Genotypic data for nine microsatellite loci for the seagrass Zostera muelleri collections from Lake Macquarie, NSW, Australia

Seagrasses are ecosystem engineers that offer important habitat for a large number of species and provide a range of ecosystem services. Many seagrass ecosystems are dominated by a single species; with research showing that genotypic diversity at fine spatial scales plays an important role in maintaining a range of ecosystem functions. However, for most seagrass species, information on fine-scale patterns of genetic variation in natural populations is lacking. In this study we use a hierarchical sampling design to determine levels of genetic and genotypic diversity at different spatial scales (centimeters, meters, kilometers) in the Australian seagrass Zostera muelleri. Our analysis shows that at fine-spatial scales (< 1 m) levels of genotypic diversity are relatively low (R (Plots) = 0.37 ± 0.06 SE), although there is some intermingling of genotypes. At the site (10's m) and meadow location (km) scale we found higher levels of genotypic diversity (R (sites) = 0.79 ± 0.04 SE; R (Locations) = 0.78 ± 0.04 SE). We found some sharing of genotypes between sites within meadows, but no sharing of genotypes between meadow locations. We also detected a high level of genetic structuring between meadow locations (FST = 0.278). Taken together, our results indicate that both sexual and asexual reproduction are important in maintaining meadows of Z. muelleri. The dominant mechanism of asexual reproduction appears to occur via localised rhizome extension, although the sharing of a limited number of genotypes over the scale of 10's of metres could also result from the localised dispersal and recruitment of fragments. The large number of unique genotypes at the meadow scale indicates that sexual reproduction is important in maintaining these populations, while the high level of genetic structuring suggests little gene flow and connectivity between our study sites. These results imply that recovery from disturbances will occur through both sexual and asexual regeneration, but the limited connectivity at the landscape-scale implies that recovery at meadow-scale losses is likely to be limited.

Assessing the physiological responses of the gastropod Crepidula fornicata to predicted ocean acidification and warming

Organisms inhabiting coastal waters naturally experience diel and seasonal physico-chemical variations. According to various assumptions, coastal species are either considered to be highly tolerant to environmental changes or, conversely, living at the thresholds of their physiological performance. Therefore, these species are either more resistant or more sensitive, respectively, to ocean acidification and warming. Here, we focused on Crepidula fornicata, an invasive gastropod that colonized bays and estuaries on northwestern European coasts during the 20th century. Small (<3 cm in length) and large (>4.5 cm in length), sexually mature individuals of C. fornicata were raised for 6 months in three different pCO2 conditions (390 µatm, 750 µatm, and 1400 µatm) at four successive temperature levels (10°C, 13°C, 16°C, and 19°C). At each temperature level and in each pCO2 condition, we assessed the physiological rates of respiration, ammonia excretion, filtration and calcification on small and large individuals. Results show that, in general, temperature positively influenced respiration, excretion and filtration rates in both small and large individuals. Conversely, increasing pCO2 negatively affected calcification rates, leading to net dissolution in the most drastic pCO2 condition (1400 µatm) but did not affect the other physiological rates. Overall, our results indicate that C. fornicata can tolerate ocean acidification, particularly in the intermediate pCO2 scenario. Moreover, in this eurythermal species, moderate warming may play a buffering role in the future responses of organisms to ocean acidification.

Somatic mosaicism in Fanconi anemia: Evidence of genotypic reversion in lymphohematopoietic stem cells

