cpDNA barcoding by combined End-Point and Real-Time PCR analyses to identify and quantify the main contaminants of oregano (Origanum vulgare L.) in commercial batches

Oregano (Origanum vulgare L.) is a flowering plant that belongs to the mint family (Lamiaceae). It is used as a culinary herb and is often commercialized as a fine powder or a mixture of small fragments of dried leaves, which makes morphological recognition difficult. Like other commercial preparations of drugs and spices, the contamination of oregano mixtures with vegetable matter of lower quality, or the use of generic misleading names, are frequent and stress the need to develop a molecular traceability system to easily, quickly, and cheaply unveil these scams. The DNA-based analytical approach known as cpDNA barcoding is particularly suited for fraud identification in crop plant species (fresh products and food derivatives), and it represents a promising traceability tool as an alternative or complement to traditional detection methods. In the present study, we used a combined approach based on both qualitative and quantitative cpDNA barcoding with end-point and real-time polymerase chain reaction (PCR) analyses to assess the type and degree of contamination in commercial batches of common oregano. In a preliminary qualitative screening, we amplified, cloned, and sequenced a number of universal trnH-psbA- and trnL-barcoded regions, to identify the main contaminants in the samples under investigation. On the basis of these findings, we then developed and validated a species-specific and sequence-targeted method of testing for the quantitative assessment of contaminants, using trnL gene intron assays. Surprisingly, the results obtained in our case study indicated an almost total absence of O. vulgare in the commercial batches analyzed, but a high presence of group I contaminants (Satureja pilosa Velen.), and a moderate presence of group II contaminants (Cistus lanidifer L./Cistus albidus)

Genomics of flower identity in grapevine (Vitis vinifera L.)

The identity of the four characteristic whorls of typical eudicots, namely, sepals, petals, stamens, and carpels, is specified by the overlapping action of homeotic genes, whose single and combined contributions have been described in detail in the so-called ABCDE model. Continuous species-specific refinements and translations resulted in this model providing the basis for understanding the genetic and molecular mechanisms of flower development in model organisms, such as Arabidopsis thaliana and other main plant species. Although grapevine (Vitis vinifera L.) represents an extremely important cultivated fruit crop globally, studies related to the genetic determinism of flower development are still rare, probably because of the limited interest in sexual reproduction in a plant that is predominantly propagated asexually. Nonetheless, several studies have identified and functionally characterized some ABCDE orthologs in grapevine. The present study is intended to provide a comprehensive screenshot of the transcriptional behavior of 18 representative grapevine ABCDE genes encoding MADS-box transcription factors in a developmental kinetic process, from preanthesis to the postfertilization stage and in different flower organs, namely, the calyx, calyptra, anthers, filaments, ovary, and embryos. The transcript levels found were compared with the proposed model for Arabidopsis to evaluate their biological consistency. With a few exceptions, the results confirmed the expression pattern expected based on the Arabidopsis data

Co-localization of PTEN and E-cadherin in canine mammary hyperplasias and benign and malignant mammary tumours

Fifty-four canine mammary lesions (15 hyperplasias, 7 adenomas and 32 carcinomas) were submitted to immunohistochemical analysis for the evaluation of PTEN and E-cadherin co-expression. Subjects bearing mammary carcinomas were also submitted to a 2-year follow-up study to compare immunohistochemical results with overall survival All the hyperplastic samples stained positive for both markers, 100% of adenomas were positive for PTEN and 86% for E-cadherin, and 69% and 34% of carcinomas were positive for PTEN and E-cadherin, respectively. Statistical analysis showed a positive correlation between these two proteins both considering all (p <0.01) or malignant tumours (p <0.05). The female dogs bearing tumours positively-stained for both markers had a longer overall survival (p <0.05) and absence of lymphatics invasion (p <0.05). Simultaneous double immunofluorescence confirmed the co-localization of the two proteins in neoplastic cells. Results reported in this study confirm the tumor suppressor effect of these two molecules

The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants

Fennel is a plant species of both agronomic and pharmaceutical interest that is characterized by a shortage of genetic and molecular data. Taking advantage of NGS technology, we sequenced and annotated the first fennel leaf transcriptome using material from four different lines and two different bioinformatic approaches: de novo and genome-guided transcriptome assembly. A reference transcriptome for assembly was produced by combining these two approaches. Among the 79,263 transcripts obtained, 47,775 were annotated using BLASTX analysis performed against the NR protein database subset with 11,853 transcripts representing putative full-length CDS. Bioinformatic analyses revealed 1,011 transcripts encoding transcription factors, mainly from the BHLH, MYB-related, C2H2, MYB, and ERF families, and 6,411 EST-SSR regions. Single-nucleotide variants of SNPs and indels were identified among the 8 samples at a frequency of 0.5 and 0.04 variants per Kb, respectively. Finally, the assembled transcripts were screened to identify genes related to the biosynthesis of t-anethole, a compound well-known for its nutraceutical and medical properties. For each of the 11 genes encoding structural enzymes in the t-anethole biosynthetic pathway, we identified at least one transcript showing a significant match. Overall, our work represents a treasure trove of information exploitable both for marker-assisted breeding and for in-depth studies on thousands of genes, including those involved in t-anethole biosynthesis

