Determination of E. gracilis mRNA base composition using high-pressure liquid chromatography.

The purine and pyrimidine bases of E. gracilis have been separated using a high-pressure liquid chromatograph (HPLC). Each base was unambiguously identified by its characteristic elution profile and UV absorption spectrum. This method allows for the study of the base composition of mRNAs altered by pathological processes, exemplified here by the analysis and comparison of mRNAs from zinc sufficient and deficient organisms.     

Snow depth manipulation and its influence on soil frost and water dynamics in a northern hardwood forest

Climate change will likelyresult in warmer winter temperatures leading toless snowfall in temperate forests. Thesechanges may lead to increases in soil freezingbecause of lack of an insulating snow cover andchanges in soil water dynamics during theimportant snowmelt period. In this study, wemanipulated snow depth by removing snow for twowinters, simulating the late development of thesnowpack as may occur with global warming, toexplore the relationships between snow depth,soil freezing, soil moisture, and infiltration.We established four sites, each with two pairedplots, at the Hubbard Brook Experimental Forest(HBEF) in New Hampshire, U.S.A. and instrumentedall eight plots with soil and snow thermistors,frost tubes, soil moisture probes, and soillysimeters. For two winters, we removed snowfrom the designated treatment plots untilFebruary. Snow in the reference plots wasundisturbed. The treatment winters (1997/1998 and1998/1999) were relatively mild, withtemperatures above the seasonal norm and snowdepths below average. Results show the treatedplots accumulated significantly less snow andhad more extensive soil frost than referenceplots. Snow depth was a strong regulator ofsoil temperature and frost depth at all sites.Soil moisture measured by time domainreflectometry probes and leaching volumescollected in lysimeters were lower in thetreatment plots in March and April compared tothe rest of the year. The ratio of leachatevolumes collected in the treatment plots tothat in the reference plots decreased as thesnow ablation seasons progressed. Our data showthat even mild winters with low snowfall,simulated by snow removal, will result inincreased soil freezing in the forests at theHBEF. Our results suggest that a climate shifttoward less snowfall or a shorter duration ofsnow on the ground will produce increases insoil freezing in northern hardwood forests.Increases in soil freezing will haveimplications for changes in soil biogeochemicalprocesses.     

Ouabain sensitivity is linked to ras -transformation in human HOS cells

Mouse cells transformed by the retroviral oncogene v-Ki- ras are significantly more sensitive to the toxic effects of 1mM ouabain than are their nontransformed counterparts. We have extended these findings to a human cell line (HOS). HOS cells (ATCC CRL 1543) are relatively resistant to treatment with 1 microM ouabain while KHOS cells (transformed by Kirsten murine sarcoma virus) are extremely sensitive. Two flat revertant cell lines isolated from the KHOS line and lacking the v- ras gene sequences are resistant to ouabain. This effect may be observed morphologically and can also be demonstrated by dye exclusion and plating efficiency tests. In addition, the toxic effects of ouabain may be rapidly and efficiently quantitated in a 51Cr-release assay. This differential lethality may be used to enrich the proportion of non-transformed revertants in populations of mutagen-treated transformed cells.     

The effect of deprivation on variations in general practitioners' referral rates: a cross sectional study of computerised data on new medical and surgical outpatient referrals in Nottinghamshire.

OBJECTIVE: To determine the effect of deprivation on variations in general practitioners'' referral rates using the Jarman underprivileged area (UPA(8)) score as a proxy measure. DESIGN: Cross sectional survey of new medical and surgical referrals from general practices to hospitals (determined from hospital activity data). SETTING: All of the 183 general practices in Nottinghamshire and all of the 19 hospitals in Trent region. MAIN OUTCOME MEASURES: The relation between the referral rates per 1000 registered patients and the practice population''s UPA(8) score (calculated on the basis of electoral ward), with adjustment for the number of partners, percentage of patients aged over 65 years, and fundholding status of each practice. RESULTS: There was a significant independent association between deprivation, as measured by the UPA(8) score, and high total referral rates and high medical referral rates (P < 0.0001). The UPA(8) score alone explained 23% of the total variation in total referral rates and 32% of the variation in medical referral rates. On multivariate analysis, where partnership size, fundholding status, and percentage of men and women aged over 65 years were included, the UPA(8) score explained 29% and 35% of the variation in total and medical referral rates respectively. CONCLUSION: Of the variables studied, the UPA(8) score was the strongest predictor of variations in referral rates. This association is most likely to be through a link with morbidity, although it could reflect differences in patients'' perceptions, doctors'' behaviour, or the use and provision of services.     