Somatic mosaicism has been observed previously in the lymphocyte population of patients with Fanconi anemia (FA). To identify the cellular origin of the genotypic reversion, we examined each lymphohematopoietic and stromal cell lineage in an FA patient with a 2815–2816ins19 mutation in FANCA and known lymphocyte somatic mosaicism. DNA extracted from individually plucked peripheral blood T cell colonies and marrow colony-forming unit granulocyte–macrophage and burst-forming unit erythroid cells revealed absence of the maternal FANCA exon 29 mutation in 74.0%, 80.3%, and 86.2% of colonies, respectively. These data, together with the absence of the FANCA exon 29 mutation in Epstein–Barr virus-transformed B cells and its presence in fibroblasts, indicate that genotypic reversion, most likely because of back mutation, originated in a lymphohematopoietic stem cell and not solely in a lymphocyte population. Contrary to a predicted increase in marrow cellularity resulting from reversion in a hematopoietic stem cell, pancytopenia was progressive. Additional evaluations revealed a partial deletion of 11q in 3 of 20 bone marrow metaphase cells. By using interphase fluorescence in situ hybridization with an MLL gene probe mapped to band 11q23 to identify colony-forming unit granulocyte–macrophage and burst-forming unit erythroid cells with the 11q deletion, the abnormal clone was exclusive to colonies with the FANCA exon 29 mutation. Thus, we demonstrate the spontaneous genotypic reversion in a lymphohematopoietic stem cell. The subsequent development of a clonal cytogenetic abnormality in nonrevertant cells suggests that ex vivo correction of hematopoietic stem cells by gene transfer may not be sufficient for providing life-long stable hematopoiesis in patients with FA.

Mathematical approach for predicting non-negative tristimulus values using the CAT02 chromatic adaptation transform

It has been reported that for certain colour samples, the chromatic adaptation transform CAT02 imbedded in the CIECAM02 colour appearance model predicts corresponding colours with negative tristimulus values (TSVs), which can cause problems in certain applications. To overcome this problem, a mathematical approach is proposed for modifying CAT02. This approach combines a non-negativity constraint for the TSVs of corresponding colours with the minimization of the colour differences between those values for the corresponding colours obtained by visual observations and the TSVs of the corresponding colours predicted by the model, which is a constrained non-linear optimization problem. By solving the non-linear optimization problem, a new matrix is found. The performance of the CAT02 transform with various matrices including the original CAT02 matrix, and the new matrix are tested using visual datasets and the optimum colours. Test results show that the CAT02 with the new matrix predicted corresponding colours without negative TSVs for all optimum colours and the colour matching functions of the two CIE standard observers under the test illuminants considered. However, the accuracy with the new matrix for predicting the visual data is approximately 1 CIELAB colour difference unit worse compared with the original CAT02. This indicates that accuracy has to be sacrificed to achieve the non-negativity constraint for the TSVs of the corresponding colours.

Maps (pdf) and raster images (tif) of predicted rural land cover suitability under current (2010) conditions and future climate scenarios

This study projects land cover probabilities under climate change for corn (maize), soybeans, spring and winter wheat, winter wheat-soybean double cropping, cotton, grassland and forest across 16 central U.S. states at a high spatial resolution, while also taking into account the influence of soil characteristics and topography. The scenarios span three oceanic-atmospheric global circulation models, three Representative Concentration Pathways, and three time periods (2040, 2070, 2100). As climate change intensifies, the suitable area for all six crops display large northward shifts. Total suitable area for spring wheat, followed by corn and soybeans, diminish. Suitable area for winter wheat and for winter wheat-soybean double-cropping expand northward, while cotton suitability migrates to new, more northerly, locations. Suitability for forest intensifies in the south while yielding to crops in the north; grassland intensifies in the western Great Plains as crop suitability diminishes. To maintain current broad geographic patterns of land use, large changes in the thermal response of crops such as corn would be required. A transition from corn-soybean to winter wheat-soybean doubling cropping is an alternative adaptation.

Using the effect size to model change in preference values from descriptive health status

Objectives: This pilot study describes a modelling approach to translate group-level changes in health status into changes in preference values, by using the effect size (ES) to summarize group-level improvement. Methods: ESs are the standardized mean difference between treatment groups in standard deviation (SD) units. Vignettes depicting varying severity in SD decrements on the SF-12 mental health summary scale, with corresponding symptom severity profiles, were valued by a convenience sample of general practitioners (n = 42) using the rating scale (RS) and time trade-off methods. Translation factors between ES differences and change in preference value were developed for five mental disorders, such that ES from published meta-analyses could be transformed into predicted changes in preference values. Results: An ES difference in health status was associated with an average 0.171-0.204 difference in preference value using the RS, and 0.104-0.158 using the time trade off. Conclusions: This observed relationship may be particular to the specific versions of the measures employed in the present study. With further development using different raters and preference measures, this approach may expand the evidence base available for modelling preference change for economic analyses from existing data.

