Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays

Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we introduce and validate a targeted probabilistic method for analyzing probe reliability directly from expression data and independently of the noise source. This provides insights into the various sources of probe-level noise and gives tools to guide probe design.     

The Contribution of Weight Status to Black-White Differences in Mortality

This article examines the contribution of weight status to black-white (B-W) differences in mortality at ages 40–79 using data from the National Health and Nutrition Examination Survey. We measured body mass index (BMI) based on the highest BMI attained and contrasted the contribution of BMI to that of smoking and educational attainment. We estimated both additive and multiplicative models. In addition to estimating regression coefficients we asked what would happen to B-W differences in mortality if blacks had the BMI distribution of whites, the smoking prevalence of whites, or the educational distribution of whites. B-W differences in BMI account for close to 30 percent of the B-W difference in female mortality but only about 1 percent of the B-W difference in male mortality at ages 40–79. In contrast, smoking makes a much larger contribution to the B-W difference in male (17 percent) than female (6 percent) mortality. Differences in educational attainment in turn explain 19 to 25 percent of the B-W mortality difference among men and women, respectively. Our results underscore the importance of two key risk factors as well as educational attainment in generating B-W differences in mortality.     

Genetic variance and covariance patterns for body weight and energy balance characters in an advanced intercross population of mice

We estimated heritabilities and genetic correlations for a suite of 15 characters in five functional groups in an advanced intercross population of over 2000 mice derived from a cross of inbred lines selected for high and low heat loss. Heritabilities averaged 0.56 for three body weights, 0.23 for two energy balance characters, 0.48 for three bone characters, 0.35 for four measures of adiposity, and 0.27 for three organ weights, all of which were generally consistent in magnitude with estimates derived in previous studies. Genetic correlations varied from -0.65 to +0.98, and were higher within these functional groups than between groups. These correlations generally conformed to a priori expectations, being positive in sign for energy expenditure and consumption (+0.24) and negative in sign for energy expenditure and adiposity (-0.17). The genetic correlations of adiposity with body weight at 3, 6, and 12 weeks of age (-0.29, -0.22, -0.26) all were negative in sign but not statistically significant. The independence of body weight and adiposity suggests that this advanced intercross population is ideal for a comprehensive discovery of genes controlling regulation of mammalian adiposity that are distinct from those for body weight.     

Recycling of aluminum can in terms of Life Cycle Inventory (LCI)

Background, Aims and Scope  Life Cycle Assessment is a technique for evaluating the environmental performance of a given product by: identifying and quantifying the energy and raw materials used in its manufacturing process, as well as the emissions of pollutants to water, soil, and air inherent in this production, use and disposal, and evaluating the environmental impact associated with the use of energy and materials and the emissions of pollutants, thus identifying opportunities to improve the system in order to optimize the environmental performance of the product. CETEA (Packaging Technology Center) has conducted a Life Cycle Assessment — LCA study of aluminum can with emphasis in life cycle inventory, collecting data for the reference years 2000–2002. The goal of this paper is to present part of this complete study, focusing the influence of aluminium recycling rate on the Life Cycle Inventory (LCI) of aluminum beverage cans in Brazil. Methods  The adopted methodology was based on the recommendations of SETAC — Society of Environmental Toxicology and Chemistry and the ISO 14040 Standard, approved by the Sub-Committee 05 of the Environmental Administration Technical Committee, TC-207, from ISO — INTERNATIONAL ORGANIZATION FOR STANDARDIZATION [1,2]. Data storage and modeling were performed by employing the PIRA Environmental Management System — PEMS [3]. Results  Taking into account the impact categories adopted in this study, it has been shown that recycling helps to improve the aluminium can environmental profile measured as LCI data. Discussion  For the transformed aluminium products, the recycling rate affects the values of the environmental parameters inventoried, but not in the same proportion, since the contribution of other stages of the product system life cycle and the recycling process remain unchanged, including the yield of this process. In general, the recycling balance is always positive due to the importance of the stages that precede the packaging production and the problem of increasing the municipal waste volume. Conclusions  The advantages of the recycling are obviously concentrated on the inventoried parameters related to the primary aluminum production and to the package disposal. The verified benefits of the recycling increase with the recycling rate enhancement. However, the effects on the inventory do not have the same magnitude of the recycling rate. This happens due to the relative contributions of the other life cycle stages, such as the transportation and sheet or can production. In agreement with the presented results, it is possible to conclude that the aluminum can recycling reduces part of the consumption of natural resources and the emissions associated to the stages previous to the production of the packaging. The parameters specifically related to the stage of aluminum production suffer reduction directly proportional to the increase of the recycling rate. In this way, all of the efforts made to increase the recycling rate will have a positive contribution to the LCI of the aluminum can. Recommendations  It is worth pointing out that LCA studies are iterative and dynamic. The data can always be refined, substituted or complemented with updated information in order to improve the representativeness of the analyzed sector. Perspectives  From this study, the aluminum sector in Brazil is able to quantify the benefits of future actions for environmental improvement of the Brazilian aluminum industry, as well as to contribute technically to Environmental Labeling initiatives regarding aluminum products. ESS-Submission Editor: Alain Dubreuil (dubreuil@nrcan.gc.ca)     

