Erratum

Genetic characterization of grape (Vitis vinifera L.) germplasm from Southeast Anatolia by SSR markersVitis 50 (3), 99-106 (2011

Magnetic properties of triethylene glycol coated CoFe2O4 and Mn0.2Co0.8Fe2O4 NP's synthesized by polyol method

AbstractIn this study, we reported on the structural and magnetic properties of TEG-CoFe2O4 and TEG-Mn0.2Co0.8Fe2O4 nanocomposites produced by the glycothermal reaction (polyol). X-ray diffraction (XRD), transmission electron microscopy (TEM) and vibration sample magnetometer (VSM) analysis have been carried out in order to understand the effect of Mn2+ into CoFe2O4 and it was observed that the addition of Mn2+ tends to reduce the crystallite size, increase the ao (cell parameter) and increase the TB. The presence of adsorbed polyol entities on the surface of the CoFe2O4 and Mn0.2Co0.8Fe2O4 NP's was also proven by TG measurements. FT-IR analysis suggested the presence of adsorbed TEG molecules on the surface of CoFe2O4 and Mn0.2Co0.8Fe2O4 NP's

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.

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.

Natural history of Arabidopsis thaliana and oomycete symbioses

Molecular ecology of plant–microbe interactions has immediate significance for filling a gap in knowledge between the laboratory discipline of molecular biology and the largely theoretical discipline of evolutionary ecology. Somewhere in between lies conservation biology, aimed at protection of habitats and the diversity of species housed within them. A seemingly insignificant wildflower called Arabidopsis thaliana has an important contribution to make in this endeavour. It has already transformed botanical research with deepening understanding of molecular processes within the species and across the Plant Kingdom; and has begun to revolutionize plant breeding by providing an invaluable catalogue of gene sequences that can be used to design the most precise molecular markers attainable for marker-assisted selection of valued traits. This review describes how A. thaliana and two of its natural biotrophic parasites could be seminal as a model for exploring the biogeography and molecular ecology of plant–microbe interactions, and specifically, for testing hypotheses proposed from the geographic mosaic theory of co-evolution

FMR investigations of half-metallic ferromagnets

Thin films of various half-metallic ferromagnets, such as chromium dioxide (CrO 2) and Heusler alloys (Co 2Cr 0.6Fe 0.4Al, Co 2MnSi) have been investigated by ferromagnetic resonance (FMR) technique. It is demonstrated that FMR is a very efficient method to study the nanoscale magnetic properties, in particular to probe the magnetic anisotropy and magnetic inhomogeneities of ferromagnetic thin films. Epitaxial CrO 2 thin films of various thicknesses (25-535 nm) have been deposited on TiO 2(100) substrates by chemical vapor deposition process. It is shown that the magnetic behavior of the CrO 2 films results from a competition between the magnetocrystalline and strain anisotropies. For the ultrathin CrO 2 film (25 nm) the magnetic easy axis switches from the c-direction to the b-direction of the rutile structure. Thin-film Co 2Cr 0.6Fe 0.4Al samples (25 nm or 100 nm) have been grown by DC magnetron sputtering either on unbuffered SiO 2(100) substrates or on the substrates capped by a 50 nm thick V buffer layer. The effects of the vanadium buffer layer and of the film thickness are revealed by FMR studies of the Co 2Cr 0.6Fe 0.4Al samples. Well-resolved multiple spin-wave modes are observed in the unbuffered Co 2Cr 0.6Fe 0.4Al sample with a thickness of 100 nm and the exchange stiffness constant has been estimated. Thin films of Co 2MnSi (4-100 nm) have been grown by DC sputtering on silicon substrates on top of a 42 nm thick V seed layer and capped either by Al 2O 3 or by Co and V layers. A set of the 80 nm thick films has been annealed at different temperatures in the range of 425-550°C. FMR studies of the Co 2MnSi samples shows that at the fixed annealing temperature (450°C) the highest magnetization is observed in the sample with a thickness of 61 nm, while the thicker samples (100 nm) reveal not only a lower magnetization but greater magnetic inhomogeneity as well. An annealing treatment at T ≥ 450°C is essential to obtain higher magnetization as well as uniform magnetic properties in the Co 2MnSi films. Weak SWR modes have also been observed in the thick Heusler films. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA

Phylogenetic Study of Plant Q-type C2H2 Zinc Finger Proteins and Expression Analysis of Poplar Genes in Response to Osmotic, Cold and Mechanical Stresses

Plant Q-type C2H2 zinc finger transcription factors play an important role in plant tolerance to various environmental stresses such as drought, cold, osmotic stress, wounding and mechanical loading. To carry out an improved analysis of the specific role of each member of this subfamily in response to mechanical loading in poplar, we identified 16 two-fingered Q-type C2H2-predicted proteins from the poplar Phytozome database and compared their phylogenetic relationships with 152 two-fingered Q-type C2H2 protein sequences belonging to more than 50 species isolated from the NR protein database of NCBI. Phylogenetic analyses of these Q-type C2H2 proteins sequences classified them into two groups G1 and G2, and conserved motif distributions of interest were established. These two groups differed essentially in their signatures at the C-terminus of their two QALGGH DNA-binding domains. Two additional conserved motifs, MALEAL and LVDCHY, were found only in sequences from Group G1 or from Group G2, respectively. Functional significance of these phylogenetic divergences was assessed by studying transcript accumulation of six poplar C2H2 Q-type genes in responses to abiotic stresses; but no group specificity was found in any organ. Further expression analyses focused on PtaZFP1 and PtaZFP2, the two genes strongly induced by mechanical loading in poplars. The results revealed that these two genes were regulated by several signalling molecules including hydrogen peroxide and the phytohormone jasmonate

Sense and Antisense Transcripts of Convergent Gene Pairs in Arabidopsis thaliana Can Share a Common Polyadenylation Region

The Arabidopsis genome contains a large number of gene pairs that encode sense and antisense transcripts with overlapping 3′ regions, indicative for a potential role of natural antisense transcription in regulating sense gene expression or transcript processing. When we mapped poly(A) transcripts of three plant gene pairs with long overlapping antisense transcripts, we identified an unusual transcript composition for two of the three gene pairs. Both genes pairs encoded a class of long sense transcripts and a class of short sense transcripts that terminate within the same polyadenylation region as the antisense transcripts encoded by the opposite strand. We find that the presence of the short sense transcript was not dependent on the expression of an antisense transcript. This argues against the assumption that the common termination region for sense and antisense poly(A) transcripts is the result of antisense-specific regulation. We speculate that for some genes evolution may have especially favoured alternative polyadenylation events that shorten transcript length for gene pairs with overlapping sense/antisense transcription, if this reduces the likelihood for dsRNA formation and transcript degradation

RBPDB: a database of RNA-binding specificities

The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. To build RBPDB, we performed a literature search for experimental binding data for all RNA-binding proteins (RBPs) with known RNA-binding domains in four metazoan species (human, mouse, fly and worm). In total, RPBDB contains binding data on 272 RBPs, including 71 that have motifs in position weight matrix format, and 36 sets of sequences of in vivo-bound transcripts from immunoprecipitation experiments. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites. RBPDB is freely available, without registration at http://rbpdb.ccbr.utoronto.ca/