Measuring natural and sexual selection on breeding values of male display traits in Drosophila serrata

Fundamental to many theories of sexual selection is the expectation that sexual traits, which males use in an attempt to increase mating success, confer costs as well as benefits to individual males. Although evolution of exaggerated male traits is predicted to be halted, by costs applied by natural selection, there is a lack of empirical work devoted to quantitatively establishing whether natural selection opposes sexual selection generated by the preferences of females. In this study, we quantified natural and sexual selection gradients on breeding values for cuticular hydrocarbon (CHC) components of male contact pheromones in Drosophila serrata. As male sexual traits may often be environmentally condition dependent, breeding values were used in the selection analysis to remove the possibility of environmental correlations between the measured trait and fitness biasing estimates of selection. The direction of natural selection was found to oppose sexual selection on a subset of CHCs examined. Opposing natural and sexual selection suggests that further evolution of the male pheromone may in part be limited by costs associated with attractive male CHC blends.

Genotypic and environmentally derived variation in the cell wall composition of Miscanthus in relation to its use as a biomass feedstock

Fifteen Miscanthus genotypes grown in five locations across Europe were analysed to investigate the influence of genetic and environmental factors on cell wall composition. Chemometric techniques combining near infrared reflectance spectroscopy (NIRS) and conventional chemical analyses were used to construct calibration models for determination of acid detergent lignin (ADL), acid detergent fibre (ADF), and neutral detergent fibre (NDF) from sample spectra. Results generated were subsequently converted to lignin, cellulose and hemicellulose content and used to assess the genetic and environmental variation in cell wall composition of Miscanthus and to identify genotypes which display quality traits suitable for exploitation in a range of energy conversion systems. The NIRS calibration models developed were found to predict concentrations with a good degree of accuracy based on the coefficient of determination (R2), standard error of calibration (SEC), and standard error of cross-validation (SECV) values. Across all sites mean lignin, cellulose and hemicellulose values in the winter harvest ranged from 76–115 g kg-1, 412–529 g kg-1, and 235–338 g kg-1 respectively. Overall, of the 15 genotypes Miscanthus x giganteus and Miscanthus sacchariflorus contained higher lignin and cellulose concentrations in the winter harvest. The degree of observed genotypic variation in cell wall composition indicates good potential for plant breeding and matching feedstocks to be optimised to different energy conversion processes.

Genotypic and antimicrobial characterisation of Propionibacterium acnes isolates from surgically excised lumbar disc herniations

The anaerobic skin commensal Propionibacterium acnes is an underestimated cause of human infections and clinical conditions. Previous studies have suggested a role for the bacterium in lumbar disc herniation and infection. To further investigate this, five biopsy samples were surgically excised from each of 64 patients with lumbar disc herniation. P. acnes and other bacteria were detected by anaerobic culture, followed by biochemical and PCR-based identification. In total, 24/64 (38%) patients had evidence of P. acnes in their excised herniated disc tissue. Using recA and mAb typing methods, 52% of the isolates were type II (50% of culture-positive patients), while type IA strains accounted for 28% of isolates (42% patients). Type III (11% isolates; 21% patients) and type IB strains (9% isolates; 17% patients) were detected less frequently. The MIC values for all isolates were lowest for amoxicillin, ciprofloxacin, erythromycin, rifampicin, tetracycline, and vancomycin (≤1mg/L). The MIC for fusidic acid was 1-2 mg/L. The MIC for trimethoprim and gentamicin was 2 to ≥4 mg/L. The demonstration that type II and III strains, which are not frequently recovered from skin, predominated within our isolate collection (63%) suggests that the role of P. acnes in lumbar disc herniation should not be readily dismissed. © 2013 Jess Rollason et al.