Reproducibility-optimized test statistic for ranking genes in microarray studies

A principal goal of microarray studies is to identify the genes showing differential expression under distinct conditions. In such studies, the selection of an optimal test statistic is a crucial challenge, which depends on the type and amount of data under analysis. While previous studies on simulated or spike-in datasets do not provide practical guidance on how to choose the best method for a given real dataset, we introduce an enhanced reproducibility-optimization procedure, which enables the selection of a suitable gene- anking statistic directly from the data. In comparison with existing ranking methods, the reproducibilityoptimized statistic shows good performance consistently under various simulated conditions and on Affymetrix spike-in dataset. Further, the feasibility of the novel statistic is confirmed in a practical research setting using data from an in-house cDNA microarray study of asthma-related gene expression changes. These results suggest that the procedure facilitates the selection of an appropriate test statistic for a given dataset without relying on a priori assumptions, which may bias the findings and their interpretation. Moreover, the general reproducibilityoptimization procedure is not limited to detecting differential expression only but could be extended to a wide range of other applications as well.     

In vitro repression of n- -acetyl-L-ornithinase synthesis in Escherichia coli

Summary Development of a system for in vitro synthesis of N--acetyl-L-ornithinase of E. coli has made it possible to detect the argR gene product, i.e., the arginine repressor, in cell extracts.     

Fibroblast growth factor 8b causes progressive stromal and epithelial changes in the epididymis and degeneration of the seminiferous epithelium in the testis of transgenic mice

Transgenic (Tg) mice expressing human fibroblast growth factor 8b (FGF8-b) under the probasin promoter (Tg [Pbsn-FGF8] L2-L5Elo; hereafter referred to as FGF8-b-Tg) were shown to produce FGF8-b at high levels in the prostate and epididymis and at lower levels in the testis. The present study examined the effects of FGF8-b expression on the epididymis and testis. In old (age, >6 mo) FGF8-b-Tg mice, epididymides were frequently enlarged, with epithelial and stromal hypercellularity progressing upon aging to epithelial dysplasia and malignant transformation of stroma. In addition, oligospermia, dilatation of the duct, and inflammation were frequently observed in the epididymides. In association with the epididymal changes, some FGF8-b-Tg mice presented a degenerative seminiferous epithelium of the testis. Consistent with this observation, infertile males were found in two FGF8-b-Tg mouse lines. Masson trichrome staining and immunohistochemical analysis of smooth muscle actin, laminin, and androgen receptor revealed that changes in the epididymal stroma closely resembled those previously found in the prostates of the FGF8-b-Tg mice. Genes previously found to be upregulated in the prostate of FGF8-b-Tg mice, such as osteopontin (Spp1) connective tissue growth factor (Ctgf), apolipoprotein D (Apod), and FGF receptor 1c (Fgfr1-c), were also upregulated in the epididymides, suggesting that similar molecular mechanisms were active in both tissues. However, unlike in the prostate, the changes in the epididymal epithelium of the FGF8-b-Tg mice did not progress into invasive carcinoma. The results suggest that prolonged and enhanced FGF signaling induces dramatic changes in the epididymis and testis that lead to infertility in a portion of the FGF8-b-Tg males.     

Titmice are a better indicator of bird density in Northern European than in Western European forests

Population sizes of many birds are declining alarmingly and methods for estimating fluctuations in species’ abundances at a large spatial scale are needed. The possibility to derive indicators from the tendency of specific species to co‐occur with others has been overlooked. Here, we tested whether the abundance of resident titmice can act as a general ecological indicator of forest bird density in European forests. Titmice species are easily identifiable and have a wide distribution, which makes them potentially useful ecological indicators. Migratory birds often use information on the density of resident birds, such as titmice, as a cue for habitat selection. Thus, the density of residents may potentially affect community dynamics. We examined spatio‐temporal variation in titmouse abundance and total bird abundance, each measured as biomass, by using long‐term citizen science data on breeding forest birds in Finland and France. We analyzed the variation in observed forest bird density (excluding titmice) in relation to titmouse abundance. In Finland, forest bird density linearly increased with titmouse abundance. In France, forest bird density nonlinearly increased with titmouse abundance, the association weakening toward high titmouse abundance. We then analyzed whether the abundance (measured as biomass) of random species sets could predict forest bird density better than titmouse abundance. Random species sets outperformed titmice as an indicator of forest bird density only in 4.4% and 24.2% of the random draws, in Finland and France, respectively. Overall, the results suggest that titmice could act as an indicator of bird density in Northern European forest bird communities, encouraging the use of titmice observations by even less‐experienced observers in citizen science monitoring of general forest bird density.