Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

Background: Abiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stressadaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses. Results: A total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, shortterm, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues. Conclusions: The large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods

Simple sequence repeat-based assessment of genetic diversity in 'Dimrit' and 'Gemre' grapevine accessions from Turkey

It is widely believed that Turkey has played an important role in the evolution of modern day grapes due to its unique geographical location with close proximity to the regions of grape diversity. Despite this, the rich grape germplasm found in Turkey has not been sufficiently analyzed genetically. In this study, 31 grapevine accessions from 'Dimrit' (or 'Dilmit') and 'Gemre' grape groups were genetically analyzed at eight SSR (microsatellite) loci (VVS2, VVMD5, VVMD7, VVMD24, VVMD27, VVMD28, VrZAG62 and VrZAG79) and for a number of ampeolographic characteristics. These analyses identified sufficient genetic diversity between these two grape groups that, in general, clustered separately in the dendrogram constructed based on the SSR data. However, the ecogeographical distribution and genetic relationship of the genotypes did not show any significant correlation. Two 'Gemre' accessions were determined as genetically identical. In addition, one case of synonym and several cases of homonym genotypes were identified. The results reported here are important first steps towards better characterization of these grape genotypes and would aid future germplasm management and breeding efforts.

Genetic characterization of grape (Vitis vinifera L.) germplasm from Southeast Anatolia by SSR markers

Southeast Anatolia is located in close proximity to the center of origin of grapes and is an important grape producing area of Turkey. The important location of this region for grape genetic diversity together with its diverse ecological conditions may have led to the development of grape germplasm that is unique to this region. However, so far little has been done to genetically analyze this grape germplasm. In this study, we genetically analyzed 55 grape cultivars originating from six different provinces of this region using 14 simple sequence repeat (SSR) loci and a number of ampeolographic characteristics. Based on these analyses, one case of synonymous and four cases of homonymous grape cultivars were identified. The contribution of our results to better characterization of the grape germplasm of the region as well as future germplasm management and breeding efforts is discussed.

PPAR-alpha L162V polymorphism in human hepatocellular carcinoma

Background/aims: Several lines of evidence suggest that peroxisome proliferator-activated receptor alpha may be involved in hepatocarcinogenesis. L162V polymorphism of the peroxisome proliferator-activated receptor alpha gene enhances the transactivation activity of this transcription factor. The aim of this study was to determine the frequency and clinical correlates of peroxisome proliferator-activated receptor alpha L162V polymorphism in hepatitis virus-induced hepatocellular carcinoma. Methods: 90 hepatocellular carcinoma patients diagnosed at Ankara University Gastroenterology Clinic between January 2002 and July 2003 and 80 healthy controls with normal body mass index, blood chemistry and with negative viral serology were included. peroxisome proliferator-activated receptor alpha L162V polymorphism was determined by PCR-RFLP. Results: hepatocellular carcinoma etiologies were as follows: 56 HBV, 12 HBV+HDV, 22 HCV. Eighty-seven patients (97%) were cirrhotic, and 60 patients (67.5%) had advanced tumors. In 83 (92%) of 90 hepatocellular carcinoma patients, gene segment including polymorphic region could be amplified by PCR (50 HBV, 12 HBV+HDV, 21 HCV) and 6 of them (7.2%, all infected with HBV) had L162V polymorphism, while 2 (2.5%) of 80 controls had this polymorphism (p=0.162). This trend became more remarkable when only HBV (HBV+HDV)-infected patients were compared with controls (6/62, 9.7% vs. 2/80, 2.5%, respectively, p=0.071). Five of 6 patients with L162V had advanced disease. Conclusions: Peroxisome proliferator-activated receptor alpha L162V polymorphism tends to occur in HBV-induced epatocellular carcinoma and is absent in HCV-related epatocellular carcinoma. These findings may show clues for the existence of different carcinogenesis mechanisms in these two common etiologies. Frequent occurrence of advanced disease in patients with L162V polymorphism suggests a role for this polymorphism in tumor progression

Parametric amplification with weak-link nonlinearity in superconducting microresonators

Nonlinear kinetic inductance in a high Q superconducting coplanar waveguide microresonator can cause a bifurcation of the resonance curve. Near the critical pumping power and frequency for bifurcation, large parametric gain is observed for signals in the frequency band near resonance. We show experimental results on signal and intermodulation gain which are well described by a theory of the parametric amplification based on a Kerr nonlinearity. Phase dependent gain, or signal squeezing, is verified with a homodyne detection scheme.Comment: Submitted to Physica Scripta, topical issue: Nobel Symposium on Quantum Bits, 2009. 10 pages, 5 figures. Version 2 contains a few new sentences about the current-phase relation of weak link

Yttria-Stabilized Zirconia Assisted Green Electrochemical Preparation of Silicon from Solid Silica in Calcium Chloride Melt

A novel integrated cell with O2-|YSZ|Pt|O2(air) reference and counter electrodes was constructed using a short yttria-stabilized zirconia solid electrolyte (YSZ) tube. Combining with cyclic voltammetry and potentiostatic electrolysis methods, green electrochemical preparation of Si from solid SiO2 in CaCl2 melt at 1173 K was studied via an experimental apparatus containing the novel integrated cell under completely carbon-free conditions; the effect of electrolysis time on the morphology of the Si product was also investigated by scanning electron microscopy with energy dispersive x-ray spectroscopy (SEM-EDS). The results show that the morphology of the product obtained from potentiostatic electrolysis at a low overpotential (− 1.6 V) undergoes an evolution from SiO2 raw powder with different sizes to aggregates of spherical particles and small particles with partial reduction, and then to Si nuclei, and finally to Si wires or flakes. The morphology of electrolytic products has little relation with that of SiO2 raw powder and may be controlled by applying different potentials. Furthermore, the longer the electrolysis time, the more the Si wires grow, and the higher the Si purity overall. It is feasible that the experimental apparatus without the sealed stainless steel reactor and any carbonaceous materials can be used to prepare Si from solid SiO2 in CaCl2 melt and release O2 gas at the same time

Etkileşimli kitap okuma: Korunmaya muhtaç çocukların alıcı ve İfade edici dil becerilerine etkileri

The purpose of this study was to investigate the effectiveness of the "Dialogic Book Reading Program (DBRP)" on the receptive and expressive language skills of 4-5- year-old children who were in need of protection. The study included nine children (4 girls and 5 boys) living in an orphanage and who were identified as developmentally delayed based on the results of Denver Developmental Screening Test II. Children's language skills were pre- and post tested. Results showed that DBRP was effective to improve expressive language skills (number of different words) of participating children. Findings were discussed based on the results of previous research

Optimizations of EFIE and MFIE Combinations in Hybrid Formulations of Conducting Bodies

We present generalized hybrid surface integral-equation formulations for three-dimensional conductors with arbitrary shapes. The proposed formulations are based on flexible applications of the electric-field integral equation and the magnetic field integral equation with varying combinations on different regions of the given objects. As a proof of concept, we demonstrate hybrid formulations using two-region maps and their parametric analysis. We show that hybrid formulations may enable optimal solutions in terms of accuracy and efficiency, in comparison to the conventional CFIE implementations with fixed combination parameters