Global transcript analysis of rice leaf and seed using SAGE technology.

We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice (Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (approximately 70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (approximately 3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non-typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion ( approximately 80%) of the abundant tags (> or = 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.

A regime view of the North Atlantic Oscillation and its response to anthropogenic forcing

The distribution of the daily wintertime North Atlantic Oscillation (NAO) index in the 40-yr ECMWF Re-Analysis (ERA-40) is significantly negatively skewed. Dynamical and statistical analyses both suggest that this skewness reflects the presence of two distinct regimes—referred to as “Greenland blocking” and “subpolar jet.” Changes in both the relative occurrence and in the structure of the regimes are shown to contribute to the long-term NAO trend over the ERA-40 period. This is contrasted with the simulation of the NAO in 100-yr control and doubled CO2 integrations of the third climate configuration of the Met Office Unified Model (HadCM3). The model has clear deficiencies in its simulation of the NAO in the control run, so its predictions of future behavior must be treated with caution. However, the subpolar jet regime does become more dominant under anthropogenic forcing and, while this change is small it is clearly statistically significant and does represent a real change in the nature of NAO variability in the model.

Variability of the North Atlantic eddy-driven jet stream

Much of the atmospheric variability in the North Atlantic sector is associated with variations in the eddy-driven component of the zonal flow. Here we present a simple method to specifically diagnose this component of the flow using the low-level wind field (925–700 hpa ). We focus on the North Atlantic winter season in the ERA-40 reanalysis. Diagnostics of the latitude and speed of the eddy-driven jet stream are compared with conventional diagnostics of the North Atlantic Oscillation (NAO) and the East Atlantic (EA) pattern. This shows that the NAO and the EA both describe combined changes in the latitude and speed of the jet stream. It is therefore necessary, but not always sufficient, to consider both the NAO and the EA in identifying changes in the jet stream. The jet stream analysis suggests that there are three preferred latitudinal positions of the North Atlantic eddy-driven jet stream in winter. This result is in very good agreement with the application of a statistical mixture model to the two-dimensional state space defined by the NAO and the EA. These results are consistent with several other studies which identify four European/Atlantic regimes, comprising three jet stream patterns plus European blocking events.

Peptides generated ex vivo from serum proteins by tumor-specific exopeptidases are not useful biomarkers in ovarian cancer

BACKGROUND: The serum peptidome may be a valuable source of diagnostic cancer biomarkers. Previous mass spectrometry (MS) studies have suggested that groups of related peptides discriminatory for different cancer types are generated ex vivo from abundant serum proteins by tumor-specific exopeptidases. We tested 2 complementary serum profiling strategies to see if similar peptides could be found that discriminate ovarian cancer from benign cases and healthy controls. METHODS: We subjected identically collected and processed serum samples from healthy volunteers and patients to automated polypeptide extraction on octadecylsilane-coated magnetic beads and separately on ZipTips before MALDI-TOF MS profiling at 2 centers. The 2 platforms were compared and case control profiling data analyzed to find altered MS peak intensities. We tested models built from training datasets for both methods for their ability to classify a blinded test set. RESULTS: Both profiling platforms had CVs of approximately 15% and could be applied for high-throughput analysis of clinical samples. The 2 methods generated overlapping peptide profiles, with some differences in peak intensity in different mass regions. In cross-validation, models from training data gave diagnostic accuracies up to 87% for discriminating malignant ovarian cancer from healthy controls and up to 81% for discriminating malignant from benign samples. Diagnostic accuracies up to 71% (malignant vs healthy) and up to 65% (malignant vs benign) were obtained when the models were validated on the blinded test set. CONCLUSIONS: For ovarian cancer, altered MALDI-TOF MS peptide profiles alone cannot be used for accurate diagnoses.

Hay strewing, brush harvesting of seed and soil disturbance as tools for the enhancement of botanical diversity in grasslands

Since the middle of the last century agricultural intensification within Europe has led to a drastic decline in the extent of botanically diverse grasslands. Whilst measures to enhance the diversity of agriculturally-improved grasslands are in place, success has often been limited. One of the primary factors limiting success is the paucity of sources of propagules of desirable species in the surrounding landscape. The restoration of two contrasting grassland types lowland hay meadow and chalk grassland) was examined using a replicated block experiment to assess the effectiveness of two methods of seed application (hay strewing and brush harvesting) and two methods of pre-treatment disturbance (power harrowing and turf stripping). The resulting changes in botanical composition were monitored for 4 years. Seed addition by both methods resulted in significant temporal trends in plant species composition and increases in plant species richness, which were further enhanced by disturbance. Power harrowing increased the effectiveness of the seed addition treatments at the lowland hay meadow site. At the chalk grassland site a more severe disturbance created by turf stripping was used and shown to be preferable. Whilst both hay strewing and brush harvesting increased plant species richness, hay strewing was more effective at creating a sward similar to that of the donor site. Soil disturbance and seed application rate at the recipient site and timing of the hay cut at the donor site are all factors to be considered prior to the commencement of restoration management. (c) 2006 Elsevier Ltd. All rights reserved.

Managing arable weeds for biodiversity

As a result of the recent intensification of crop production, the abundance and diversity of UK arable weeds adapted to cultivated land have declined, with an associated reduction in farmland birds. A number of questions need to be addressed when considering how these declines can be reversed. Firstly, can the delivery of crop production and biodiversity be reconciled by spatially separating cropping from designated wildlife areas? A number of subsidised environmental schemes in the UK take this approach and are focused on establishing vegetation cover on uncropped land. However, because of the lack of regular disturbance in these habitats, they are dominated by perennials and they therefore have limited potential for promoting the recovery of annual weed populations. A number of farmland bird species also rely on the provision of resources in field centres, and it is therefore likely that the recovery of their populations will rely on weed management options targeted at the cropped areas of the field. This raises two further questions. Firstly, is it possible to identify beneficial weed species that are relatively poor competitors with the crop and also have biodiversity value? Secondly, are the tools available to manage these species at acceptable levels while controlling pernicious weeds? A number of approaches are being employed to answer these questions, including predicting yield loss from weed competition models and exploiting herbicide selectivity. The further development of these tools is crucial if farmer opposition to managing weeds in crops is to be overcome. (c) 2007 Society of Chemical Industry.