Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions.

Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types corresponding to former classifications based on opines detected in diseased plants, while the T-DNA gene content more finely separate opine types in 18 T-DNA organizations. This classification was supported by the phylogeny of T-DNA oncogenes of Ti plasmids. The five gene organizations found in Ti/Ri vir regions was supported by the phylogeny of common vir genes. The vir organization was found to be likely an ancestral plasmid trait separating "classic" Ti plasmids (with one or two T-DNAs) and "Ri and vine-Ti" plasmids. A scenario generally supported by the repABC phylogeny. T-DNAs likely evolved later with the acquisition of opine characteristics as last steps in the Ti/Ri plasmid evolution. This novel evolutionary classification of Ti/Ri plasmids was found to be relevant for accurate crown gall and hairy root epidemiology.

Chemical characterization and nutritional quality investigations of healthy extra virgin olive oil flavored with chili pepper.

The production of extra virgin olive oil (EVOO) flavored with diverse spices, herbs, fruits, and vegetables or natural aromas is believed to provide advantageous properties considering either the high nutritional value or biological activity in addition to the flavoring and industrial aspects. The biological activities including antioxidant and antimicrobial properties of Tunisian EVOO obtained from "Chemlali" variety and mixed with chili pepper were investigated. Molecular analyses, including the detection of twelve olive-infecting viruses and Pseudomonas savastanoi pv savastanoi, were performed to ensure that the samples were obtained from healthy olive trees and EVOO quality was not affected. Quality parameters like free acidity, peroxide number, oxidative stability, and specific absorption at K232 nm and K270 nm were also investigated and no significant variation was revealed. The content of minor compounds such as chlorophylls, carotenoids, and total phenols showed minor changes. However, the profiles of the volatile compounds showed remarkable differences, which appeared to be the main factor for the observed variability in consumer acceptance. The results showed for the first time high quantities of polyphenols and ortho-diphenols. Four colorimetric methods were used for the determination of the antioxidant activity, namely DPPH, ABTS, FRAP, and ß-carotene test. Compared to the control, a higher level of antioxidant activity was observed for the flavored EVOO. Furthermore, significant results were obtained in the antimicrobial tests. The quality parameters of the mixture showed no alteration compared to the control. Finally, all the measurements and the chemical characterization gave a scientific basis for food technology innovation of new food products.

Chemical composition, Fatty acids profile and Biological properties of Thymus capitatus (L.) Hoffmanns, essential Oil.

T. capitatus is widely used in traditional medicine in Tunisia. The main goal of this study was to evaluate the phytochemical composition, the fatty acids profile, the antioxidant, antibacterial, and antifungal activities as well as the cytotoxic potential of the essential oil (EO) of this plant. The identification and the quantification of the different constituents of the tested EO was determined by gas chromatography-mass spectrometry (GC-MS). Antioxidant activities were evaluated by spectrophotometric methods and chemical tests. HCT 116 cells were used to evaluate the cytotoxic effect of the EO. The microdilution method was conducted to evaluate the antibacterial activity. Poisoned food method was used to test the antifungal activities against fungi species such Aspergillus niger and Aspergillus flavus. The EO presented several components, mainly monoterpenes. Results revealed that T. capitatus EO is not cytotoxic and showed excellent antioxidant activity with a dose dependent manner. Regarding antimicrobial activity, T. capitatus EO was efficient against all tested bacteria and fungi.

Establishment of a Sensitive qPCR Methodology for Detection of the Olive-Infecting Viruses in Portuguese and Tunisian Orchards.

