Ekrem Dündar

Phenolics profiles of olive fruits (Olea europaea L.) and oils from Ayvalık, Domat and Gemlik varieties at different ripening stages

Phenolic compounds in olive fruit and oils obtained from Ayvalık, Domat and Gemlik olive varieties collected at different ripening periods were evaluated by High Performance Liquid Chromatography (HPLC). Gallic acid and p-cumaric acid were identified for Ayvalık and Domat at each period of ripening, respectively. In addition, gallic acid, p-cumaric acid, sinapinic and apigenin acids were detected in Gemlik olive fruit. Hydroxytyrosol, rutin, oleoropein, luteolin, tyrosol, vanilic acid and gallic acid in Ayvalık olive fruit in all ripening periods were determined. The tyrasol contents varied between 0.18 to 1.57mg/kg. Luteolin contents of olive oils ranged at the levels between 0.12 to 2.28mg/kg. In contrast, oils had the lowest syringic, p-cumaric, chlorogenic and ferulic acids. Vanillic acid contents of oils ranged between 0.08 to 2.38mg/kg.

Crimean-Congo hemorrhagic fever virus in various ixodid tick species from a highly endemic area.

Ticks are major vectors of numerous diseases affecting animals and humans. Presence of various tick-borne pathogens such as Crimean-Congo hemorrhagic fever virus (CCHFV) in various tick species was documented. CCHF is a severe tick-borne illness caused by the CCHFV which is a member of the Nairovirus genus (family: Bunyaviridae). Presence of CCHFV was shown in the most prevalent ixodid tick species such as Hyalomma marginatum and Rhiphicephalus bursa in Turkey. In the present study, prevalence and species diversity of ixodid ticks carrying CCHFV in Tokat province where CCHF is highly endemic were determined by using real-time reverse transcription-polymerase chain reaction (RRT-PCR). As a result, 15 out 745 ticks from various hosts (2%) were found to be CCHFV positive. The CCHFV positive ticks were Haemaphysalis concinna, Hyalomma anatolicum, Hyalomma detritum, Hyalomma marginatum, Hyalomma turanicum, Rhipicephalus bursa, and Rhiphicephalus turanicus indicating that multiple ixodid tick species may contribute to transmission of CCHFV to humans and animals in Turkey.

Species Diversity of Ixodid Ticks Feeding on Humans in Amasya, Turkey: Seasonal Abundance and Presence of Crimean-Congo Hemorrhagic Fever Virus

ABSTRACT Ticks (Acari: Ixodidae) are important pests transmitting tick-borne diseases such as Crimean-Congo hemorrhagic fever (CCHF) to humans. Between 2002 and 2009, numerous CCHF cases were reported in Turkey, including Amasya province. In the current study, species diversity, seasonal abundance of ticks, and presence of CCHF virus (CCHFV) in ticks infesting humans in several districts of Amasya province were determined. In the survey, a total of 2,528 ixodid ticks were collected from humans with tick bite from April to November 2008 and identified to species. Hyalomma marginatum (18.6%), Rhipicephalus bursa (10.3%), Rhipicephalus sanguineus (5.7%), Rhipicephalus (Boophilus) annulatus (2.2%), Dermacentor marginatum (2.5%), Haemaphysalis parva (3.6%), and Ixodes ricinus (1.6%) were the most prevalent species among 26 ixodid tick species infesting humans in Amasya province. Hyalomma franchinii Tonelli & Rondelli, 1932, was a new record for the tick fauna of Turkey. The most abundant species were the members of Hyalomma and Rhipicephalus through summer and declined in fall, whereas relative abundances of Ixodes and Dermacentor ticks were always low on humans in the province. Of 25 Hyalomma tick pools tested, seven pools were CCHFV positive by reverse transcription-polymerase chain reaction. Results indicated diversity of ixodid tick species infesting humans was very high, abundance of ticks changed by season, and ticks infesting humans had potential for transmitting CCHFV.

Nutrition Metabolism Plays an Important Role in the Alternate Bearing of the Olive Tree (Olea europaea L.)

The olive tree (Olea europaea L.) is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between ”on year” and “off year” leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree.

Genome of wild olive and the evolution of oil biosynthesis

Significance We sequenced the genome and transcriptomes of the wild olive (oleaster). More than 50,000 genes were predicted, and evidence was found for two relatively recent whole-genome duplication events, dated at approximately 28 and 59 Mya. Whole-genome sequencing, as well as gene expression studies, provide further insights into the evolution of oil biosynthesis, and will aid future studies aimed at further increasing the production of olive oil, which is a key ingredient of the healthy Mediterranean diet and has been granted a qualified health claim by the US Food and Drug Administration. Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.

Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayvalık.

