One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Unsteady flow around two square cylinders in staggered arrangements

Paper presented at the 7th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, Turkey, 19-21 July, 2010.In this study, the flow around two staggered square cylinders, placed in a uniform flow field, has been studied. The numerical simulations have been performed by use of a commercial CFD software Fluent. The Reynolds number, defined as a function of cylinder width D, has been chosen as 100 and 200. In the simulations, the dimensionless distance P/D, between the cylinder centers was changed from 2 to 5, and the incidence angle 8 also has been changed from 0' to 90' by 25' increments. In order to evaluate the flow field, isovorticity curves were obtained at different values of dimensionless distance P/D and incidence angle 8. The deviation of the mean drag coefficients and of the square root values of the lift coefficient with P/D and 8 also determined. The power spectrums of the lift coefficient have been obtained for different flow fields.ksb201

Complete down-regulation is not mandatory for good assisted reproductive treatment cycle outcomes

WOS: 000186099600011PubMed ID: 14557012Objective: To determine the implications and predictive value of estradiol concentrations following pituitary down-regulation with gonadotrophin releasing hormone agonists in women undergoing controlled ovarian hyperstimulation for assisted reproductive technology. Study design: A total of 277 patients undergoing ovarian hyperstimulation for intracytoplasmic sperm injection (ICSI) were enrolled into the study and the patients were divided into four groups according to estradiol levels on the initial day of stimulation of which group-A consisted of the patients who had less than or equal to25 pg/ml (n = 90), group-B with levels between 26 and 50 pg/ml (n = 104), group-C with levels between 51 and 75 pg/ml (n = 67) and group-D with levels greater than or equal to76-90 pg/ml (n = 16) and the results were compared. The primary outcome measures included ovarian response and the clinical pregnancy rates. Results: The clinical pregnancy rates in groups-A, 13, C and D were 33.3% (30/90), 26.0% (27/104), 35.8% (24/67), and 25.0% (4/16), respectively, and there was no statistically significant difference (P = 0.482). The mean number of oocytes retrieved in groups were (9.7 +/- 5.8, 10.3 +/- 6.5, 11.0 +/- 6.8, and 12.1 +/- 6.6), respectively (P = 0.453) and the fertilization rates in groups-A, 13, C and D were found to be similar (75, 80,73 and 79%, respectively; P = 0.658). Conclusion: Complete and deep desensitization obviously seems not to be mandatory for successful stimulation in wassisted reproductive technology cycles. (C) 2003 Elsevier Ireland Ltd. All rights reserved

Lipid peroxidation, DNA damage and coenzyme Q10 in lung cancer patients - Markers for risk assessment?

Objectives: Early diagnosis and prevention is very important for lung cancer patients. Previous studies have emphasized that the level of coenzyme Q10 (CoQ10), present primarily in mitochondria, decreases with age and is low in patients with chronic diseases. Our goal was to find out if there is any relationship between lung cancer and CoQ10 and lipid peroxidation levels. Design and Methods: Blood samples from lung cancer patients were collected. Total and oxide CoQ10 levels, 8-OHdG (product of DNA damage), and malondialdehyde (MDA) levels (lipid peroxidation) were analyzed with high performance liquid chromatography (HPLC). Results: The MDA level (P<0.001) and DNA damage rate (8-OHdG) (P<0.001) was higher in cancer patients than in the control group; in contrast, theCoQ10 enzyme level was significantly lower (P<0.001). Conclusion: The results suggest that the aforementioned parameters can be useful for lung cancer risk assessment