Sensitive detection of viruses in olive orchards is actually of main importance since these pathogenic agents cannot be treated, their dissemination is quite easy, and they can have eventual negative effects on olive oil quality. The work presented here describes the development and application of a new SYBR® Green-based real-time quantitative PCR (qPCR) analysis for specific and reliable quantification of highly spread olive tree viruses: Olive latent virus 1 (OLV-1), Tobacco necrosis virus D (TNV-D), Olive mild mosaic virus (OMMV), and Olive leaf yellowing-associated virus (OLYaV). qPCR methodology revealed high specificity and sensitivity, estimated in the range of 0.8-8 copies of the virus genome, for the studied viruses. For validation of the method, total RNA and double strand RNA (dsRNA) from naturally infected trees were used. In a first trial, dsRNAs from trees of cv. "Galega vulgar" from a Portuguese orchard, were subjected to qPCR and from the 30 samples tested, 26 were TNV-D and/or OMMV-positive and 25 were OLV-1 positive. In a second trial, total RNA from trees of different cultivars from Tunisian orchards, were here tested by qPCR and all viruses were detected. From the 33 samples studied, the most prevalent virus detected in Tunisia orchards was OLV-1 (31 samples diagnosed), followed by OLYaV (20 samples diagnosed), and finally the combination in last TNV-D and/or OMMV (12 samples diagnosed). In both trials, qPCR demonstrated to be effective and sensitive, even when using total RNA as template. qPCR through the use of a SYBR® Green methodology enabled, for the first time, a reliable, sensitive, and reproducible estimation of virus accumulation in infected olive trees, in which viruses are usually in low titres, that will allow gaining new insights in virus biology essential for disease control and give an important contribution for establishment of sanitary certification of olive propagative material.

Pathogenicity, Phylogenetic relationship and NGS based identification and assembly of tumorigenic Agrobacterium radiabacter plasmidic and chromosomic reads isolated from Prunus duclcis.

Although many Agrobacterium radiobacter strains have already been identified, only a few genomes of strains belonging to genomovar G4 have been sequenced so far. In this study, we report the first virulent genome sequence of Agrobacterium radiobacter strain tun 183, which is highly virulent to almond specie. The genome size was estimated to be 5.53 Mb, with 57.9%GC content. In total, 6486 genes encoding proteins and 61 genes encoding RNAs were identified in this genome. Comparisons with the available sequenced genomes of genomovar G4 as well as with other A. sp. were conducted, revealing a hexapartite genome containing circular and linear chromosomes in addition to two accessory plasmids and a tumor inducing plasmid (pTi) in strain tun 183. The phylogenetic analysis of recA gene clearly showed the clustering of tun 183 strain within genomovar G4, supporting the monophyly within this genomovar.

Antioxidant, Antimicrobial and the Phenolic Content of Infusion, Decoction and Methanolic Extracts of Thyme and Rosmarinus Species.

BACKGROUND: The plant species Rosmarinus officinalis (RO), Thymus algeriensis (TA) and Thymus capitatus (TC) are widely used in traditional medicine in Tunisia. Their bioactivities have been reported before and particularly referred to their essential oils. The main objective of this work was to assess the phytochemical composition, the antioxidant activity, the antibacterial, antifungal, and cytotoxic potential of these 3 plants. METHOD: The High Performance Liquid Chromatography (HPLC), chemical tests and spectrophotometric methods were used for screening, quantification of phytochemicals and for antioxidant activities. Extracts were evaluated for antibacterial potential by the microdilution method. Antifungal activities were tested using the Poisoned food method against: Aspergillus niger and Aspergillus flavus. The cytotoxic potential of the plant extracts was checked using HCT 116 cultures. RESULTS: Results revealed that aqueous extracts are not toxic compared to the methanolic extracts. Phenolic compounds were detected and these extracts showed excellent antioxidant activity presenting dose-dependent relationship. For antibacterial potential, all tested strains are more sensitive to Thymus extracts than Rosmarinus extracts. However, for antifungal activities, only Rosmarinus extracts inhibited mycelial growth. HPLC analysis allowed the identification of ten compounds with the abundance of gallic acid. CONCLUSION: This study showed important bioactivities (antioxidant, antimicrobial, and safety potential) of the plant species RO, TA and TC used in traditional medicine.

A new QRT-PCR assay designed for the differentiation between elements provided from Agrobacterium sp. in GMOs plant events and natural Agrobacterium sp. bacteria.

The question asked in the present work was how to differentiate between contamination of field samples with and GM plants contained sequences provided from this bacterium in order to avoid false positives in the frame of the detection and the quantification of GMO. For this, new set of primers and corresponding TaqMan Minor Groove Binder (MGB) probes were designed to target Agrobacterium sp. using the tumor-morphology-shooty gene (TMS1). Final standard curves were calculated for each pathogen by plotting the threshold cycle value against the bacterial number (log (colony forming units) per milliliter) via linear regression. The method designed was highly specific and sensitive, with a detection limit of 10CFU/ml. No significant cross-reaction was observed. Results from this study showed that TaqMan real-time PCR, is potentially an effective method for the rapid and reliable quantification of Agrobacterium sp. in samples containing GMO or non GMO samples.