A comparison study reveals important features of agreement and disagreement between summarized DNA and RNA data obtained from renal cell carcinoma

Cytogenetic abnormalities, such as DNA amplifications and deletions, often lead to significant changes in gene expression levels within a chromosomal region. Instead of generating additional DNA copy number data, one method to identify DNA copy number abnormalities has been to search existing gene expression data for regional perturbations in gene expression. However, it is not clear how well this surrogate method performs in the examination of individual tumors and how we can use both DNA and RNA data to identify candidate genes that may be mutated. Here we report a comparison study using summarized DNA and RNA data to identify chromosomal abnormalities in human samples. Forty-four tissue samples from patients diagnosed as having renal cell carcinoma (RCC) were collected, together with 15 normal kidney samples as controls, and for each sample the genome-wide DNA and RNA data were obtained for comparison using Affymetrix 100K SNP and HGU133plus2 gene expression chips, respectively. The DNA and RNA data was summarized by both chromosome arm and cytogenetic banding patterns and compared. The result of this analysis revealed that the two summarized data sets used to identify cytogenetic changes agreed well. However, some differences between the two were also identified. These differences of large-scale gene expression deregulation without evidence of the comparable DNA copy number alterations may be the result of known mechanisms, such as large-scale methylation or chromosome inactivation, or may be the result of some new mechanism of DNA-RNA translation. The usefulness of the combined data set for identifying regions of mutated genes is also discussed.     

Genomic location and characterisation of MIC genes in cattle

Major histocompatibility complex (MHC) class I chain-related (MIC) genes have been previously identified and characterised in human. They encode polymorphic class I-like molecules that are stress-inducible, and constitute one of the ligands of the activating natural killer cell receptor NKG2D. We have identified three MIC genes within the cattle genome, located close to three non-classical MHC class I genes. The genomic position relative to other genes is very similar to the arrangement reported in the pig MHC region. Analysis of MIC cDNA sequences derived from a range of cattle cell lines suggest there may be four MIC genes in total. We have investigated the presence of the genes in distinct and well-defined MHC haplotypes, and show that one gene is consistently present, while configuration of the other three genes appears variable.     

Reductions in entrée energy density increase children's vegetable intake and reduce energy intake

The energy density (ED; kcal/g) of an entrée influences children's energy intake (EI), but the effect of simultaneously changing both ED and portion size of an entrée on preschool children's EI is unknown. In this within-subject crossover study, 3- to 5-year-old children (30 boys, 31 girls) in a daycare facility were served a test lunch once/week for 4 weeks. The amount and type of vegetables and cheeses incorporated into the sauce of a pasta entrée were manipulated to create two versions that varied in ED by 25% (1.6 or 1.2 kcal/g). Across the weeks, each version of the entrée was served to the children in each of two portion sizes (400 or 300 g). Lunch, consumed ad libitum, also included carrots, applesauce, and milk. Decreasing ED of the entrée by 25% significantly (P<0.0001) reduced children's EI of the entrée by 25% (63.1+/-8.3 kcal) and EI at lunch by 17% (60.7+/-8.9 kcal). Increasing the proportion of vegetables in the pasta entrée increased children's vegetable intake at lunch by half of a serving of vegetables (P<0.01). Decreasing portion size of the entrée by 25% did not significantly affect children's total food intake or EI at lunch. Therefore, reducing the ED of a lunch entrée resulted in a reduction in children's EI from the entrée and from the meal in both portion size conditions. Decreasing ED by incorporating more vegetables into recipes is an effective way of reducing children's EI while increasing their vegetable intake.     

Resource Abundance and Invasiveness: A Simple Model

The 'invasiveness' of an alien species depends partly on its ability to become abundant and widespread in its new environment. While competitiveness may be an important component of this ability, so too is the abundance of resource or habitat. First, the local carrying capacity will depend on the local favourability of the habitat, hence the global density will depend on how widespread the habitat is. Second, and more subtly, the local density will also be affected by the global extent of favourable habitat, because of losses occasioned by dispersal when the population redistributes; these losses should be fewer the greater the contiguous area of favourable habitat or the more patches of such habitat across the landscape. Here we describe a model which demonstrates how habitat availability affects an invading speciesèquilibrium abundance, hence its invasiveness. The model shows that local density is likely to be an increasing function of global habitat abundance, and global density to be a non-linear, concave-up function of global habitat abundance. Examples are given to support the model's predictions, taken largely from alien species in New Zealand.     

