic absorption spectroscopy in aceto Balsamico tradizionale di Modena

A comparison of different digestion procedures has been carried out for the analysis of metal concentration in samples of vinegars and Aceto Balsamico Tradizionale of Modena (ABTM) coming from an unique barrel set. In particular, classical wet, dry ashing, and closed vessel microwave digestion procedure have been utilized and compared for each investigated species. In a few cases, direct metal determination on ABTM (without treatment procedure) is proposed as possible alternative to sample manipulation. Flame atomic absorption spectrometry was used for the quantification of iron and zinc, while graphite furnace atomic absorption spectrometry was used for all the other elements (i.e., chromium, manganese, cobalt, nickel, copper, cadmium, and lead). The comparison among the different sample treatments was carried out by the use of statistical and chemometric tools. In particular, principal component analysis and ANOVA approaches were used to discriminate between the diverse analytical methods. Furthermore, for all the dissolving techniques, the analytical metal recovery was always evaluated by the application of the recovery function on the same sample matrix. In general, the recoveries were fairly good, ranging from 90 to 103%, except for Cd and Pb with dry ashing, which showed recovery values close to 55% and 67%, respectively. As regards the metals concentration of the investigated samples, the experimental data reveal for some species the presence of concentration slightly over the legal limit fixed for wine and wine vinegar.