Transcriptome pathways in leaf and root of grapevine genotypes with contrasting drought tolerance

Most of the world’s wine-producing regions are subjected to seasonal drought,and,in the light of the dramatic climate-change events occurring in recent years, the selection of resistant rootstocks is becoming a crucial factor for the development of sustainable agricultural models to ensure optimal grape berry development and ripening. In this study, roots and leaves of 101.14 (drought-susceptible) and M4 (drought-tolerant) rootstocks were sampled in progressive drought and mRNA-seq profiles were evaluated. Physiological characterization indicated that only M4 was able to maintain high leaf transpiration and net assimilation rates under severe stress conditions. Statistical analyses, carried out on mRNA-seq data, highlighted that “treatment” (water stress) and “genotype” (rootstock-genotype) seem to be the main variables explaining differential gene expression in roots and leaves tissues, respectively. Upon water-stress, roots and leaves of the tolerant genotype M4 exhibit a higher induction of stilbenes (i.e., STS) and flavonoids (e.g., CHS, F3H, FLS) biosynthetic genes. Moreover, the higher expression of STS genes in M4 is coupled with an up-regulation of WRKYs transcription factors. STS genes promoter regions, extracted from whole genome of M4 and 101.14, highlighted a higher number of WBOX cis elements (binding site for WRKYs) in the tolerant genotype

MOD derived pyrochlore films as buffer layer for all-chemical YBCO coated conductors

We report a detailed study performed on La2Zr2O7 (LZO) pyrochlore material grown by Metal-Organic Decomposition (MOD) method as buffer layers for YBa2Cu3O7-x (YBCO) coated conductors. High quality epitaxial LZO thin films have been obtained on single crystal (SC) and Ni-5%at.W substrates. In order to evaluate structural and morphological properties, films have been characterized by means of X-ray diffraction analyses (XRD), atomic force microscope (AFM) and scanning electron microscope (SEM). Precursors solutions and heat treatments have been studied by thermogravimetric analyses (TG-DTA-DTG) and infrared spectra (FT-IR) with the aim of optimizing the annealing process. Thin films of YBCO have been deposited by pulsed laser ablation (PLD) on this buffer layers. The best results obtained on SC showed YBCO films with critical temperature values above 90 K, high self field critical current density values (Jc > 1 MA/cm2) and high irreversibility field values (8.3 T) at 77 K together with a rather high depinning frequency vp (0.5 T, 77 K)>44 GHz as determined at microwaves. The best results on Ni-5%at.W has been obtained introducing in the heat treatment a pyrolysis process at low temperature in air in order to remove the residual organic part of the precursor solution

Dissecting the effect of soil on plant phenology and berry transcriptional plasticity in two Italian grapevine varieties (Vitis vinifera L.)

Grapevine embodies a fascinating species as regards phenotypic plasticity and genotype-per-environment interactions. The terroir, namely the set of agri-environmental factors to which a variety is subjected, can influence the phenotype at the physiological, molecular, and biochemical level, representing an important phenomenon connected to the typicality of productions. We investigated the determinants of plasticity by conducting a field-experiment where all terroir variables, except soil, were kept as constant as possible. We isolated the effect of soils collected from different areas, on phenology, physiology, and transcriptional responses of skin and flesh of a red and a white variety of great economic value: Corvina and Glera. Molecular results, together with physio-phenological parameters, suggest a specific effect of soil on grapevine plastic response, highlighting a higher transcriptional plasticity of Glera in respect to Corvina and a marked response of skin compared to flesh. Using a novel statistical approach, we identified clusters of plastic genes subjected to the specific influence of soil. These findings could represent an issue of applicative value, posing the basis for targeted agricultural practices to enhance the desired characteristics for any soil/cultivar combination, to improve vineyards management for a better resource usage and to valorize vineyards uniqueness maximizing the terroir-effect

Rotating-Coil Measurement System for Small-Bore-Diameter Magnet Characterization

Rotating-coil measurement systems are widely used to measure the multipolar fields of particle accelerator magnets. This paper presents a rotating-coil measurement system that aims at providing a complete data set for the characterization of quadrupole magnets with small bore diameters (26 mm). The PCB magnetometer design represents a challenging goal for this type of transducer. It is characterized by an aspect ratio 30% higher than the state of the art, imposed by the reduced dimension of the external radius of the rotating shaft and the necessity of covering the entire magnet effective length (500 mm or higher). The system design required a novel design for the mechanical asset, also considering the innovation represented by the commercial carbon fiber tube, housing the PCB magnetometer. Moreover, the measurement system is based primarily on standard and commercially available components, with simplified control and post-processing software applications. The system and its components are cross-calibrated using a stretched-wire system and another rotating-coil system. The measurement precision is established in a measurement campaign performed on a quadrupole magnet characterized by an inner bore diameter of 45 mm