Ben F Koop

Summary

Affiliation: University of Victoria
Country: Canada

Publications

  1. pmc A salmonid EST genomic study: genes, duplications, phylogeny and microarrays
    Ben F Koop
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W3N5, Canada
    BMC Genomics 9:545. 2008
  2. pmc Genomic resources for sea lice: analysis of ESTs and mitochondrial genomes
    Motoshige Yasuike
    Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5, Canada
    Mar Biotechnol (NY) 14:155-66. 2012
  3. ncbi request reprint Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis
    Ben J G Sutherland
    Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
    BMC Genomics 15:200. 2014
  4. pmc Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka)
    Scott A Pavey
    National Park Service, Katmai National Park PO Box 7, King Salmon, AK 99613, USA
    BMC Ecol 11:31. 2011
  5. pmc Rainbow smelt (Osmerus mordax) genomic library and EST resources
    K R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada
    Mar Biotechnol (NY) 10:487-91. 2008
  6. pmc A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers
    Thomas Moen
    CIGENE Centre of Integrative Genetics, As, Norway
    BMC Genomics 9:223. 2008
  7. pmc A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects
    Jim Thorsen
    Department of Basic Sciences and Aquatic Medicine, Section of Genetics, Norwegian School of Veterinary Science, P O Box 8146 Dep, N 0033 Oslo, Norway
    BMC Genomics 6:50. 2005
  8. pmc Analysis of the conservation of synteny between Fugu and human chromosome 12
    Alexandre Montpetit
    Division of Hematology Oncology, Charles Bruneau Cancer Center, Sainte Justine Hospital, 3175 Cote Ste Catherine, Montreal, QC, H3T 1C5, Canada
    BMC Genomics 4:30. 2003
  9. pmc Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome
    Nicole L Quinn
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
    BMC Genomics 9:404. 2008
  10. pmc High gene expression of inflammatory markers and IL-17A correlates with severity of injection site reactions of Atlantic salmon vaccinated with oil-adjuvanted vaccines
    Stephen Mutoloki
    Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Sciences, Oslo, Norway
    BMC Genomics 11:336. 2010

