Population structure of Staphylococcus aureus isolated from bulk tank goat's milk.

The presence of Staphylococcus aureus in raw milk can represent a potential threat to human health, due to the introduction of pathogenic strains into dairy food supply chain. The present study was performed to investigate the genetic variation among S. aureus strains isolated from bulk tank goat's milk. The virulence profiles were also assessed to link the isolates with the potential source of milk contamination. A population study was performed on 60 strains using distance-based methods such as pulsed-field gel electrophoresis (PFGE), and the output was analyzed using Structure statistical software (University of Chicago; http://pritch.bsd.uchicago.edu/structure.html ). This Bayesian clustering model tool allows one to assign individuals into a population with no predefined structure. In order to assess partition of genetic variability among isolates, groups obtained by Structure were also investigated using analysis of molecular variance. S. aureus was recovered in 60 out of 78 samples (76.9%) collected from 26 farms. According to PFGE analysis, the strains were divided into 25 different pulsotypes and grouped into two main clusters. Restriction profiles, analyzed by Structure, allowed us to identify two distinct S. aureus genetic groups. Within each group, the strains showed a high coefficient of membership. A great part of genetic variability was attributable to within-groups variation. On the basis of the virulence profile, 45% of the isolates were linked to "animal" biovar, while 6.7% could be assigned to "human" biovar. Out of 60 strains, 27 were characterized by in vitro production of either enterotoxins A (5.0%), C (38.3%), or D (1.7%). The present study showed a high prevalence of bulk tank goat's milk contamination with S. aureus of animal origin. The presence in goat's milk of S. aureus strains able to produce enterotoxins and their potential introduction into dairy chain may represent a serious threat to human health.

PRGdb: a bioinformatics platform for plant resistance gene analysis.

PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. The complete database includes a set of 73 manually curated reference R-genes, 6308 putative R-genes collected from NCBI and 10463 computationally predicted putative R-genes. Thanks to a user-friendly interface, data can be examined using different query tools. A home-made prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. New putative R-gene classes containing unknown domain combinations were discovered and characterized. The development of the PRG platform represents an important starting point to conduct various experimental tasks. The inferred cross-link between genomic and phenotypic information allows access to a large body of information to find answers to several biological questions. The database structure also permits easy integration with other data types and opens up prospects for future implementations.

Geographical variation of the chemical composition in essential oils extracted from Sardinian Salvia verbenaca.

Salvia verbenaca is a perennial herbaceous plant well appreciated as medicinal herb which can be found in Mediterranean area, Europe, Africa and Asia. In this study, S. verbenaca flowers and leaves were collected in six different geographical areas of Sardinia (Italy). Information about the variation of the chemical composition of plants grown in different locations were obtained from gas chromatography analysis of the extracted essential oils. Gas chromatography analysis detected 33 compounds, which have been grouped in oxygenated monoterpenes, monoterpene hydrocarbons, sesquiterpenes and other compounds. The chemical composition of each group resulted significantly affected by sampling site in terms of geography and altitude. Concerning the geographical distribution of the detected chemicals, sesquiterpenes were found in considerable amount in three localities, monoterpenes hydrocarbons in two and other compounds were predominant only in one site. Regarding the altitude level, monoterpenes, sesquiterpenes and other compounds were predominant, respectively, at medium and medium-high altitude.

Stabilising fluoride in contaminated soils with monocalcium phosphate and municipal solid waste compost: microbial, biochemical and plant growth impact.

