Plant growth-promoting bacteria (PGPBs) and copper (II) oxide (CuO) nanoparticle ameliorates DNA damage and DNA Methylation in wheat (Triticum aestivum L.) exposed to NaCl stress

Journal of Plant Biochemistry and Biotechnology - Wheat is the second important cereal crop worldwide due to nutritional composition and role in meeting daily energy needs. Salinity is an abiotic...     

Genetic diversity of Amsonia orientalis

Amsonia orientalis Decne. (Apocynaceae), is a rare and threatened plant species which is located only in a constricted area in northeast of Greece and northwest of Turkey in the world. Although phylogenetic analysis depending on nucleotide sequences of genes from different sources (nucleus, mitochondria and chloroplast) became a major tool for classification of plant species, there is still a big lack of information about A. orientalis in the international molecular data bases such as NCBI. In the current study, we phylogenetically analyzed three commonly used molecular markers (18S rDNA, 18S-28S rDNA-ITS region and trnL-F intergenic spacer) from A. orientalis samples collected from Turkey to determine the genetic diversity and also to question the systematic position of A. orientalis. As a result, A. orientalis samples clearly showed close relation with Alyxieae tribe rather than Vinceae. And this result brings the necessity to reconsider the morphological characters that have used to delimit the tribes of Rauvolfioideae.     

Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions

Key message

Development of models to predict genotype by environment interactions, in unobserved environments, using environmental covariates, a crop model and genomic selection. Application to a large winter wheat dataset.

Abstract

Genotype by environment interaction (G*E) is one of the key issues when analyzing phenotypes. The use of environment data to model G*E has long been a subject of interest but is limited by the same problems as those addressed by genomic selection methods: a large number of correlated predictors each explaining a small amount of the total variance. In addition, non-linear responses of genotypes to stresses are expected to further complicate the analysis. Using a crop model to derive stress covariates from daily weather data for predicted crop development stages, we propose an extension of the factorial regression model to genomic selection. This model is further extended to the marker level, enabling the modeling of quantitative trait loci (QTL) by environment interaction (Q*E), on a genome-wide scale. A newly developed ensemble method, soft rule fit, was used to improve this model and capture non-linear responses of QTL to stresses. The method is tested using a large winter wheat dataset, representative of the type of data available in a large-scale commercial breeding program. Accuracy in predicting genotype performance in unobserved environments for which weather data were available increased by 11.1 % on average and the variability in prediction accuracy decreased by 10.8 %. By leveraging agronomic knowledge and the large historical datasets generated by breeding programs, this new model provides insight into the genetic architecture of genotype by environment interactions and could predict genotype performance based on past and future weather scenarios.     

Cold-induced genetic instability in micropropagated Pistacia lentiscus L. plantlets

Genetic stability of plants during in vitro propagation and conservation is one of the important aspects of plant biotechnology. In the present study, micropropagated P. lentiscus L. shoot cultures, which are cultivated for the mastic resin, have been cold stored up to 12 months at 4 °C in the dark for different durations (2, 4, 6, 8, 10 and 12 months) and genetic alterations in cold storage conditions were evaluated. Growth parameters such as proliferation rate, shoot numbers per explant, shoot lengths and shoot forming capacity were also calculated. Since the highest proliferation rate (100 %) was obtained in 6?month-stored shoot cultures without any severe influence of cold stress on proliferation ability, amplified fragment length polymorphism (AFLP) and inter-retrotransposon amplified polymorphism (IRAP) marker systems were used to determine genetic stability in the plantlets after this storage period. Totally, 702 scorable bands were produced by 10 AFLP primer pairs. Genetic similarity value of the non-stored (control) plant and cold-stored clones ranged from 0.66 to 0.84 with a mean of 0.74. In the case of IRAP, 159 bands were produced by 8 IRAP primers. Genetic similarity value of the non-stored plant and cold-stored clones varied from 0.65 to 0.83 and the average genetic similarity value was determined as 0.72. The genetic similarity indices revealed that genetic variability was similar in both techniques. Our results showed that tissue culture and especially cold storage of P. lentiscus L. may result transposons activation, thus could cause genetic instability.     

Variation in Capsidiol Sensitivity between Phytophthora infestans and Phytophthora capsici Is Consistent with Their Host Range

Plants protect themselves against a variety of invading pathogenic organisms via sophisticated defence mechanisms. These responses include deployment of specialized antimicrobial compounds, such as phytoalexins, that rapidly accumulate at pathogen infection sites. However, the extent to which these compounds contribute to species-level resistance and their spectrum of action remain poorly understood. Capsidiol, a defense related phytoalexin, is produced by several solanaceous plants including pepper and tobacco during microbial attack. Interestingly, capsidiol differentially affects growth and germination of the oomycete pathogens Phytophthora infestans and Phytophthora capsici, although the underlying molecular mechanisms remain unknown. In this study we revisited the differential effect of capsidiol on P. infestans and P. capsici, using highly pure capsidiol preparations obtained from yeast engineered to express the capsidiol biosynthetic pathway. Taking advantage of transgenic Phytophthora strains expressing fluorescent markers, we developed a fluorescence-based method to determine the differential effect of capsidiol on Phytophtora growth. Using these assays, we confirm major differences in capsidiol sensitivity between P. infestans and P. capsici and demonstrate that capsidiol alters the growth behaviour of both Phytophthora species. Finally, we report intraspecific variation within P. infestans isolates towards capsidiol tolerance pointing to an arms race between the plant and the pathogens in deployment of defence related phytoalexins.     