Collaborators

Detail Information

Publications45

  1. pmc A salmonid EST genomic study: genes, duplications, phylogeny and microarrays
    Ben F Koop
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W3N5, Canada
    BMC Genomics 9:545. 2008
    ..A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish...
  2. pmc Genomic resources for sea lice: analysis of ESTs and mitochondrial genomes
    Motoshige Yasuike
    Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5, Canada
    Mar Biotechnol (NY) 14:155-66. 2012
    ..This report represents the largest genomic resource for any copepod species to date...
  3. ncbi request reprint Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis
    Ben J G Sutherland
    Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
    BMC Genomics 15:200. 2014
    ..gorbuscha, profiling hematocrit, blood cortisol concentrations, and transcriptomic responses of the anterior kidney and skin to the infection...
  4. pmc Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka)
    Scott A Pavey
    National Park Service, Katmai National Park PO Box 7, King Salmon, AK 99613, USA
    BMC Ecol 11:31. 2011
    ..In turn we predict that morphology and expressed genes promote burst swimming in riverine sockeye and continuous swimming in lake-type sockeye...
  5. pmc Rainbow smelt (Osmerus mordax) genomic library and EST resources
    K R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada
    Mar Biotechnol (NY) 10:487-91. 2008
    ..They also facilitate identification of genes important to fish and direct us toward new technologies for other studies in fish biology...
  6. pmc A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers
    Thomas Moen
    CIGENE Centre of Integrative Genetics, As, Norway
    BMC Genomics 9:223. 2008
    ..We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers...
  7. pmc A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects
    Jim Thorsen
    Department of Basic Sciences and Aquatic Medicine, Section of Genetics, Norwegian School of Veterinary Science, P O Box 8146 Dep, N 0033 Oslo, Norway
    BMC Genomics 6:50. 2005
    ..Furthermore, large-scale mapping can utilize highly redundant libraries in genome projects, and hence provide valuable data on the genome structure...
  8. pmc Analysis of the conservation of synteny between Fugu and human chromosome 12
    Alexandre Montpetit
    Division of Hematology Oncology, Charles Bruneau Cancer Center, Sainte Justine Hospital, 3175 Cote Ste Catherine, Montreal, QC, H3T 1C5, Canada
    BMC Genomics 4:30. 2003
    ..The human chromosome 12p12 is frequently deleted in various hematological malignancies and solid tumors, but the actual tumor suppressor gene remains unidentified...
  9. pmc Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome
    Nicole L Quinn
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
    BMC Genomics 9:404. 2008
    ....
  10. pmc High gene expression of inflammatory markers and IL-17A correlates with severity of injection site reactions of Atlantic salmon vaccinated with oil-adjuvanted vaccines
    Stephen Mutoloki
    Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Sciences, Oslo, Norway
    BMC Genomics 11:336. 2010
    ..qPCR was also used to examine the expression of additional genes known to be important in the adaptive immune response...
  11. pmc Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar)
    Morten F Lukacs
    Department of Basic Science and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo, Norway
    BMC Genomics 8:251. 2007
    ..To evaluate if only MHC or also closely linked genes contributed to the observed resistance we ventured into sequencing of the duplicated MHC class I regions of Atlantic salmon...
  12. pmc Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)
    Roy G Danzmann
    Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
    BMC Genomics 9:557. 2008
    ..We describe the organization of the 4R chromosomal segments of the proto-ray-finned fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies with two model species of 3R ray-finned fishes...
  13. pmc Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
    Morten F Lukacs
    Centre for Ecology and Evolutionary Synthesis, Dept of Biology, University of Oslo, Norway
    BMC Genomics 11:154. 2010
    ..A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region...
  14. pmc Comparative genomic analysis of Atlantic salmon, Salmo salar, from Europe and North America
    Krzysztof P Lubieniecki
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
    BMC Genet 11:105. 2010
    ..We set out to construct a linkage map for a North American Atlantic salmon family and to compare this map with the well developed map for European Atlantic salmon...
  15. pmc Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss)
    Ruth B Phillips
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
    BMC Genet 10:46. 2009
    ..The purpose of this study was to integrate the Atlantic salmon's linkage map and karyotype and to compare the chromosome map with that of rainbow trout...
  16. pmc A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.)
    Stuart G Jantzen
    Center for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada
    BMC Res Notes 4:88. 2011
    ..abstract:..
  17. pmc GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets
    Stuart G Jantzen
