Using otoliths to determine daily growth rate and size-selective mortality of juvenile salmon in Nanaimo, British Columbia

Available evidence suggests that interannual variability in the recruitment of Pacific salmon is related to survival in the first few months juveniles spend at sea. Differential growth of smolts during this stage is often thought to result in interannual differences in marine survival, as those fish that grow faster may be less vulnerable to predators or physiological and environmental stressors associated with overwintering (i.e. the 'differential growth' hypothesis). Due to the limitations of traditional techniques, however, only rarely has salmon growth been reliably characterized during the early marine stage. Using juvenile chum salmon (Oncorhynchus keta) collected in the Nanaimo area (1999-2001), I demonstrate that otoliths provide a powerful means of examining the early life history of individual salmon in the field. I used a fluorescent marker to validate the daily periodicity of otolith increment formation, and the formation of a marine entry check. I then back-calculated size-atmarine- entry for each chum smolt to provide individual estimates of early marine growth rate from the summers of 1999 and 2000. Mean daily growth rates were significantly higher, and size-at-entry significantly larger, in 1999 (0.084 cm day"1, 4.48 cm) than in 2000 (0.076 cm day"1, 3.97 cm). 1999 was also a year of significantly higher gut fullness and lower sea surface temperatures. By comparing growth rate frequencies across trips, I found evidence for size-selective mortality of slow growing fish in the midsummer of 2000. These patterns are consistent with the "differential growth hypothesis". In years of unfavourable ocean conditions, juvenile salmon may experience slower growth and higher rates of size-selective predation (possibly due to low food availability or quality). This, in turn, may lead to below average survival and recruitment in these years.Science, Faculty ofEarth, Ocean and Atmospheric Sciences, Department ofGraduat

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data

Abstract Background Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in unaffected individuals as polymorphisms. Affymetrix GeneChip whole genome sampling analysis (WGSA) combined with 100 K single nucleotide polymorphism (SNP) genotyping arrays is one of several microarray-based approaches that are now being used to detect such structural genomic changes. The popularity of this technology and its associated open source data format have resulted in the development of an increasing number of software packages for the analysis of copy number changes using these SNP arrays. Results We evaluated four publicly available software packages for high throughput copy number analysis using synthetic and empirical 100 K SNP array data sets, the latter obtained from 107 mental retardation (MR) patients and their unaffected parents and siblings. We evaluated the software with regards to overall suitability for high-throughput 100 K SNP array data analysis, as well as effectiveness of normalization, scaling with various reference sets and feature extraction, as well as true and false positive rates of genomic copy number variant (CNV) detection. Conclusion We observed considerable variation among the numbers and types of candidate CNVs detected by different analysis approaches, and found that multiple programs were needed to find all real aberrations in our test set. The frequency of false positive deletions was substantial, but could be greatly reduced by using the SNP genotype information to confirm loss of heterozygosity.</p

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data

Background: Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in unaffected individuals as polymorphisms. Affymetrix GeneChip whole genome sampling analysis (WGSA) combined with 100 K single nucleotide polymorphism (SNP) genotyping arrays is one of several microarray-based approaches that are now being used to detect such structural genomic changes. The popularity of this technology and its associated open source data format have resulted in the development of an increasing number of software packages for the analysis of copy number changes using these SNP arrays. Results: We evaluated four publicly available software packages for high throughput copy number analysis using synthetic and empirical 100 K SNP array data sets, the latter obtained from 107 mental retardation (MR) patients and their unaffected parents and siblings. We evaluated the software with regards to overall suitability for high-throughput 100 K SNP array data analysis, as well as effectiveness of normalization, scaling with various reference sets and feature extraction, as well as true and false positive rates of genomic copy number variant (CNV) detection. Conclusion: We observed considerable variation among the numbers and types of candidate CNVs detected by different analysis approaches, and found that multiple programs were needed to find all real aberrations in our test set. The frequency of false positive deletions was substantial, but could be greatly reduced by using the SNP genotype information to confirm loss of heterozygosity.Medical Genetics, Department ofMedicine, Faculty ofPathology and Laboratory Medicine, Department ofOther UBCNon UBCReviewedFacult

The Resurgence of India

Recent economic growth in India has raised its potential to be an economic giant, along with the United States and China. One unique aspect of the Indian economy is that tremendous economic growth has been achieved despite weak infrastructure, resource shortages, and other travails that restrict growth in emerging economies. Recent economic explanations suggest that institutions supporting the economy and economic development are vital to sustained economic growth and may even be more important than infrastructure development. Examining the historic context of the Indian economy, we contend that vital market institutions were always present in India and that economic reforms have unleashed the full potential of these institutions. Using some industry examples, the authors argue that economic policies that strengthen market institutions may be more important compared to conventional policies geared toward infrastructure development

Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation

The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically detectable chromosomal abnormalities are the most frequently recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy-number variants. We studied 100 children with idiopathic mental retardation and normal results of standard chromosomal analysis, by use of whole-genome sampling analysis with Affymetrix GeneChip Human Mapping 100K arrays. We found de novo deletions as small as 178 kb in eight cases, de novo duplications as small as 1.1 Mb in two cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy-number variants as conventional cytogenetic analysis can in people with mental retardation