This study evaluated the influence of a municipal solid waste compost (MSWC) and monocalcium phosphate (MCP), alone or combined, on the mobility, toxicity, bioavailability and health risk of fluoride (1000 mg F-·kg-1) in an artificially polluted soil (pH 7.85). The addition of MCP (0.2% w/w) and MSWC (1% w/w) (alone and combined) to the contaminated soil reduced water-soluble (e.g. by more than 50% in MCP and MCP + MSWC-treated soils) and exchangeable F- fractions and increased the residual one. The addition of MSWC and MSWC + MCP to the contaminated soil significantly increased microbial biomass C (SMB-C; 1.3-3.6-fold) while all treatments increased the abundance of culturable heterotrophic bacteria (up to twofold in MSWC + MCP). Overall, dehydrogenase, ß-glucosidase, urease and phosphomonoesterase activities were enhanced in treated soils and positively correlated with SMB-C, but not with labile F-. All treatments increased carrot yield (up to 3.4-fold in MSWC + MCP), while bean growth was significantly enhanced only by MCP and MCP + MSWC (~ twofold). The opposite trend applied for F- uptake which was especially reduced in the edible part of carrot after soil amendment. A limited influence of MCP and MSWC on hazard quotient (HQ), due to bean and carrot consumption, was also recorded (i.e. HQ generally > 1). Results suggest that MCP and MSWC can be used in the recovery of soil chemical, microbial and biochemical status of F-rich agricultural soils. They also indicate that the bean and carrot cultivars employed in this study are likely unsuitable in such soils due to high F- uptake in edible parts.

Biochemical Characterization and Effects of Cooking Methods on Main Phytochemicals of Red and Purple Potato Tubers, a Natural Functional Food.

Potato is a staple food crop and an important source of dietary energy. Its tubers contain several essential amino acids, vitamins, minerals and phytochemicals that contribute to the nutritional value of this important product. Recently, scientific interest has focused on purple and red potatoes that, due to the presence of anthocyanins, may be considered as natural powerful functional food. The aim of this study was to evaluate the characteristics of pigmented varieties, the types of anthocyanins accumulated and the level of both beneficial phytochemicals (vitamin C and chlorogenic acids, CGAs) and anti-nutritional compounds (glycoalkaloids) following various cooking methods. The analyses described the presence of a mix of several acylated anthocyanins in pigmented tubers along with high level of CGA. The amount of antioxidants was differently affected by heat treatments according to the type of molecule and the cooking methods used. In some cases, the beneficial compounds were made more available by heat treatments for the analytical detection as compared to raw materials. Data reported here describe both the agronomic properties of these pigmented varieties and the effects of food processing methods on bioactive molecules contained in this natural functional food. They may provide useful information for breeders aiming to develop new varieties that could include desirable agronomical and industrial processing traits.

A nematode demographics assay in transgenic roots reveals no significant impacts of the Rhg1 locus LRR-Kinase on soybean cyst nematode resistance.

BACKGROUND: Soybean cyst nematode (Heterodera glycines, SCN) is the most economically damaging pathogen of soybean (Glycine max) in the U.S. The Rhg1 locus is repeatedly observed as the quantitative trait locus with the greatest impact on SCN resistance. The Glyma18g02680.1 gene at the Rhg1 locus that encodes an apparent leucine-rich repeat transmembrane receptor-kinase (LRR-kinase) has been proposed to be the SCN resistance gene, but its function has not been confirmed. Generation of fertile transgenic soybean lines is difficult but methods have been published that test SCN resistance in transgenic roots generated with Agrobacterium rhizogenes. RESULTS: We report use of artificial microRNA (amiRNA) for gene silencing in soybean, refinements to transgenic root SCN resistance assays, and functional tests of the Rhg1 locus LRR-kinase gene. A nematode demographics assay monitored infecting nematode populations for their progress through developmental stages two weeks after inoculation, as a metric for SCN resistance. Significant differences were observed between resistant and susceptible control genotypes. Introduction of the Rhg1 locus LRR-kinase gene (genomic promoter/coding region/terminator; Peking/PI 437654-derived SCN-resistant source), into rhg1- SCN-susceptible plant lines carrying the resistant-source Rhg4+ locus, provided no significant increases in SCN resistance. Use of amiRNA to reduce expression of the LRR-kinase gene from the Rhg1 locus of Fayette (PI 88788 source of Rhg1) also did not detectably alter resistance to SCN. However, silencing of the LRR-kinase gene did have impacts on root development. CONCLUSION: The nematode demographics assay can expedite testing of transgenic roots for SCN resistance. amiRNAs and the pSM103 vector that drives interchangeable amiRNA constructs through a soybean polyubiqutin promoter (Gmubi), with an intron-GFP marker for detection of transgenic roots, may have widespread use in legume biology. Studies in which expression of the Rhg1 locus LRR-kinase gene from different resistance sources was either reduced or complemented did not reveal significant impacts on SCN resistance.