    Department of Biology and Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada
    BMC Res Notes 4:267. 2011
    ..abstract:..
  18. pmc Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome
    Jong S Leong
    Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada
    BMC Genomics 11:279. 2010
    ....
  19. doi request reprint EST and mitochondrial DNA sequences support a distinct Pacific form of salmon louse, Lepeophtheirus salmonis
    Ryosuke Yazawa
    Centre for Biomedical Research, University of Victoria, P O Box 3020 STN CSC, Victoria, BC, V8W 3N5, Canada
    Mar Biotechnol (NY) 10:741-9. 2008
    ..The genetic differences may help explain apparent differences in pathogenicity and environmental sensitivity documented for the Atlantic and Pacific forms of L. salmonis...
  20. pmc Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar
    Motoshige Yasuike
    Department of Biology, University of Victoria, Victoria, British Columbia, Canada
    BMC Genomics 11:486. 2010
    ..1 Mb) and IGH-B (0.9 Mb) loci. In addition, over 7,000 cDNA clones from the IgH variable (VH) region have been sequenced and analyzed...
  21. pmc Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2
    Kristian R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada
    BMC Genomics 9:522. 2008
    ....
  22. pmc Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray
    Kristian R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada
    BMC Genomics 6:126. 2005
    ..In order to evaluate the utility of the microarray, a number of hybridization techniques and screening methods have been developed and tested...
  23. doi request reprint Functional adaptive diversity of the Atlantic salmon T-cell receptor gamma locus
    Ryosuke Yazawa
    Centre for Biomedical Research, University of Victoria, PO Box 3020 STN CSC, Victoria, British Columbia, V8W 3N5 Canada
    Mol Immunol 45:2150-7. 2008
    ..The identification and characterization of the functional TCRgamma 1 along with the associated TCR alpha/delta locus suggest that Atlantic salmon have a functional gammadelta T-cell immune component...
  24. pmc Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene
    Eric B Rondeau
    Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
    BMC Genomics 14:452. 2013
    ..The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable...
  25. doi request reprint Regulation, expression and characterization of aromatase (cyp19b1) transcripts in ovary and testis of rainbow trout (Oncorhynchus mykiss)
    Kristian R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
    Comp Biochem Physiol B Biochem Mol Biol 155:118-25. 2010
    ..The function of these different 5'-UTRs may be for regulation of cyp19b1 at particular developmental stages or to specify control in distinct gonadal cell-types...
  26. pmc Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics
    Matthew L Rise
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5 Canada
    Genome Res 14:478-90. 2004
    ..A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids...
  27. ncbi request reprint Striking antigen recognition diversity in the Atlantic salmon T-cell receptor alpha/delta locus
    Ryosuke Yazawa
    Centre for Biomedical Research, University of Victoria, PO Box 3020 STN CSC, Victoria, BC, Canada V8W 3N5
    Dev Comp Immunol 32:204-12. 2008
    ..Cumulatively, the genomic and expression data suggest that the Atlantic salmon T-cell receptor has enormous capacity to recognize a wide diversity of antigens...
  28. pmc Regulation and expression of sexual differentiation factors in embryonic and extragonadal tissues of Atlantic salmon
    Kristian R von Schalburg
    Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
    BMC Genomics 12:31. 2011
    ..Although the function of these factors in sexual differentiation have been defined, their roles in early development before sexual fate decisions and in tissues beyond the brain or gonad are essentially unknown...
  29. pmc Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire
    Nicole L Quinn
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    BMC Genomics 11:539. 2010
    ....
  30. doi request reprint Identification of genes associated with heat tolerance in Arctic charr exposed to acute thermal stress
    Nicole L Quinn
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    Physiol Genomics 43:685-96. 2011
    ..Our results highlight the importance of using more than one approach to identify candidate genes, particularly when examining a complicated trait such as UTT in a highly complex genome for which there is no reference genome...
  31. pmc Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein
    Peter N D Hunt
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
    BMC Genomics 6:165. 2005
    ..Here we investigate the genomic structure and expression of zonadhesin-like genes in three species of fish...
  32. pmc Transcriptomics of coping strategies in free-swimming Lepeophtheirus salmonis (Copepoda) larvae responding to abiotic stress
    Ben J G Sutherland
    Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5
    Mol Ecol 21:6000-14. 2012
    ..The results further our understanding of the tolerances of L. salmonis copepodids to salinity and temperature gradients and may assist in the development of salmon louse management strategies...
  33. doi request reprint Differentiating size-dependent responses of juvenile pink salmon (Oncorhynchus gorbuscha) to sea lice (Lepeophtheirus salmonis) infections
