Using the ratio of means as the effect size measure in combining results of microarray experiments

Background  

Development of efficient analytic methodologies for combining microarray results is a major challenge in gene expression analysis. The widely used effect size models are thought to provide an efficient modeling framework for this purpose, where the measures of association for each study and each gene are combined, weighted by the standard errors. A significant disadvantage of this strategy is that the quality of different data sets may be highly variable, but this information is usually neglected during the integration. Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference) when sample sizes in each group are small.     

Surface soil chemical and physical patterns in a brigalow–Dawson gum forest,central Queensland

Brigalow (Acacia harpophylla)–Dawson gum (Eucalyptus cambageana) open forests are predominantly supported by solodic soils in central Queensland. This report describes relations between some physical, chemical and morphological properties of surface soils (0–0.10 m) within a virgin brigalow–Dawson gum forest. Soil property gradients were found to radiate horizontally from tree-dominated to non-vegetated areas, indicative of a vegetation-induction process. These reflect the importance of litterfall organic matter in determining soil fertility and soil physical conditions at this site. The decomposition of litterfall is probably responsible for significant increases in soil organic carbon (C), total nitrogen (N) and total sulphur (S) concentrations with increasing vegetation canopy cover. The composition of soil organic matter appears constant across the study area, as similar soil C:N:S ratios were recorded across all vegetation canopy classes. Soil salinity, total phosphorus, mineral nitrogen, cation exchange capacity, exchangeable calcium and exchangeable potassium levels also increased with increasing vegetation canopy cover. Surface soil physical properties were also related to vegetation canopy cover. Bulk density and the < 20 μm dispersion ratio decreased while soil micro-relief and A hor?izon depth increased with increasing vegetation canopy cover. Organic C, through inverse relations with bulk density and the < 20 μm dispersion ratio, appears to enhance soil porosity and aggregate stability, indicating the role of organic matter in the stabilization of larger virgin soil aggregates. The close association between virgin forest and surface soil fertility is seen to have implications for changes in land-use, with a decline in nutrient availability, soil aggregate stability and productivity following forest clearing.     

Applying the genetic theories of ageing to the cytoplasm: cytoplasmic genetic covariation for fitness and lifespan

Two genetic models exist to explain the evolution of ageing – mutation accumulation (MA) and antagonistic pleiotropy (AP). Under MA, a reduced intensity of selection with age results in accumulation of late‐acting deleterious mutations. Under AP, late‐acting deleterious mutations accumulate because they confer beneficial effects early in life. Recent studies suggest that the mitochondrial genome is a major player in ageing. It therefore seems plausible that the MA and AP models will be relevant to genomes within the cytoplasm. This possibility has not been considered previously. We explore whether patterns of covariation between fitness and ageing across 25 cytoplasmic lines, sampled from a population of Drosophila melanogaster, are consistent with the genetic associations predicted under MA or AP. We find negative covariation for fitness and the rate of ageing, and positive covariation for fitness and lifespan. Notably, the direction of these associations is opposite to that typically predicted under AP.     

Comparative use patterns of plant resources in rural areas of South Africa and Zimbabwe

Documentation of use patterns of plants across national boundaries is of relevance in understanding the importance of plant resources to livelihood strategies of different ethnic groups. Plant resources have gained prominence as a natural asset through which families derive food, firewood, income, medicines and timber, enabling particularly poor communities to achieve self-sufficiency. The objective of this study was to investigate the trends in plant usage in South Africa and Zimbabwe. An ethnobotanical investigation was conducted between January 2012 and January 2013 in the Limpopo Province, South Africa and the Midlands Province, Zimbabwe. The study used questionnaire surveys and interviews with a total of 143 participants to explore plant use patterns in South Africa and Zimbabwe. A total of 98 plant species were identified, with Zimbabwe contributing 70 species and 47 species from South Africa. The uses were classified into 15 categories, major use categories were firewood, food plants, medicine and timber. Food plant was a major plant use category in Zimbabwe, contributing 55.1%, followed by medicinal plants (36.8%), firewood (35.7%) and timber (31.6%). In contrast, firewood was the major plant use category in South Africa, contributing 18.4%, followed by food plants (17.3%), medicinal (14.3%) and timber (1.0%). Comparison of the two countries demonstrated remarkable differences in plant use patterns. The results showed that rural households in Zimbabwe were more reliant on plant resources than their counterparts in South Africa. Such a trend could be attributed to a close relationship between the local people, and their natural and agricultural environment leading to a rich knowledge base on plants, plant use and related practices. This comparative analysis strengthens the firm belief that utilization of plant resources represents an important shared heritage, preserved over the centuries, which must be exploited in order to provide further new and useful body of ethnobotanical knowledge.