Ingrid Burgetz - Academia.edu (original) (raw)

Papers by Ingrid Burgetz

Canadian aquaculture: R&D review - 2011., 2011

Evolutionary Bioinformatics, 2006

In comparative genomic studies, syntenic groups of homologous sequence in the same order have bee... more In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that orthologous gene copies are more likely to share the same genome positions and share the same gene neighbors. In this study we have defined positional homologs as those that also have homologous neighboring genes and we investigated the usefulness of this distinction for bacterial comparative genomics. We considered the identification of positionaly homologous gene pairs in bacterial genomes using protein and DNA sequence level alignments and found that the positional homologs had on average relatively lower rates of substitution at the DNA level (synonymous substitutions) than duplicate homologs in different genomic locations, regardless of the level of protein sequence divergence (measured with non-synonymous substitution rate). Since gene order conservation can indicate accuracy of orthology assignments, we also considered the effect of imposing certain alignment quality requirements on the sensitivity and specificity of identification of protein pairs by BLAST and FASTA when neighboring information is not available and in comparisons where gene order is not conserved. We found that the addition of a stringency filter based on the second best hits was an efficient way to remove dubious ortholog identifications in BLAST and FASTA analyses. Gene order conservation and DNA sequence homology are useful to consider in comparative genomic studies as they may indicate different orthology assignments than protein sequence homology alone.

Journal of Experimental Biology, 1998

Lactate and phosphocreatine concentrations were monitored in the white muscle of rainbow trout On... more Lactate and phosphocreatine concentrations were monitored in the white muscle of rainbow trout Oncorhynchus mykiss following swimming at 70, 80 and 100 % of critical swimming speed (Ucrit) using 31P-nuclear magnetic resonance (NMR) spectroscopy. Lactate was detected following swimming at all speeds, but its concentration was greatest following swimming at 80 and 100 %Ucrit. Phosphocreatine stores were reduced following swimming at 70 and 80 %Ucrit, but were further depleted following swimming at 100 %Ucrit. Following swimming at 70 and 80 %Ucrit, lactate concentrations were higher in the rostral, relative to the caudal, musculature, whereas phosphocreatine stores were least depleted in the mid, relative to the rostral and caudal, musculature. There were no differences among muscle locations in concentrations of lactate and phosphocreatine following swimming to 100 %Ucrit. Our results indicate that anaerobic metabolism is required to support swimming at speeds equal to and greater th...

The editors would like to thank the members of Working Group 24 for their contributions to the co... more The editors would like to thank the members of Working Group 24 for their contributions to the country reports, and to Mark Higgins (Fisheries and Oceans Canada), S.V. Mikhaylov (TINRO-Center), Norihisa Oseko and Motohiko Sano (Fisheries Research Agency), and Christa Speekmann and Stan Bruntz (U.S. Department of Agriculture) for their contributions to section 3. Laura Hoberecht and Michael Rust are also gratefully acknowledged for constructive comments on the U.S. reports in sections 1 and 2. PICES Scientific Report No.

The extent of anaerobic metabolism required to support sub-maximal swimming below the critical sw... more The extent of anaerobic metabolism required to support sub-maximal swimming below the critical swimming speed ( U ^ in rainbow trout (Oncorhynchus mykiss) was investigated by monitoring the concentration of lactate and phosphocreatine within the white muscle. Trout were swum to 70%, 80% and 100% of U c r i t. Lactate and phosphocreatine were measured using conventional methods, from the white muscle of exercised trout and sockeye salmon (O. nerka), and the chemical shift of inorganic phosphate (Pi) and quantity of phosphocreatine from the muscle were determined using 3 P nuclear magnetic resonance (NMR) spectroscopy. The predictive relationship between lactate and Pi is described by the second-order regression equation: lactate (umols g" tissue)=856.38-306.67*P/+27.80*P/ (r=0.834). The relationship between the phosphocreatine (PCr) estimate obtained using 3 P-NMR and the concentration of intramuscular PCr is described by the equation: PCr (umols g" tissue)=0.562+0.021 *PCr...

Aquaculture Environment Interactions, 2020

Cultured Atlantic salmon Salmo salar are of international socioeconomic value, and the process of... more Cultured Atlantic salmon Salmo salar are of international socioeconomic value, and the process of domestication has resulted in significant behavioural, morphological, and allelic differences from wild populations. Substantial evidence indicates that direct genetic interactions or interbreeding between wild and escaped farmed Atlantic salmon occurs, genetically altering wild salmon and reducing population viability. However, genetic interactions may also occur through ecological mechanisms (e.g. disease, parasites, predation, competition), both in conjunction with and in the absence of interbreeding. Here we examine existing evidence for ecological and non-reproductive genetic interactions between domestic Atlantic salmon and wild populations and the potential use of genetic and genomic tools to resolve these impacts. Our review identified examples of genetic changes resulting from ecological processes, predominately through pathogen or parasite transmission. In addition, many examp...

Aquaculture Environment Interactions, 2019

Genetic interactions (i.e. hybridization) between wild and escaped Atlantic salmon Salmo salar fr... more Genetic interactions (i.e. hybridization) between wild and escaped Atlantic salmon Salmo salar from aquaculture operations have been widely documented, yet the ability to incorporate predictions of risk into aquaculture siting advice has been limited. Here we demonstrate a model-based approach to assessing these potential genetic interactions using a salmon aquaculture expansion scenario in southern Newfoundland as an example. We use an eco-genetic individual-based Atlantic salmon model (IBSEM) parameterized for southern Newfoundland populations, with regional environmental data and field-based estimates of survival, to explore how the proportion of escapees relative to the size of wild populations could potentially influence genetic and demographic changes in wild populations. Our simulations suggest that both demographic decline and genetic change are predicted when the percentage of escapees in a river relative to wild population size is equal to or exceeds 10% annually. The occu...

Canadian Journal of Fisheries and Aquatic Sciences, 2000

We analyzed historical data on the age structure and abundance of males in 22 populations of sock... more We analyzed historical data on the age structure and abundance of males in 22 populations of sockeye salmon (Oncorhynchus nerka) in the Fraser River, British Columbia, to determine geographical and temporal patterns of precocial maturation, its relationship with growth and maturation at other ages, and the value of precocial males as indicators of year-class strength. Most Fraser sockeye males spend two winters at sea before maturing at 3-5 years of age. Precocial males return to spawn at 2, 3, or 4 years of age (ages 0.1, 1.1, and 2.1) and comprised &amp;amp;amp;lt;1 to &amp;amp;amp;gt;33% of male brood year returns among populations. Precocity was lowest among populations that spawned far upstream and highest among populations spawning to the west of the main Fraser River and was not correlated with migration distance. Precocial maturation was related to growth during the second summer in the ocean to brood line and to brood line abundance. The combination of brood line, abundance, and size of precocial males accounted for more than 75% of the variation in total returns in four populations, suggesting that these variables might be used to predict abundance 1 year in advance.