    Ben J G Sutherland
    Centre for Biomedical Research, University of Victoria, British Columbia, Canada
    Comp Biochem Physiol Part D Genomics Proteomics 6:213-23. 2011
    ..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...
  34. pmc Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids
    Johan G de Boer
    Centre for Biomedical Research, University of Victoria, Victoria, BC V8W 2Y2 Canada
    BMC Genomics 8:422. 2007
    ..We analyzed the DNA sequence of several large loci in Salmo salar and other species for the presence of DNA transposon families...
  35. ncbi request reprint Expression of morphogenic genes in mature ovarian and testicular tissues: potential stem-cell niche markers and patterning factors
    Kristian R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
    Mol Reprod Dev 73:142-52. 2006
    ..This report provides evidence for local regulation by various morphogens and their potential to control distinct programs of gene expression in the gametes and their accessory cells during gametogenesis...
  36. ncbi request reprint The genomic sequence of the bovine T cell receptor gamma TRG loci and localization of the TRGC5 cassette
    Melanie L Conrad
    University of Victoria, Centre for Biomedical Research, Victoria, British Columbia, Canada V8W 3N5
    Vet Immunol Immunopathol 115:346-56. 2007
    ..The location of the TRGC5 cassette is conclusively described in 5' of the TRG1 locus. Analysis of 17 TRGV belonging to 10 different subgroups, 8 TRGJ and 6 TRGC genes is conducted which comprises the most comprehensive list to date...
  37. ncbi request reprint Comparative analysis of the paired immunoglobulin-like receptor (PILR) locus in six mammalian genomes: duplication, conversion, and the birth of new genes
    Michael D Wilson
    Centre for Biomedical Research, Department of Biology, University of Victoria, British Columbia, Canada
    Physiol Genomics 27:201-18. 2006
    ..Overall, we demonstrate that the PILR locus is dynamically evolving via multiple evolutionary mechanisms in several mammalian genomes...
  38. ncbi request reprint A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary
    Kristian R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada V8W 3N5
    Biol Reprod 72:687-99. 2005
    ..We also report unequivocal evidence for expression of the transcripts that encode the common glycoprotein alpha, LH beta, FSH beta, thyroid-stimulating hormone beta, and retinol-binding protein in both the ovary and testis of trout...
  39. ncbi request reprint Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss
    Ben J G Sutherland
    Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia, V8W 3N5, Canada
    Mol Ecol 23:1952-64. 2014
    ..The best smoltification marker candidate was protein s100a4, expression of which was highly correlated with Na(+) , K(+) ATPase (NKA) activity and smolt-like morphology in pre- and postrelease trout gills...
  40. ncbi request reprint Microarray analysis reveals differences in expression of cell surface and extracellular matrix components during development of the trout ovary and testis
    Kristian R von Schalburg
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada V8W 3N5
    Comp Biochem Physiol Part D Genomics Proteomics 3:78-90. 2008
    ....
  41. pmc ARS2 is a conserved eukaryotic gene essential for early mammalian development
    Michael D Wilson
    Centre for Biomedical Research, University of Victoria, P O Box 3020 Station CSC, Victoria, BC, Canada
    Mol Cell Biol 28:1503-14. 2008
    ..The analysis of data from several independent protein-protein interaction studies in mammals, combined with functional studies of its Arabidopsis ortholog, SERRATE, suggests that this essential process is related to RNA metabolism...
  42. doi request reprint Sex-specific expression and localization of aromatase and its regulators during embryonic and larval development of Atlantic salmon
    Kristian R von Schalburg
    Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada Electronic address
    Comp Biochem Physiol B Biochem Mol Biol 168:33-44. 2014
    ..As well, immunolabeling of skeletal muscle by CYP19B1 throughout the study reveals probable neurogenic activity associated with peripheral radial glial cells and the growing embryonic musculature. ..
  43. ncbi request reprint TCR and CD3 antibody cross-reactivity in 44 species
    Melanie L Conrad
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada V8W 3N5
    Cytometry A 71:925-33. 2007
    ..These antibodies may be used for further immunity research in species with less well-characterized immune systems...
  44. ncbi request reprint Transcriptional responses in a Drosophila defensive symbiosis
    Phineas T Hamilton
    Department of Biology, University of Victoria, PO Box 1800, STN CSC, Victoria, British Columbia, Canada, V8W 2Y2
    Mol Ecol 23:1558-70. 2014
    ..Protection via the production of toxins may be a widely used and important mechanism in heritable defensive symbioses in insects. ..
  45. pmc Sequence analysis and organization of the Neodiprion abietis nucleopolyhedrovirus genome
    Simon P Duffy
    Department of Biology, University of Victoria, Victoria, BC, Canada V8W 2Y2
    J Virol 80:6952-63. 2006
    ..Analyses of ORF upstream sequences identified potential temporally distinct genes on the basis of putative promoter elements...