New neural network classification method for individuals ancestry prediction from SNPs data.

Artificial Neural Network (ANN) algorithms have been widely used to analyse genomic data. Single Nucleotide Polymorphisms(SNPs) represent the genetic variations, the most common in the human genome, it has been shown that they are involved in many genetic diseases, and can be used to predict their development. Developing ANN to handle this type of data can be considered as a great success in the medical world. However, the high dimensionality of genomic data and the availability of a limited number of samples can make the learning task very complicated. In this work, we propose a New Neural Network classification method based on input perturbation. The idea is first to use SVD to reduce the dimensionality of the input data and to train a classification network, which prediction errors are then reduced by perturbing the SVD projection matrix. The proposed method has been evaluated on data from individuals with different ancestral origins, the experimental results have shown the effectiveness of the proposed method. Achieving up to 96.23% of classification accuracy, this approach surpasses previous Deep learning approaches evaluated on the same dataset.

Protective effect of Bacillus amyloliquefaciens against infections of Citrus aurantium seedlings by Phoma tracheiphila.

Isolate TEB1 an antagonistic endophytic bacterium, obtained from citrus leaves and identified as Bacillus amyloliquefaciens by 16S rDNA sequencing, was used for the biological control of mal secco disease of Citrus aurantium seedlings caused by the mitosporic fungus Phoma tracheiphila. The isolate TEB1 exhibited a good in vitro activity against P. tracheiphila in dual cultures as well as with the well diffusion method. C. aurantium seedlings watered with a suspension of TEB1 cells showed a reduction of 53.61 and 48.63% in disease severity and incidence, respectively. A PCR test with specific primers was performed 365 days after inoculation and P. tracheiphila was detected along the whole stem in inoculated control plant while no amplification product was obtained in TEB1 treated seedlings. Molecular analysis of TEB1 revealed a positive amplification of fenD and ituC genes responsible of the biosynthesis of fengycin and iturin lipopeptides, respectively. Moreover, observations by optical microscope showed that TEB1 reduced by 55% the germination of P. tracheiphila conidia and exhibited a marked effect on mycelia structure. Data suggest that lipopeptides produced by the bacterium interact with the cytoplasmic membrane of the fungus causing pore formation. TEB1 appears a potential candidate for the biological control of citrus mal secco disease.

First Report of Mature Citrus Trees Being Affected by Fusarium Wilt in Tunisia.

Citrus is an important crop in Tunisia and over 98% of trees of all varieties are grafted on sour orange rootstock. Since September 2010, unusual wilt symptoms have been observed in Takilsa, Bni-Khaled, and Manzel Bouzalfa fields that eventually caused tree death. The disease was observed on 10- to 25-year-old trees of sweet orange (Citrus sinensis) 'Washington Navel' and on 'Clementine' tangerines (C. tangerina) 'Cassar,' 'Hernandina,' and 'MA3,' all grafted on sour orange (C. aurantum) 'Bigarade Gou Tou.' The most conspicuous symptoms were wilting of sections of the canopy, chlorosis and epinasty of young leaves, and discoloration of vascular tissue. No root rot was observed. The problem was widespread with a disease incidence of 45 to 67%. Similar symptoms were described by Timmer et al. (2) on Mexican lime (C. aurantiifolia) nursery plants and some other species of citrus. Three representative isolates of Fusarium oxysporum Schlechtend.:Fr. from crown were single-spored and identified by the production of characteristic, three- to five-celled, sickle-shaped macroconidia with foot-shaped basal cells, ellipsoid microconidia borne in false heads on short monophialides, and chlamydospores in culture (1). The internal transcribed spacer (ITS) region of rDNA and the elongation factor (TEF 1-α) were amplified with primers ITS1/ITS4 and (TEF1/TEF2), respectively. GenBank accessions of ITS region are KC282838, KC282839, and KC282840, for TEF 1-α region are KF531633, KF537336, and KF537337, showed 99% homology with isolates of F. oxysporum in Fusarium-ID data. Pathogenicity tests were conducted on 7-month-old seedlings of sour orange using 10 plants for each of the three isolates. Prior to inoculation, roots were scraping with a sterile scalpel and plants were dipped in a conidial suspension of F. oxysporum (106 conidia ml-1) for 10 min. Each seedling was planted in a separate pot containing 0.7 liter of sterile soil. Non-inoculated plants with scraped roots dipped in sterile distilled water served as controls. Plants were irrigated and placed in a greenhouse at 24 ± 2°C and 12-h photoperiod. One month after inoculation, leaf chlorosis was observed and 2 months later, 90% of inoculated plants presented a severe wilt. Symptoms on infected plants were similar to those observed in the field. F. oxysporum was successfully re-isolated from the stems, thereby completing Koch's postulates. Genomic DNA was isolated from the re-isolations and PCR amplification of the ITS region was performed with the same primers. There was 100% nucleotide identity with sequences of the original isolates. To our knowledge, this is the first report of fusarium wilt of citrus trees in Tunisia. The pathogen may represent a new form species because previously, the disease was only reported from lime and lemon. References: (1) J. F. Leslie and B. A. Summerell. Page 256 in: The Fusarium Laboratory Manual. Blackwell Publishing Professional, Hoboken, NJ, 2006. (2) L. W. Timmer et al. Phytopathology 72:698, 1982.

