Genome of Wild Olive and the Evolution of Oil Biosynthesis

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 similar to 28 and similar to 59 Mya. These events contributed to the expansion and neo-functionalization 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

Molecular and Physiological Analysis of Putative Amino Acid Transporters in Arabidopsis Thaliana

120 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2003.Amino acids are the currency of nitrogen exchange in plants and their physiological and molecular analysis is essential. The objective of this thesis was to identify and analyze plant amino acid transporters using the model plant Arabidopsis thaliana. A valine resistant T-DNA insertion mutant was first analyzed for this purpose. The mutant plant was isolated after screening 4900 T-DNA insertion mutants by growing them on media containing toxic (1 mM) concentration of valine (Chen, 1997). The mutant was also resistant to azaserine suggesting it was valine uptake mutant rather than a loss of feedback inhibition mutant of acetohydroxy acid synthase. Segregation analysis suggested, however, that the T-DNA insertion was not linked to the valine resistance phenotype. The analysis also revealed a poor penetrance of the valine resistance phenotype. Therefore I switched to transposon insertion mutants to analyze plant amino acid transporters. After analyzing a number transposants, I found that ten independent transposons inserted in the same gene, At2g01170. Taking advantage of this opportunity, I used these transposants to analyze the putative amino acid transporter At2g01170. First I examined the GUS expression patterns, and found a completely different GUS staining pattern for each transposant. Detailed analysis revealed that only those transposants having insertions at the 3' end of the gene yield GUS expression. A chemotropism insensitivity was also observed in mutants of At2g01170. The transposants displaying the phenotype also were those having insertions at the same (3') site of the gene, suggesting the importance of this part for the proper function of the gene. Biochemical analysis of At2g01170 was also performed using 14C-labeled amino acid transport and plate growth experiments in yeast, and revealed a bidirectional transport activity for which the gene was named BAT1 (B&barbelow;idirectional A&barbelow;mino Acid T&barbelow;ransporter 1). BAT1 import and export activity appears to be affected by pH in parallel with the age of the yeast cells. Although some bidirectional amino acid transporters from other organisms have been reported (Hosie et al., 2001; Boulland et al., 2003), BAT1 appears to be the first example from plants, and hence represents a new class of amino acid transporters in plants.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Morphological, karyological and phylogenetic evaluation of Cyclotrichium: a piece in the tribe Mentheae puzzle

WOS: 000279624500002The genus Cyclotrichium, a member of the tribe Mentheae subtribe Menthinae (Lamiaceae, Nepetoideae), was analysed with respect to morphological revision, phylogenetic analysis, and cytogenetic properties. All species of the genus were investigated for morphological characters and ITS (internal transcribed spacers) of nrDNA sequence comparison (except C. hausknechtii for ITS). Six members of the genus were also analysed for chromosome numbers. The combined results strongly suggested that Cyclotrichium is a separate genus in Nepetoideae with distinct morphological, phylogenetic, and cytogenetic characteristics. For intrageneric phylogeny of Cyclotrichium, 3 groups were recognised: 1. C. niveum; 2. C. origanifolium; and 3. the remaining 6 species. Clinopodium s.l. and Mentha appear to be most closely related to Cyclotrichium. The phylogenetic relationship of Cyclotrichium with Clinopodium s.l., Mentha, Micromeria, Melissa, and Satureja is discussed. This is the first report on the somatic chromosome numbers of 6 Cyclotrichium species and phylogenetic analysis of Cyclotrichium based on (nrDNA) ITS sequences.TUBITAK [104T293]; Balikesir University; SYNTHESYS [GB-TAF-3087]This research was supported by TUBITAK (grant number 104T293), Balikesir University and the SYNTHESYS program (GB-TAF-3087). Special thanks to the curators of MB, E, G, K, W, WU and Turkish herbaria for letting us examine their specimens. Further thanks to E and Prof. Dr. Bayram Yildiz providing us with plant materials for DNA extraction

Genome-wide identification of alternate bearing-associated microRNAs (miRNAs) in olive (<it>Olea europaea</it> L.)

<p>Abstract</p> <p>Background</p> <p>Alternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year"), followed by a low-yield or even no crop the following year <b>(</b>"off-year"). Several factors may affect the balance between such developmental phase-transition processes. Among them are the microRNA (miRNA), being gene-expression regulators that have been found to be involved as key determinants in several physiological processes.</p> <p>Results</p> <p>Six olive (<it>Olea europaea</it> L. cv. Ayvalik variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves (”on year” and ”off year” leaves in July and in November, respectively) and sequenced by high-throughput Illumina sequencing. The RNA was retrotranscribed and sequenced using the high-throughput Illumina platform. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in the olive. In addition, 38 putative novel miRNAs were discovered in the datasets. Expression of olive tree miRNAs varied greatly among the six libraries, indicating the contribution of diverse miRNA in balancing between reproductive and vegetative phases. Predicted targets of miRNA were categorized into 108 process ontology groups with significance abundance. Among those, potential alternate bearing-associated processes were found, such as development, hormone-mediated signaling and organ morphogenesis. The KEGG analyses revealed that the miRNA-targeted genes are involved in seven main pathways, belonging to carbohydrate metabolism and hormone signal-transduction pathways.</p> <p>Conclusion</p> <p>A comprehensive study on olive miRNA related to alternate bearing was performed. Regulation of miRNA under different developmental phases and tissues indicated that control of nutrition and hormone, together with flowering processes had a noteworthy impact on the olive tree alternate bearing. Our results also provide significant data on the miRNA-fruit development interaction and advance perspectives in the miRNA profile of the olive tree.</p

