Structure of PSI, PSII and antennae complexes from yellow-green alga Xanthonema debile

Photosynthetic carbon fixation by Chromophytes is one of the significant components of a carbon cycle on the Earth. Their photosynthetic apparatus is different in pigment composition from that of green plants and algae. In this work we report structural maps of photosystem I, photosystem II and light harvesting antenna complexes isolated from a soil chromophytic alga Xanthonema debile (class Xanthophyceae). Electron microscopy of negatively stained preparations followed by single particle analysis revealed that the overall structure of Xanthophytes’ PSI and PSII complexes is similar to that known from higher plants or algae. Averaged top-view projections of Xanthophytes’ light harvesting antenna complexes (XLH) showed two groups of particles. Smaller ones that correspond to a trimeric form of XLH, bigger particles resemble higher oligomeric form of XLH.     

Mammalian Ino80 mediates double-strand break repair through its role in DNA end strand resection

Chromatin modifications/remodeling are important mechanisms by which cells regulate various functions through providing accessibility to chromatin DNA. Recent studies implicated INO80, a conserved chromatin-remodeling complex, in the process of DNA repair. However, the precise underlying mechanism by which this complex mediates repair in mammalian cells remains enigmatic. Here, we studied the effect of silencing of the Ino80 subunit of the complex on double-strand break repair in mammalian cells. Comet assay and homologous recombination repair reporter system analyses indicated that Ino80 is required for efficient double-strand break repair. Ino80 association with chromatin surrounding double-strand breaks suggested the direct involvement of INO80 in the repair process. Ino80 depletion impaired focal recruitment of 53BP1 but did not impede Rad51 focus formation, suggesting that Ino80 is required for the early steps of repair. Further analysis by using bromodeoxyuridine (BrdU)-labeled single-stranded DNA and replication protein A (RPA) immunofluorescent staining showed that INO80 mediates 5'-3' resection of double-strand break ends.     

DNA methylation changes associated with risk factors in tumors of the upper aerodigestive tract

Cancers of the upper aerodigestive tract (UADT) are common forms of malignancy associated with tobacco and alcohol exposures, although human papillomavirus and nutritional deficiency are also important risk factors. While somatically acquired DNA methylation changes have been associated with UADT cancers, what triggers these events and precise epigenetic targets are poorly understood. In this study, we applied quantitative profiling of DNA methylation states in a panel of cancer-associated genes to a case-control study of UADT cancers. Our analyses revealed a high frequency of aberrant hypermethylation of several genes, including MYOD1, CHRNA3 and MTHFR in UADT tumors, whereas CDKN2A was moderately hypermethylated. Among differentially methylated genes, we identified a new gene (the nicotinic acetycholine receptor gene) as target of aberrant hypermethylation in UADT cancers, suggesting that epigenetic deregulation of nicotinic acetycholine receptors in non-neuronal tissues may promote the development of UADT cancers. Importantly, we found that sex and age is strongly associated with the methylation states, whereas tobacco smoking and alcohol intake may also influence the methylation levels in specific genes. This study identifies aberrant DNA methylation patterns in UADT cancers and suggests a potential mechanism by which environmental factors may deregulate key cellular genes involved in tumor suppression and contribute to UADT cancers.Key words: DNA methylation, upper aerodigestive tract, cancer, risk factors, biomarkers     

A new genomic resource dedicated to wood formation in Eucalyptus

Background  

Renowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. Thus, there is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs) from genes involved in wood formation in Eucalyptus would provide a valuable resource.     

Root-induced acidification and excess cation uptake by N2-fixing Lupinus albus grown in phosphorus-deficient soil

Plant and Soil - White lupin plants (Lupinus albus L. cv. Kiev) were grown in soil columns under controlled conditions at 20/12?°C (12/12 h) for 76 d to investigate the effect of...     

Zn fertilization improves water use efficiency,grain yield and seed Zn content in chickpea

In a number of the major chickpea-growing areas in the world, rainfed crops of chickpeas are often grown on soils with low available zinc (Zn). Consequently, chickpea crops can be challenged by soil water deficits and Zn deficiency coincidentally during the growing season. The interaction between these stresses was examined in two glasshouse experiments using genotypes differing in Zn efficiency. Water stress was imposed during podding. Increasing the level of Zn resulted in large and significant increases in vegetative growth up to podding. Applying Zn increased grain yields when the plants were well watered, but not under water stress, except for the Zn-efficient and drought-resistant genotype ICC-4958. Harvest indices were generally reduced as the supply of Zn and water increased. Applying Zn increased water use and water use efficiency of chickpea. Yields were reduced by water stress, largely due to fewer pods set per plant. Losses from water stress were greatest at the highest level of Zn, which was attributed to the limited soil volume afforded by the pots and the rapid development of stress in the larger plants grown at adequate levels of Zn. However, at each level of Zn, the loss in yield from water stress tended to be less in a Zn-efficient genotype. The major factor determining the distribution of Zn in the plant was the supply of Zn, while differences due to water stress and genotype were relatively small. Two-thirds of the Zn present in the plant at maturity was accumulated after the start of podding and this was little affected by water stress. The proportion of Zn in the roots of Zn-deficient plants was less than that in Zn-adequate plants. As the Zn supply increased, Zn accumulation was higher in leaves than in the stem and reproductive parts, due to combined effect of both higher Zn concentration and higher dry matter. At maturity, senesced leaves and pod walls had relatively lower concentrations of Zn compared to leaves and pods at the start of podding in all Zn treatments. In contrast, the Zn content in the stem either increased or remained unchanged. At maturity, Zn accumulation in plant organs generally increased with increasing Zn supply, but the largest proportion of Zn was found in the seeds, which is a beneficial nutritional trait for human nutrition.     

Crops and genotypes differ in efficiency of potassium uptake and use

Cultivars with increased efficiency of uptake and utilization of soil nutrients are likely to have positive environmental effects through reduced usage of chemicals in agriculture. This review assesses the available literature on differential uptake and utilization efficiency of K in farming systems. Large areas of agricultural land in the world are deficient in K (e.g. 3/4 of paddy soils in China, 2/3 of the wheatbelt in Southern Australia), with export in agricultural produce (especially hay) and leaching (especially in sandy soils) contributing to lowering of K content in the soil. The capacity of a genotype to grow and yield well in soils low in available K is K efficiency. Genotypic differences in efficiency of K uptake and utilization have been reported for all major economically important plants. The K-efficient phenotype is a complex one comprising a mixture of uptake and utilization efficiency mechanisms. Differential exudation of organic compounds to facilitate release of non-exchangeable K is one of the mechanisms of differential K uptake efficiency. Genotypes efficient in K uptake may have a larger surface area of contact between roots and soil and increased uptake at the root–soil interface to maintain a larger diffusive gradient towards roots. Better translocation of K into different organs, greater capacity to maintain cytosolic K⁺ concentration within optimal ranges and increased capacity to substitute Na⁺ for K⁺ are the main mechanisms underlying K utilization efficiency. Further breeding for increased K efficiency will be dependent on identification of suitable markers and compounding of efficiency mechanisms into locally adapted germplasm.