Papers by Stuart Jantzen
A number of genetic resources have been developed for use with the Sablefish (Anoplopoma fimbriai... more A number of genetic resources have been developed for use with the Sablefish (Anoplopoma fimbriai), an economically important wild, and more recently, cultured species in the Pacific Northwest. Combined data from EST library sequencing and Illumina RNAseq has resulted in the addition of 35973 transcripts to the NCBI database. PCR primers were developed to target DNA polymorphisms; 463 primer pairs were developed to target simple-sequence repeats, and 406 primer pairs were developed to detect single-nucleotide polymorphisms (SNPs). Along with 13 previously published microsatellite primer pairs (Aggarwal et al., 2011), these were used with DNA from two Sablefish families (progeny = 83, 96) to construct a first-generation linkage map using LINKMFEX (V2.3); 227 microsatellite and 133 SNP loci were mapped across 25 linkage groups, with a total coverage of 1334 cM in the merged map. BLATing the marker sequences against the Stickleback (Gasterosteus aculeatus) genome (Assembly Feb.2006; UC...
Marine Biotechnology, 2012
Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an impor... more Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an important economic market in North America, South America, and Northern Europe. Infections with sea lice can result in significant production losses. A compilation of genomic information on different genera of sea lice is an important resource for understanding their biology as well as for the study of population genetics and control strategies. We report on over 150,000 expressed sequence tags (ESTs) from five different species Pacific Lepeophtheirus salmonis (49,672 new ESTs in addition to 14,994 previously reported ESTs), Atlantic L. salmonis (57,349 ESTs), Caligus clemensi (14,821 ESTs), Caligus rogercresseyi (32,135 ESTs), and Lernaeocera branchialis (16,441
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2011
Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, i... more Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, incur a wide variety of consequences depending upon host sensitivity. Juvenile pink salmon (Oncorhynchus gorbuscha) migrate from natal freshwater systems to the ocean at a young age relative to other Pacific salmon, and require rapid development of appropriate defenses against marine pathogens. We analyzed the early transcriptomic responses of naïve juvenile pink salmon of sizes 0.3 g (no scales), 0.7 g (mid-scale development) and 2.4 g (scales fully developed) six days after a low-level laboratory exposure to L. salmonis copepodids. All infected size groups exhibited unique transcriptional profiles. Inflammation and inhibition of cell proliferation was identified in the smallest size class (0.3 g), while increased glucose absorption and retention was identified in the middle size class (0.7 g). Tissue-remodeling genes were also up-regulated in both the 0.3 g and 0.7 g size groups. Profiles of the 2.4 g size class indicated cell-mediated immunity and possibly parasite-induced growth augmentation. Understanding a size-based threshold of resistance to L. salmonis is important for fisheries management. This work characterizes molecular responses reflecting the gradual development of innate immunity to L. salmonis between the susceptible (0.3 g) and refractory (2.4 g) pink salmon size classes.
BMC Research Notes, 2011
Background: The increased accessibility of gene expression tools has enabled a wide variety of ex... more Background: The increased accessibility of gene expression tools has enabled a wide variety of experiments utilizing transcriptomic analyses. As these tools increase in prevalence, the need for improved standardization in processing and presentation of data increases, as does the need to guard against interpretation bias. Gene Ontology (GO) analysis is a powerful method of interpreting and summarizing biological functions. However, while there are many tools available to investigate GO enrichment, there remains a need for methods that directly remove redundant terms from enriched GO lists that often provide little, if any, additional information. Findings: Here we present a simple yet novel method called GO Trimming that utilizes an algorithm designed to reduce redundancy in lists of enriched GO categories. Depending on the needs of the user, this method can be performed with variable stringency. In the example presented here, an initial list of 90 terms was reduced to 54, eliminating 36 largely redundant terms. We also compare this method to existing methods and find that GO Trimming, while simple, performs well to eliminate redundant terms in a large dataset throughout the depth of the GO hierarchy. Conclusions: The GO Trimming method provides an alternative to other procedures, some of which involve removing large numbers of terms prior to enrichment analysis. This method should free up the researcher from analyzing overly large, redundant lists, and instead enable the concise presentation of manageable, informative GO lists. The implementation of this tool is freely available at:
Aquaculture, 2011
The ectoparasitic sea louse, Lepeophtheirus salmonis (Krøyer), has caused great concern for both ... more The ectoparasitic sea louse, Lepeophtheirus salmonis (Krøyer), has caused great concern for both wild salmon fisheries and the salmon aquaculture industry. Identifying the population structure of this parasite is important for better understanding its dispersal capabilities and controlling louse infections. Most of the sea lice population studies carried out to date have been focused on Atlantic Ocean L. salmonis where host parasite interactions may be quite different than those in the Pacific Ocean. In this study we examined the genetic population structure of sea lice from 12 Pacific Ocean samples ranging from the Bering Sea to southern Vancouver Island using 27 microsatellite and 87 single nucleotide polymorphisms (SNPs) from 25 loci. Louse samples were analyzed for genetic differentiation among farmed and wild host salmon in addition to temporal differentiation from 2007 to 2009 and spatial differentiation over the entire sampling range. Our analyses failed to resolve significant population structure in L. salmonis for any of these three comparisons. Our results therefore support a hypothesis of high migration and panmixis of L. salmonis within the studied area of the Pacific Ocean.
BMC Genomics, 2010
Background: Salmonids are one of the most intensely studied fish, in part due to their economic a... more Background: Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution.