Enhanced Functionality and Bio-Accessibility of Composite Pomegranate Peel Extract-Enriched Boba Balls

“Boba balls” or pearls have recently gained popularity for beverages or food toppings. “Boba balls” could be developed into functional foods by the encapsulation of bioactive compounds. In this study, gelatin/sodium alginate composite “Boba balls” enriched with pomegranate peel extract (PPE) at different concentrations (0, 1, 2, and 3%) were prepared. They were characterized in terms of physical, rheological, textural, morphological, and sensory properties, as well as in vitro digestion, bio-accessibility, and release kinetic of PPE. Adding PPE improved the “Boba” mix’s viscoelasticity and decreased the “Boba balls”’ hardness. The increasing PPE ratio significantly (p \u3c 0.05) increased the antioxidant capacity and total phenolic content. The addition of PPE preserved the spherical shape of the “Boba balls”, and as the PPE ratio increased, new junction zones were observed in SEM images. The in vitro digestibility of PPE was significantly (p \u3c 0.05) improved by preserving PPE from the mouth and gastric medium, and “Boba balls” showed the highest release and bio-accessibility in the intestinal medium. Consequently, PPE as a by-product could be successfully used at 2% concentration for enhancing the functionality and bio-accessibility of “Boba balls” without affecting sensory properties

Enhanced Functionality and Bio-Accessibility of Composite Pomegranate Peel Extract-Enriched “Boba Balls”

“Boba balls” or pearls have recently gained popularity for beverages or food toppings. “Boba balls” could be developed into functional foods by the encapsulation of bioactive compounds. In this study, gelatin/sodium alginate composite “Boba balls” enriched with pomegranate peel extract (PPE) at different concentrations (0, 1, 2, and 3%) were prepared. They were characterized in terms of physical, rheological, textural, morphological, and sensory properties, as well as in vitro digestion, bio-accessibility, and release kinetic of PPE. Adding PPE improved the “Boba” mix’s viscoelasticity and decreased the “Boba balls”’ hardness. The increasing PPE ratio significantly (p p < 0.05) improved by preserving PPE from the mouth and gastric medium, and “Boba balls” showed the highest release and bio-accessibility in the intestinal medium. Consequently, PPE as a by-product could be successfully used at 2% concentration for enhancing the functionality and bio-accessibility of “Boba balls” without affecting sensory properties

THE MEANING AND EXTENT OF THE HUMANIST REVOLUTION IN RENAISSANCE ITALY

Bu makalenin konusu, özel olarak Rönesans dönemi İtalya'sında ortaya çıkmış olduğu şekliyle hümanist kültürün tanımlanmasıdır. Makalenin genelinde ise tarihsel bağlamındaki tanımı ve boyutları belirlenmeye çalışılan Rönesans hümanist kültürünün, modern dünya ve yaşamın da kurucu öğelerinden biri olduğuna vurgu yapılmaktadır. Filolojik karakterdeki bu tarihsel hümanizm, temelde Antik kültürün dil ve edebiyatının yeni bir coşku ile canlandırılmasıyla gerçekleşeceği umulan daha üstün ve incelmiş bir beğeni düzeyinin, insan zihniyeti ve dünya tasavvurunda iyi yönde bir gelişme sağlayacağı inancına dayanmaktadır. Bu açıdan makalede öncelikle, yeni olma iddiasındaki bu hümanist yaklaşımın kimi ana özelliklerinin Ortaçağ'daki öncülleriyle benzerlikleri ve ayrılıkları üzerinde durulmuş ve hümanistlere özgü olanın ne olduğu ortaya konulmaya çalışılmıştır. Hümanizmin gerçek kaynakları belirlendikten sonra, bunların kültür ve zihniyet üzerindeki iki önemli etkisi Rönesans tarihçiliğinin babası da sayılan Jacob Burckhardt'ın anlatısını takiben belirlenmeye gayret edilmiştir. Son olarak hümanist kültürün nihai aşaması olan, toplumsal ve siyasal alanla bağlantılı olarak yaratılan, modern bakış açılarının da temelinde olan sonuçların oluşumuna değinilmiştirThe subject of this article is the definition of humanist culture as it emerged especially in the Renaissance Italy. In general, the article also emphasizes that the Renaissance humanist culture, whose meaning and extent are tried to be defined in its historical context is one of the founding elements of the modern world and life. This historical humanism in its philological characteristic form was based on the belief that the level of distingue and refined taste that might be actualized with the revitalization of the literature of the ancient culture and languages of Greece and Rome with a new enthusiasm would also provide an improvement in the mentality and the worldview of men. In this regard, first, we dwell on the similarities and differences between some main points of this humanist approach which claims to be new and its antecedents in the Middle Ages and try to reveal what is unique to humanists. After defining the true origins of humanism, we try to determine two crucial effects of these origins on culture and mentality through the narration of Jacob Burckhardt, who is accepted as the father of Renaissance historiography. Lastly, we mention about the foundation of the results, which are the ultimate stages of humanist culture, created in connection with the social and political fields and underlie the modern viewpoint

Differentially expressed transcripts between leaves comparisons.

<p>Transcripts are grouped on the basis of their predicted biological roles.</p

List of differentially expressed transcripts associated to oxidation-reduction metabolism, carbohydrate metabolism, ion transport and homeostasis between “on” and “off” years.

<p>Fold changes were given in log2-based numbers. (-) indicates down-regulation.</p

Comparison of expression levels of selected genes calculated by qRT-PCR.

<p>Gene expressions represented are normalized to the 18S rRNA.</p