BackgroundOlive cDNA libraries to isolate candidate genes that can help enlightening the molecular mechanism of periodicity and / or fruit production were constructed and analyzed. For this purpose, cDNA libraries from the leaves of trees in “on year” and in “off year” in July (when fruits start to appear) and in November (harvest time) were constructed. Randomly selected 100 positive clones from each library were analyzed with respect to sequence and size. A fruit-flesh cDNA library was also constructed and characterized to confirm the reliability of each library’s temporal and spatial properties.ResultsQuantitative real-time RT-PCR (qRT-PCR) analyses of the cDNA libraries confirmed cDNA molecules that are associated with different developmental stages (e. g. “on year” leaves in July, “off year” leaves in July, leaves in November) and fruits. Hence, a number of candidate cDNAs associated with “on year” and “off year” were isolated. Comparison of the detected cDNAs to the current EST database of GenBank along with other non - redundant databases of NCBI revealed homologs of previously described genes along with several unknown cDNAs. Of around 500 screened cDNAs, 48 cDNA elements were obtained after eliminating ribosomal RNA sequences. These independent transcripts were analyzed using BLAST searches (cutoff E-value of 1.0E-5) against the KEGG and GenBank nucleotide databases and 37 putative transcripts corresponding to known gene functions were annotated with gene names and Gene Ontology (GO) terms. Transcripts in the biological process were found to be related with metabolic process (27%), cellular process (23%), response to stimulus (17%), localization process (8.5%), multicellular organismal process (6.25%), developmental process (6.25%) and reproduction (4.2%).ConclusionsA putative P450 monooxigenase expressed fivefold more in the “on year” than that of “off year” leaves in July. Two putative dehydrins expressed significantly more in “on year” leaves than that of “off year” leaves in November. Homologs of UDP – glucose epimerase, acyl - CoA binding protein, triose phosphate isomerase and a putative nuclear core anchor protein were significant in fruits only, while a homolog of an embryo binding protein / small GTPase regulator was detected in “on year” leaves only. One of the two unknown cDNAs was specific to leaves in July while the other was detected in all of the libraries except fruits. KEGG pathway analyses for the obtained sequences correlated with essential metabolisms such as galactose metabolism, amino sugar and nucleotide sugar metabolisms and photosynthesis. Detailed analysis of the results presents candidate cDNAs that can be used to dissect further the genetic basis of fruit production and / or alternate bearing which causes significant economical loss for olive growers.

Stachys vuralii (Lamiaceae), a New Species from North Anatolia, Turkey

Stachys vuralii Yıldız, Dirmenci & Akçiçek (Lamiaceae), a new species of the section Eriostomum is described from north Anatolia, Turkey. Detailed illustrations and taxonomic comments are provided along with a table listing the differential characters to the closely related S. byzantina and S. thirkei. Delimitations towards S. byzantina and S. thirkei and existence of putative hybrids are discussed. A phylogenetic analysis using ITS of nuclear ribosomal DNA confirmed the status of S. vuralii as a distinct species. The geographical location of S. vuralii is also presented.

Determination of tocopherol contents of some olive varieties harvested at different ripening periods

The tocopherol contents of oils obtained from Ayvalık, Domat and Gemlik olive varieties harvested at different ripening periods were evaluated by high-performance liquid chromatography. α-Tocopherol was the major tocol detected in all the studied olive oil samples. The oils extracted from olive fruits composed of 130.54–180.43 mg kg–1 α-tocopherol, 0.73–1.61 mg kg–1 β-tocopherol and 0.53–2.28 mg kg–1 γ-tocopherol for Ayvalık oil. The α-, β- and γ-tocopherol contents of Domat oil are in the ranges 95.60–125.56, 0.71–2.70 and 0.49–1.25 mg kg–1 at different harvesting periods. The α-, β- and γ-tocopherol contents of Gemlik olive oil are in the ranges 112.59–168.19, 0.94–1.21 and 0.85–2.40 mg kg–1, respectively. There were significant differences between the oils from cultivars grown in different environments.

Mining olive genome through library sequencing and bioinformatics: Novel sequences and new microsatellites

As one of the initial steps of olive (Olea europaea L.) genome analysis, a small insert genomic DNA library was constructed (digesting olive genomic DNA with SmaI and cloning the digestion products into pUC19 vector) and randomly picked 83 colonies were sequenced. Analysis of the insert sequences revealed 12 clones that have no matches to previously characterized/ confirmed sequence records, and 5 insert sequences that are completely new to any nucleotide database available. The remaining sequences had homology to previously described protein coding genes (13%), ribosomal RNAs/tRNAs (24%), phage DNA (1%) and non-functional sequences (such as “chloroplast DNA”, “Lotus chromosome 3” or “Arabidopsis chromosome 2”) that are confirmed for accuracy but have not been assigned a function (22%). Analysis of the insert sequences employing multiple bioinformatics tools including a secondary structure prediction analysis revealed potential properties such as coding regions, regulatory sequences and microsatellites that helped to extract more information especially about insert sequences with no hits to any sequence record with a described function. Our results and analyses also suggested that olive di-nucleotide microsatellites with a repeat number of three [(XY)3] could be informative and therefore should not be excluded from studies involving microsatellite analysis. Common insights extracted from multiple bioinformatics analyses suggested that the utilization of these tools can be useful for mining genomic sequences.