Effects of arbuscular mycorrhizal inoculation and fertilization on mycorrhizal Statute of Jacaranda mimosifolia D.Don cultivated in nurseries.

The effects of fertilization and the nature of the inoculum as well as the variation of the dose intake of the latter on the level of Jacaranda mimosifolia D.Don mycorhization were tested. Young plants were treated with two inoculums presenting different origins, compositions and modes of application: one is a commercial product containing Glomus irregulare, and the other is a composite indigenous inoculum resulting from trapping five species of genus Glomus and also from multiplication on mycotrophic plants: leek (Allium porrum L.) and vetch (Vicia sativa L.). For each inoculum, two doses were tested and for each dose of inoculum, four levels of fertilization based on a complete commercial fertilizer (Osmocote) were tested: 0 g/plant, 2 g/plant, 4 g/plant, and 6g/plant. Three repetitions were performed for each combination treatment of inoculum/fertilizer. One-year-old young Jacaranda plants, being about 40 cm high, were cultured under greenhouse in 10/12 cm caliber pots. After six months, all the inoculated plants were mycorrhized. According to endomycorrhizal structures found on their roots, plants receiving doses of composite indigenous inoculum reached a more advanced stage of mycorrhization than those treated with the commercial inoculum. The existence of an interaction effect between the inoculum dose and the level of fertilization on Jacaranda mycorhization rate was excluded. These two parameters of variation were studied as simple effects. The increase in commercial inoculum dose had a significant positive influence on the level of Jacaranda plants mycorrhization (P=0.05). The rate of mycorrhization jumped from 12.69% to 21.92%. Nonetheless, for plants receiving increasing doses of composite indigenous inoculum, the level of mycorrhization has varied randomly. In both instances of inoculum treatments, increasing the dose of fertilizer significantly inhibited endomycorrhizal colonization of Jacaranda roots (P=0.01). Thus, the rate of root colonization decreased from 47.43% to 2.41% for plants receiving the composite indigenous inoculums. It decreased from 32.35% to 3.95% for those treated with the commercial inoculum. Mycorrhization had a positive effect on root dry biomass of Jacaranda, as in the case of unfertilize ave the highest rates of colonization.

Up-regulation of alpha 2 beta 1 integrin cell-surface expression protects A431 cells from epidermal growth factor-induced apoptosis.

High epidermal growth factor (EGF) concentration (10(-8) M) induces inhibition of A431 cell proliferation, resulting in part from an apoptotic process. For some cells escaping this process, proliferation was associated with a decrease in apoptosis. Moreover, these surviving cells displayed marked morphological changes consisting of filopodia formation and cell aggregation. Disrupting cell-cell contacts by lowering extracellular calcium concentration reversed the resistance process, suggesting that apoptosis protection by aggregation may involve intercellular adhesion and cell-cell survival signals probably mediated by calcium-requiring molecules such as integrins. From a panel of integrins tested, only alpha 2 beta 1 integrin cell-surface expression was up-regulated after high apoptotic EGF treatment, and this up-regulation was not observed under a growth-stimulatory EGF concentration (10(-11) M). Double-labeling analysis (alpha 2 beta 1/DNA) implicated alpha 2 beta 1 integrin in the resistance process since 99% of cells that up-regulated alpha 2 beta 1 integrin survived a high dose of EGF. Moreover, the involvement of alpha 2 beta 1 integrin up-regulation in the survival of A431 cells that escape EGF-induced apoptosis was verified using the blocking anti-alpha 2 beta 1 integrin antibody, which was shown to decrease the survival of EGF-stimulated cells. Furthermore, under our culture conditions, alpha 2 beta 1 integrin-dependent cell-cell adhesion can be inhibited without affecting other cell-adhesive interactions, suggesting that alpha 2 beta 1 integrin is involved more directly in cell-cell interaction than in cell-substrate adhesion. Our results provide evidence that EGF-induced up-regulation of alpha 2 beta 1 integrin contributes to the enhancement of cell-cell adhesion, leading to cell aggregate formation, which permits the escape of A431 cells to EGF-induced death by alpha 2 beta 1 integrin signaling.