Lean and Weight Stable: Behavioral Predictors and Psychological Correlates

Objective: To examine behavioral characteristics associated with being lean and weight stable during adulthood. Research Methods and Procedures: Participants included 165 white married couples who were part of a larger longitudinal study. Participants’ height and weight were measured on three occasions at 2‐year intervals. Men and women were classified as being lean and weight stable (the target group) if they had a BMI < 25 at baseline and maintained their weight within 5% of baseline at 2nd and 4th year follow‐up. Individuals not fulfilling these criteria were included in the comparison group. Group differences in background characteristics including childhood weight status, BMI at each occasion, dieting history, and mental and physical health history were examined. In addition, multiple measures of dietary intake and physical activity were obtained and used to predict the likelihood of being in the target group. Results: Men (N = 22) and women (N = 36) in the target group had lower mean BMI scores at each occasion, were less overweight during childhood, were less likely to have dieted in the past year, and rated themselves as being more healthy than men and women in the comparison group. No differences were identified in mental health. Relative to the comparison group, women in the target group reported higher levels of physical activity and higher levels of physical activity among their spouses, and men in the target group reported healthier dietary patterns. Discussion: Results from this study suggest that being lean and weight stable in adulthood is linked to childhood weight status in combination with dietary and activity patterns during adulthood.     

Physical mapping across an avirulence locus of Phytophthora infestans using a highly representative, large-insert bacterial artificial chromosome library

The oomycete plant pathogen Phytophthora infestans is the causal agent of late blight, one of the most devastating diseases of potato worldwide. As part of efforts to clone avirulence (Avr) genes and pathogenicity factors from P. infestans, we have constructed a bacterial artificial chromosome (BAC) library from an isolate containing six Avr genes. The BAC library comprises clones with an average insert size of 98 kb and represents an estimated 10 genome equivalents. A three-dimensional pooling strategy was developed to screen the BAC library for amplified fragment length polymorphism (AFLP) markers, as this type of marker has been extensively used in construction of a P. infestans genetic map. Multiple positive clones were identified for each AFLP marker tested. The pools were used to construct a contig of 11 BAC clones in a region of the P. infestans genome containing a cluster of three avirulence genes. The BAC contig is predicted to encompass the Avr11 locus but mapping of the BAC ends will be required to determine if the Avr3 and Avr10 loci are also present in the BAC contig. These results are an important step towards the positional cloning of avirulence genes from P. infestans, and the BAC library represents a valuable resource for largescale studies of oomycete genome organisation and gene content.     

Effect of calcium ions on the processing of pro-opiomelanocortin by bovine intermediate lobe pro-opiomelanocortin-converting enzyme.

The effect of Ca2+ on the extent and pattern of processing of pro-opiomelanocortin and an N-terminal fragment by a purified pituitary secretory vesicle, soluble aspartic endoprotease, was studied. Ca2+ stimulated the first cleavage of pro-opiomelanocortin by pro-opiomelanocortin-converting enzyme to yield 21-23 kDa adrenocorticotropin and beta-lipotropin, but its effect was minimal. The production of adrenocorticotropin from the 21-23 kDa intermediate was stimulated approximately 2.3-fold in the presence of 10 mM Ca2+, and processing of beta-lipotropin to beta-endorphin was stimulated about 1.3-1.4-fold by 5-10 mM Ca2+. The production of gamma-melanotropin-immunoreactive material from bovine N-pro-opiomelanocortin(1-77) was stimulated approximately 1.3-fold at both 100 microM and 1.5-2.0 mM Ca2+. Further characterization of the gamma-melanotropin-immunoreactive material by HPLC demonstrated that the major products were gamma 3-[Lys]melanotropin and gamma 3-melanotropin at both Ca2+ concentrations. These results indicate that pro-opiomelanocortin-converting enzyme is stimulated by Ca2+.     

L-phenylisopropyladenosine (L-PIA) diminishes halothane anesthetic requirements and decreases noradrenergic neurotransmission in rats

The effect of L-phenylisopropyladenosine (L-PIA), the A1 adenosine agonist, on the depth of anesthesia was investigated in halothane-anesthetized rats. L-PIA treatment reduced the minimum anesthetic concentration (MAC) of halothane that prevented 50% of animals from moving in response to a painful stimulus by 49%. MAC experiments performed with L-PIA given in conjunction with A1 adenosine receptor antagonists which either permeate the blood-brain barrier (8-phenyltheophylline [8-PT] or do not (8-sulphophenyltheophylline [8-So-PT]) indicate that central mechanisms are involved. Noradrenergic neurotransmission was diminished following L-PIA administration in halothane-anesthetized rats in all brain regions. These data suggest that acute L-PIA treatment decreases central noradrenergic neurotransmission and may represent the mechanism for the decrease in halothane dose to achieve an anesthetic endpoint anesthetic response to halothane.