Scientific animations have tremendous potential as instruments of insight and dissemination. Howe... more Scientific animations have tremendous potential as instruments of insight and dissemination. However, audiences are often unable to determine the degree to which visualizations are informed by scientific evidence. By providing a more detailed account of source use, developers can increase the credibility of animations as scientific tools.
BMC Research Notes, 2011
Background: Atlantic salmon (Salmo salar L.) is an environmentally and economically important org... more Background: Atlantic salmon (Salmo salar L.) is an environmentally and economically important organism and its gene content is reasonably well characterized. From a transcriptional standpoint, it is important to characterize the changes in gene expression over the course of unperturbed early development, from fertilization through to the parr stage. Findings: S. salar samples were taken at 17 time points from 2 to 89 days post fertilization. Total RNA was extracted and cRNA was synthesized and hybridized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected to preliminary data analysis and submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE25938. http://www.ncbi.nlm.nih.gov/geo/query/acc. cgi?acc=GSE25938 Conclusions: Throughout the entire period of development, several thousand genes were found to be differentially regulated. This work represents the trancriptional characterization of a very large geneset that will be extremely valuable in further examination of the transcriptional changes in Atlantic salmon during the first few months of development. The expression profiles can help to annotate salmon genes in addition to being used as references against any number of experimental variables to which developing salmonids might be subjected.
Background: The sablefish (order: Scorpaeniformes) is an economically important species in commer... more Background: The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable.
Conservation Genetics Resources, 2013
We report sets of 19 and 16 microsatellite loci for the examination of the population genetics of... more We report sets of 19 and 16 microsatellite loci for the examination of the population genetics of Boreogadus saida and Arctogadus glacialis, respectively. Six of these loci were developed from a collection of 9,497 expressed sequences from B. saida while the remaining loci were found in the literature and optimized for use in B. saida and A. glacialis. The numbers of alleles observed for each locus ranged from 3 to 33 in B. saida and 1-22 in A. glacialis. Observed heterozygosities ranged from 0.02 to 0.93 in B. saida and 0.17-1.0 in A. glacialis. Species specific differences were observed for the loci providing new tools for the identification of these two morphologically similar arctic gadids. The loci presented here can be used to distinguish between the two species and fill fundamental biological knowledge gaps, thus promoting conservation of these important fishes.
Background: Salmonids are one of the most intensely studied fish, in part due to their economic a... more Background: Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution.
The salmon louse Lepeophtheirus salmonis is a marine ectoparasite of wild and farmed
BMC Genomics, 2014
Background: Salmon species vary in susceptibility to infections with the salmon louse (Lepeophthe... more Background: Salmon species vary in susceptibility to infections with the salmon louse (Lepeophtheirus salmonis). Comparing mechanisms underlying responses in susceptible and resistant species is important for estimating impacts of infections on wild salmon, selective breeding of farmed salmon, and expanding our knowledge of fish immune responses to ectoparasites. Herein we report three L. salmonis experimental infection trials of co-habited Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha, profiling hematocrit, blood cortisol concentrations, and transcriptomic responses of the anterior kidney and skin to the infection.
The phylogenetic relationships among the three subfamilies (Salmoninae, Coregoninae and Thymallin... more The phylogenetic relationships among the three subfamilies (Salmoninae, Coregoninae and Thymallinae) in the Salmonidae have not been addressed extensively at the molecular level. In this study, the whole mitochondrial genomes of two Thymallinae species, Thymallus arcticus and Thymallus thymallus were sequenced, and the published mitochondrial genome sequences of other salmonids were used for Bayesian and maximum-likelihood phylogenetic analyses. These results support an ancestral Coregoninae, branching within the Salmonidae, with Thymallinae as the sister group to Salmoninae.
Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, i... more Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, incur a wide variety of consequences depending upon host sensitivity. Juvenile pink salmon (Oncorhynchus gorbuscha) migrate from natal freshwater systems to the ocean at a young age relative to other Pacific salmon, and require rapid development of appropriate defenses against marine pathogens. We analyzed the early transcriptomic responses of naïve juvenile pink salmon of sizes 0.3 g (no scales), 0.7 g (mid-scale development) and 2.4 g (scales fully developed) six days after a low-level laboratory exposure to L. salmonis copepodids. All infected size groups exhibited unique transcriptional profiles. Inflammation and inhibition of cell proliferation was identified in the smallest size class (0.3 g), while increased glucose absorption and retention was identified in the middle size class (0.7 g). Tissue-remodeling genes were also up-regulated in both the 0.3 g and 0.7 g size groups. Profiles of the 2.4 g size class indicated cell-mediated immunity and possibly parasite-induced growth augmentation. Understanding a size-based threshold of resistance to L. salmonis is important for fisheries management. This work characterizes molecular responses reflecting the gradual development of innate immunity to L. salmonis between the susceptible (0.3 g) and refractory (2.4 g) pink salmon size classes.
Conference Presentations by Stuart Jantzen
This study examines techniques for calling attention to the random movements of two proteins with... more This study examines techniques for calling attention to the random movements of two proteins within a crowded molecular environment, while simultaneously depicting a binding event. Participants (n=148) watched one of five cued animations with or without external overlay highlighting the movements of two binding proteins. We hypothesized that one of the four external cueing treatments (linear path, velocity vectors, ghosting, and heat map) would provide students with important insights about the stochastic nature of molecular events without impeding their ability to follow the binding process. Multiple choice pre and post-test measures were collected using iClickers. While additional cueing strategies did moderate participants' understanding of interactions they failed to correct prior conceptions relating to the stochastic nature of molecular environments.
Uploads
Papers by Stuart Jantzen
Conference Presentations by Stuart Jantzen