Seed Architecture Shapes Embryo Metabolism in Oilseed Rape

Constrained to develop within the seed, the plant embryo must adapt its shape and size to fit the space available. Here, we demonstrate how this adjustment shapes metabolism of photosynthetic embryo. Noninvasive NMR-based imaging of the developing oilseed rape (Brassica napus) seed illustrates that, following embryo bending, gradients in lipid concentration became established. These were correlated with the local photosynthetic electron transport rate and the accumulation of storage products. Experimentally induced changes in embryo morphology and/or light supply altered these gradients and were accompanied by alterations in both proteome and metabolome. Tissue-specific metabolic models predicted that the outer cotyledon and hypocotyl/radicle generate the bulk of plastidic reductant/ATP via photosynthesis, while the inner cotyledon, being enclosed by the outer cotyledon, is forced to grow essentially heterotrophically. Under field-relevant high-light conditions, major contribution of the ribulose-1,5-bisphosphate carboxylase/oxygenase–bypass to seed storage metabolism is predicted for the outer cotyledon and the hypocotyl/radicle only. Differences between in vitro– versus in planta–grown embryos suggest that metabolic heterogeneity of embryo is not observable by in vitro approaches. We conclude that in vivo metabolic fluxes are locally regulated and connected to seed architecture, driving the embryo toward an efficient use of available light and space.     

Identification of quantitative trait loci contributing to yield and seed quality parameters under terminal drought in barley advanced backcross lines

Drought is a major limiting factor for barley production, especially in the primary areas of its cultivation. Wild barley represents a major source of favourable alleles for increasing the genetic variation for multiple traits including resistance to both biotic and abiotic stresses. We used advanced backcross quantitative trait locus (AB-QTL) analysis of a BC3-doubled haploid population developed between the cultivated parent Brenda (Hordeum vulgare ssp. vulgare) and the wild accession HS584 (H. vulgare ssp. spontaneum) to study the contribution of wild barley in improving various agronomic and seed quality traits under post-anthesis drought. The experiment was carried out at two different locations (IPK, Gatersleben and Nordsaat, Böhnshausen) and terminal drought was imposed by withholding water or spraying with potassium iodide at 10 days after flowering under greenhouse or field conditions, respectively. QTL analysis indicated that wild barley contributed favourably to most of the traits studied under both control and drought conditions. A total of seven hot-spot QTL regions with co-localizing QTL for various traits harboured more than 80 % of the stable QTL detected in the present study. For yield and thousand-grain weight and their respective drought tolerance indices, most of the QTL were derived from Brenda. On the other hand, for traits like seed length and seed nitrogen content, all the QTL were contributed by HS584, the parent having higher trait value. A significantly reduced carbon/nitrogen (C/N) ratio in the selected contrasting inferior lines compared to superior ones suggests that C/N ratio could be a potential parameter for screening not just seed quality parameters but also grain weight performance under terminal drought.     

Extending the coverage of spectral libraries: A neighbor‐based approach to predicting intensities of peptide fragmentation spectra

Searching spectral libraries in MS/MS is an important new approach to improving the quality of peptide and protein identification. The idea relies on the observation that ion intensities in an MS/MS spectrum of a given peptide are generally reproducible across experiments, and thus, matching between spectra from an experiment and the spectra of previously identified peptides stored in a spectral library can lead to better peptide identification compared to the traditional database search. However, the use of libraries is greatly limited by their coverage of peptide sequences: even for well‐studied organisms a large fraction of peptides have not been previously identified. To address this issue, we propose to expand spectral libraries by predicting the MS/MS spectra of peptides based on the spectra of peptides with similar sequences. We first demonstrate that the intensity patterns of dominant fragment ions between similar peptides tend to be similar. In accordance with this observation, we develop a neighbor‐based approach that first selects peptides that are likely to have spectra similar to the target peptide and then combines their spectra using a weighted K‐nearest neighbor method to accurately predict fragment ion intensities corresponding to the target peptide. This approach has the potential to predict spectra for every peptide in the proteome. When rigorous quality criteria are applied, we estimate that the method increases the coverage of spectral libraries available from the National Institute of Standards and Technology by 20–60%, although the values vary with peptide length and charge state. We find that the overall best search performance is achieved when spectral libraries are supplemented by the high quality predicted spectra.