Genetic and epigenetic dynamics affecting anthocyanin biosynthesis in potato cell culture.

Anthocyanins are antioxidant pigments widely used in drugs and food preparations. Flesh-coloured tubers of the cultivated potato Solanum tuberosum are important sources of different anthocyanins. Due to the high degree of decoration achieved by acylation, anthocyanins from potato are very stable and suitable for the food processing industry. The use of cell culture allows to extract anthocyanins on-demand, avoiding seasonality and consequences associated with land-based-tuber production. However, a well-known limit of cell culture is the metabolic instability and loss of anthocyanin production during successive subcultures. To get a general picture of mechanisms responsible for this instability, we explored both genetic and epigenetic regulation that may affect anthocyanin production in cell culture. We selected two clonally related populations of anthocyanin-producing (purple) and non-producing (white) potato cells. Through targeted molecular investigations, we identified and functionally characterized an R3-MYB, here named StMYBATV. This transcription factor can interact with bHLHs belonging to the MBW (R2R3-MYB, bHLH and WD40) anthocyanin activator complex and, potentially, may interfere with its formation. Genome methylation analysis revealed that, for several genomic loci, anthocyanin-producing cells were more methylated than clonally related white cells. In particular, we localized some methylation events in ribosomal protein-coding genes. Overall, our study explores novel molecular aspects associated with loss of anthocyanins in cell culture systems.

Effect of salinity (NaCl) on plant growth, nutrient content, and glucosinolate hydrolysis products trends in rocket genotypes.

Salinity caused by NaCl is an abiotic stress inducing morphological and metabolic disorders. The impact of salinity (0, 65 and 130 mM NaCl) on morphological traits, elemental and volatiles composition of six rocket genotypes (G1-G6) was explored. A significant reduction of shoot biomass, plant height and leaf area as function of genotype and salinity level was observed. G5 was highly affected by NaCl: at 65 and 130 mM plants were 48.6% and 59.1% shortened compared with to control. The volatiles compositions was also analyzed. Glucosinolates increased under 65 mM, then decreased at 130 mM. In G1, glucosinolates start with 7.4 (control), raised to 21.50 (65 mM) and finally dropped to 4.34 (130 mM). This trend was observed also for erucin, the major rocket's isothiocyanate. Rockets could be irrigated with saline water improving the health promoting compounds production. The evaluation of different genotype seems to be of great interest for future breeding programs.

Relationship Between Soil and Essential Oil Profiles in Salvia desoleana Populations: Preliminary Results.

Salvia desoleana is a herbaceous perennial shrub endemic of Sardinia (Italy). The leaves are a source of essential oil, used in pharmaceutical and cosmetic industries. The therapeutic function of this species has been associated to the presence of essential oils rich in α/ß-pinene, p-cimene, linalool, linalyl acetate and 1,8-cineole. Today.the industrial request of Salvia essential oils is increasing and most of the biomass is exploited from the natural populations which are under severe risk of genetic erosion. In order to improve the essential oil production, the study of the environmental parameters that influence composition, quality and quantity of the essential oils, turns out to be necessary. Soil physical and chemical structure represents one of the determinant factors in secondary metabolites production, and could also be involved in volatiles fraction composition in the same species. The main aim of this research was to explore the relationship between essential oil profiles and soil characteristics in S. desoleana populations. GC/MS analysis performed on the essential oil extracts identified 22 principal compounds, which were extremely variable among the five S. desoleana populations studied. The analysis of the essential oils revealed different compositions in the terpenes fractions: 68.2% of monoterpenes, 27.3% of sesquiterpenes and 4.5% of diterpenes. Analysis of chemical and physical soil parameters at the collection sites revealed that silt and sand contents were correlated with α-pinene and sclareol fractions and the total K20 was significantly correlated to several compounds belonging to the three terpene fractions identified. These results will provide guidelines for the in site conservation and for the improvement of the commercial value of the species.

