Generation and Analysis of Expressed Sequence Tags from Olea europaea L.

Olive (Olea europaea L.) is an important source of edible oil which was originated in Near-East region. In this study, two cDNA libraries were constructed from young olive leaves and immature olive fruits for generation of ESTs to discover the novel genes and search the function of unknown genes of olive. The randomly selected 3840 colonies were sequenced for EST collection from both libraries. Readable 2228 sequences for olive leaf and 1506 sequences for olive fruit were assembled into 205 and 69 contigs, respectively, whereas 2478 were singletons. Putative functions of all 2752 differentially expressed unique sequences were designated by gene homology based on BLAST and annotated using BLAST2GO. While 1339 ESTs show no homology to the database, 2024 ESTs have homology (under 80%) with hypothetical proteins, putative proteins, expressed proteins, and unknown proteins in NCBI-GenBank. 635 EST's unique genes sequence have been identified by over 80% homology to known function in other species which were not previously described in Olea family. Only 3.1% of total EST's was shown similarity with olive database existing in NCBI. This generated EST's data and consensus sequences were submitted to NCBI as valuable source for functional genome studies of olive

Bayesian Network as a Decision Tool for Predicting ALS Disease

Clinical diagnosis of amyotrophic lateral sclerosis (ALS) is difficult in the early period. But blood tests are less time consuming and low cost methods compared to other methods for the diagnosis. The ALS researchers have been used machine learning methods to predict the genetic architecture of disease. In this study we take advantages of Bayesian networks and machine learning methods to predict the ALS patients with blood plasma protein level and independent personal features. According to the comparison results, Bayesian Networks produced best results with accuracy (0.887), area under the curve (AUC) (0.970) and other comparison metrics. We confirmed that sex and age are effective variables on the ALS. In addition, we found that the probability of onset involvement in the ALS patients is very high. Also, a person’s other chronic or neurological diseases are associated with the ALS disease. Finally, we confirmed that the Parkin level may also have an effect on the ALS disease. While this protein is at very low levels in Parkinson’s patients, it is higher in the ALS patients than all control groups

Proteomic investigation of compatible interaction between wheat and yellow rust

WOS: 000209805600356

Proteome profiling of the compatible interaction between wheat and stripe rust

WOS: 000379860300018Over the last decade, comparative molecular profiling studies between compatible and incompatible plant-pathogen interactions have shown that susceptible response of the host to a pathogen requires factors that promote disease development. In this study, we examined proteome profiles during a compatible interaction between wheat and stripe rust. A 2D-LC system (ProteomeLab PF2D) was used for protein separation and to compare the proteome from infected and control samples. More than 700 protein peaks at each time point were compared between pathogen- and mock-inoculated samples. Selected proteins, with significant differences in abundance were identified by nanoLC-ESI- MS/MS and generated spectra were searched against the wheat protein databases from UniProt, and NCBI and the Puccinia database from The Broad Institute. In total, the identified proteins comprised of 62 % wheat and 38 % Pst proteins. All identified proteins were searched by bioinformatics-based algorithms to detect their subcellular localization and signal peptide motifs which have the potential to catch the candidate effector proteins. The wheat proteins were classified based on their function. Although a compatible interaction, many wheat proteins, such as antioxidants, PRs and cold-responsive proteins, are implicated in defense and stress tolerance. On the pathogen side, 64 proteins were identified, and included some important pathogenicity proteins that can play role in pathogen virulence and suppress the host defense. In addition, we discovered that nine proteins have a signal sequence and three of the hypothetical fungal proteins, PGTG_11681T0, PGTG_07231T0 and CBH50687.1, have been tentatively identified as candidate effectors.TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [109 T293]This study was supported by TUBITAK, COST programme 109 T293 project. We thank Kadir Akan, Aysc Yildiz and Lutfi Cetin for their help during plant inoculation and sampling. We also thank Abdulmecit Gokce and Yavuz Ozturk for their technical support for PF2D as well as Konca Bulut and Rahmi Buyukkeskin for their experimental assistance