Molecular genetic markers for abalone aquaculture

Describes the development and mapping of molecular markers in the blacklip and greenlip abalones. By means of a genome scan using a novel selective DNA pooling strategy, markers associated with growth were discovered that could potentially be applied to increase genetic gain in abalone aquaculture, whilst minimising inbreeding.

Genome sequencing: a grin without a cat

In some types of unicellular algae, the chloroplasts have their own nucleus — a legacy of the time when the chloroplast was a free-living cell. The sequence of the genome in one such nucleus is now revealed.

Effect of hydrogen/air flow rates and scan rate on the flame ionisation detection response of phopholipids, and their quantitative and qualitative analysis by Iatroscan (Mark‐6s) TLC‐FID

The combined effect of scan speed, hydrogen and air flow rates on the flame ionization detection (FID) peak response of phospholipid classes has been studied to determine the optimum levels of these parameters. The phospholipid composition of different types of commercial lecithins, as well as lecithins combined with fish oils, has been analyzed by Iatroscan TLC‐FID Mark‐6s under optimized conditions. An air flow rate of 2 L/min, a hydrogen flow rate of 150–160 mL/min, and a scan speed of 30 s/rod seem to be the ideal conditions for scanning phospholipids with complete pyrolysis in the flame in the Mark‐6 model. Increasing the scan speed rapidly decreased the FID response. A hydrogen flow rate as high as 170 mL/min could be used at relatively low air flow rates (&#x003C2 L/min) and the response declined when both air flow rate and hydrogen flow rate increased simultaneously. Both linear and curvilinear relationships had highly significant correlations (p&#x003C0.01) with the sample load. Time course reactions, including the hydrolysis of phosphatidylserine using enzymes, can be successfully monitored by the Iatroscan TLC‐FID Chromarod system.

Genome - wide association study identifies novel breast cancer susceptibility loci

Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r² > 0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P < 10^-7). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P < 0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.

Familial and genomic analyses of postural changes in systolic and diastolic blood pressure

The physiological adaptation to the erect posture involves integrated neural and cardiovascular responses that might be determined by genetic factors. We examined the familial- and individual-specific components of variance for postural changes in systolic and diastolic blood pressure in 767 volunteer nuclear adult families from the Victorian Family Heart Study. In 274 adult sibling pairs, we made a genome-wide scan using 400 markers for quantitative trait loci linked with the postural changes in systolic and diastolic pressures. Overall, systolic pressure did not change on standing, but there was considerable variation in this phenotype (SD=8.1 mm Hg). Familial analyses revealed that 25% of the variance of change in systolic pressure was attributable to genetic factors. In contrast, diastolic pressure increased by 6.3 mm Hg (SD=7.0 mm Hg) on standing and there was no evidence of contributory genetic factors. Multipoint quantitative genome linkage mapping suggested evidence (Z=3.2) of linkage of the postural change in systolic pressure to chromosome 12 but found no genome-wide evidence of linkage for the change in diastolic pressure. These findings suggest that genetic factors determine whether systolic pressure decreases or increases when one stands, possibly as the result of unidentified alleles on chromosome 12. The genetics of postural changes in systolic blood pressure might reflect the general buffering function of the baroreflex; thereby, the predisposition to sudden decreases or increases in systolic pressure might cause postural hypotension or vessel wall disruption, respectively.

Relationship between verbal working memory and the SCAN-C in children with specific language impairment

Purpose: An ongoing concern with the evaluation of auditory processing disorders is the extent that assessment instruments are influenced by higher order cognitive functions. This study examined the relationship between verbal working memory and performance on the Test for Auditory Processing Disorders in Children--Revised (SCAN-C; Keith, 2000b) in children with specific language impairment (SLI) and typically developing (TD) children.

Method: Sixteen children with SLI and 16 TD children ages 8/4 to 11 years participated in the study. The children were presented with the SCAN-C and tests measuring verbal working memory.

Results: Initial comparisons revealed that the SLI group obtained significantly lower scores than the TD group on the SCAN-C. However, after controlling for verbal working memory, significant differences between the 2 groups were no longer observed. Correlational analyses revealed that the composite score from the SCAN-C was related to all tests assessing verbal working memory.

Conclusions: Performance on the SCAN-C may be related to working memory functioning. As a consequence, it is unclear whether difficulty on this task should be viewed as a problem with auditory processing or a problem with verbal working memory.

Insights into bacterial genome composition through variable target GC content profiling

This study presents a new computational method for guanine (G) and cytosine (C), or GC, content profiling based on the idea of multiple resolution sampling (MRS). The benefit of our new approach over existing techniques follows from its ability to locate significant regions without prior knowledge of the sequence, nor the features being sought. The use of MRS has provided novel insights into bacterial genome composition. Key findings include those that are related to the core composition of bacterial genomes, to the identification of large genomic islands (in Enterobacterial genomes), and to the identification of surface protein determinants in human pathogenic organisms (e.g., Staphylococcus genomes). We observed that bacterial surface binding proteins maintain abnormal GC content, potentially pointing to a viral origin. This study has demonstrated that GC content holds a high informational worth and hints at many underlying evolutionary processes. For online Supplementary Material, see www.liebertonline.com.

Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies

Background
Automated candidate gene prediction systems allow geneticists to hone in on disease genes more rapidly by identifying the most probable candidate genes linked to the disease phenotypes under investigation. Here we assessed the ability of eight different candidate gene prediction systems to predict disease genes in intervals previously associated with type 2 diabetes by benchmarking their performance against genes implicated by recent genome-wide association studies.

Results
Using a search space of 9556 genes, all but one of the systems pruned the genome in favour of genes associated with moderate to highly significant SNPs. Of the 11 genes associated with highly significant SNPs identified by the genome-wide association studies, eight were flagged as likely candidates by at least one of the prediction systems. A list of candidates produced by a previous consensus approach did not match any of the genes implicated by 706 moderate to highly significant SNPs flagged by the genome-wide association studies. We prioritized genes associated with medium significance SNPs.

Conclusion
The study appraises the relative success of several candidate gene prediction systems against independent genetic data. Even when confronted with challengingly large intervals, the candidate gene prediction systems can successfully select likely disease genes. Furthermore, they can be used to filter statistically less-well-supported genetic data to select more likely candidates. We suggest consensus approaches fail because they penalize novel predictions made from independent underlying databases. To realize their full potential further work needs to be done on prioritization and annotation of genes.

Analysis of genome-wide association study data using the protein knowledge base

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