Seforta, an integrated tool for detecting the signature of selection in coding sequences.

BACKGROUND: The majority of amino acid residues are encoded by more than one codon, and a bias in the usage of such synonymous codons has been repeatedly demonstrated. One assumption is that this phenomenon has evolved to improve the efficiency of translation by reducing the time required for the recruitment of isoacceptors. The most abundant tRNA species are preferred at sites on the protein which are key for its functionality, a behavior which has been termed "translational accuracy". Although observed in many species, as yet no public domain software has been made available for its quantification. FINDINGS: We present here Seforta (Selection for Translational Accuracy), a program designed to quantify translational accuracy. It searches for synonymous codon usage bias in both conserved and non-conserved regions of coding sequences and computes a cumulative odds ratio and a Z-score. The specification of a set of preferred codons is desirable, but the program can also generate these. Finally, a randomization protocol calculates the probability that preferred codon combinations could have arisen by chance. CONCLUSIONS: Seforta is the first public domain program able to quantify translational accuracy. It comes with a simple graphical user interface and can be readily installed and adjusted to the user's requirements.

Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

BACKGROUND: Helichrysum italicum (Asteraceae) is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. METHODS: H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. KEY RESULTS: The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. CONCLUSIONS: The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.

Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean.

The rhg1-b allele of soybean is widely used for resistance against soybean cyst nematode (SCN), the most economically damaging pathogen of soybeans in the United States. Gene silencing showed that genes in a 31-kilobase segment at rhg1-b, encoding an amino acid transporter, an α-SNAP protein, and a WI12 (wound-inducible domain) protein, each contribute to resistance. There is one copy of the 31-kilobase segment per haploid genome in susceptible varieties, but 10 tandem copies are present in an rhg1-b haplotype. Overexpression of the individual genes in roots was ineffective, but overexpression of the genes together conferred enhanced SCN resistance. Hence, SCN resistance mediated by the soybean quantitative trait locus Rhg1 is conferred by copy number variation that increases the expression of a set of dissimilar genes in a repeated multigene segment.

The genetic diversity of Sardinian myrtle (Myrtus communis L. ) populations

Background: The myrtle (Myrtus communis) is a common shrub widespread in the Mediterranean Basin. Its fruit and leaves exhibit antioxidant, antibacterial and antifungal properties, and are used for their content of essential oils and for their medicinal properties, but most commonly as an ingredient in locally made liquor. The uncontrolled exploitation of natural stands has reduced both the species' geographical coverage and the size of individual populations. The selection of genotypes for controlled cultivation requires a characterization of the genetic diversity present both within and between populations. Results: Genotypic variation was evaluated using ISSR profiling and genetic diversity characterized using standard population genetics approaches. Two major clusters were identified: one capturing all the candidate cultivars selected from various Sardinian localities, and the other wild individuals collected from Asinara, Corsica and Surigheddu. A moderate level of gene flow between the Sardinian and Corsican populations was identified. Discriminant analysis of principal components revealed a level of separation among the wild populations, confirming the population structure identified by the clustering methods. Conclusions: The wild accessions were well differentiated from the candidate cultivars. The level of genetic variability was high. The genetic data were compatible with the notion that myrtle has a mixed pollination system, including both out-pollination by insects and self-pollination. The candidate cultivars are suggested to represent an appropriate basis for directed breeding.