Oomycetes, effectors, and all that jazz

Plant pathogenic oomycetes secrete a diverse repertoire of effector proteins that modulate host innate immunity and enable parasitic infection. Understanding how effectors evolve, translocate and traffic inside host cells, and perturb host processes are major themes in the study of oomycete-plant interactions. The last year has seen important progress in the study of oomycete effectors with, notably, the elucidation of the 3D structures of five RXLR effectors, and novel insights into how cytoplasmic effectors subvert host cells. In this review, we discuss these and other recent advances and highlight the most important open questions in oomycete effector biology.     

Estrogen-induced upregulation and 3′-UTR shortening of CDC6

3′-Untranslated region (UTR) shortening of mRNAs via alternative polyadenylation (APA) has important ramifications for gene expression. By using proximal APA sites and switching to shorter 3′-UTRs, proliferating cells avoid miRNA-mediated repression. Such APA and 3′-UTR shortening events may explain the basis of some of the proto-oncogene activation cases observed in cancer cells. In this study, we investigated whether 17 β-estradiol (E2), a potent proliferation signal, induces APA and 3′-UTR shortening to activate proto-oncogenes in estrogen receptor positive (ER+) breast cancers. Our initial probe based screen of independent expression arrays suggested upregulation and 3′-UTR shortening of an essential regulator of DNA replication, CDC6 (cell division cycle 6), upon E2 treatment. We further confirmed the E2- and ER-dependent upregulation and 3′UTR shortening of CDC6, which lead to increased CDC6 protein levels and higher BrdU incorporation. Consequently, miRNA binding predictions and dual luciferase assays suggested that 3′-UTR shortening of CDC6 was a mechanism to avoid 3′-UTR-dependent negative regulations. Hence, we demonstrated CDC6 APA induction by the proliferative effect of E2 in ER+ cells and provided new insights into the complex regulation of APA. E2-induced APA is likely to be an important but previously overlooked mechanism of E2-responsive gene expression.     

Distribution and Local Species Diversity of Freshwater Ostracoda in Relation to Habitat in the Kahramanmaraş Province of Turkey

To understand the relationship between local (alpha) diversity of ostracods and their distribution, 95 different locations were randomly sampled from southern Kahramanmaraş (Turkey) between 7 June and 31 July, 2010. Total of 46 ostracods were encountered from 68 sites. Four alpha diversity indices (Shannon‐Wiener, Menhinick, Brillouin, Margalef) individually quantified higher species diversity and evenness for three types of habitats (limnocrene springs, ponds, stream). Diversity partitioning analyses revealed a significant and substantial beta‐diversity among the sites. First axis of CCA exhibited about 71% of the correlations between species and environmental variables. Water temperature, having either a negative or positive correlation with individual species, was the most influential factor affecting diversity. Altitude did not significantly affect the numbers of species identified from the elevation ranges of 400–600 m and 800–1000 m. At least nine cosmopolitan species from 56 sites had an important contribution to local diversity. Hence, suitability of aquatic (ecological) conditions and habitat types provide better explanations for ostracod diversity than do other abiotic factors such as altitude, pH and salinity. The results may support the Habitat Diversity Hypothesis but the study needs to be expanded to different regions and cannot be generalized at the moment. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Increased 5-Lipoxygenase Immunoreactivity in the Hippocampus of Patients With Alzheimer's Disease

The proinflammatory enzyme 5-lipoxygenase (5-LOX) is upregulated in Alzheimer''s disease (AD), but its localization and association with the hallmark lesions of the disease, β-amyloid (Aβ) plaques and neurofibrillary tangles (NFTs), is unknown. This study examined the distribution and cellular localization of 5-LOX in the medial temporal lobe from AD and control subjects. The spatial relationship between 5-LOX immunoreactive structures and AD lesions was also examined. We report that, in AD subjects, 5-LOX immunoreactivity is elevated relative to controls, and its localization is dependent on the antibody-targeted portion of the 5-LOX amino acid sequence. Carboxy terminus–directed antibodies detected 5-LOX in glial cells and neurons, but less frequently in neurons with dystrophic (NFT) morphology. In contrast, immunoreactivity observed using 5-LOX amino terminus–directed antibodies was virtually absent in neurons and abundant in NFTs, neuritic plaques, and glia. Double-labeling studies showed a close association of 5-LOX–immunoreactive processes and glial cells with Aβ immunoreactive plaques and vasculature and also detected 5-LOX in tau immunoreactive and amyloid containing NFTs. Different immunolabeling patterns with antibodies against carboxy vs amino terminus of 5-LOX may be caused by post-translational modifications of 5-LOX protein in Aβ plaques and NFTs. The relationship between elevated intracellular 5-LOX and hallmark AD pathological lesions provides further evidence that neuroinflammatory pathways contribute to the pathogenesis of AD. (J Histochem Cytochem 56:1065–1073, 2008)