FHEA
Personal Chair
- About
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- Email Address
- sam.martin@abdn.ac.uk
- Telephone Number
- +44 (0)1224 272867
- School/Department
- School of Biological Sciences
Biography
2022- present Director of Research, School of Biological Sciences
2020- present Director Scottish Fish Immunology Research Centre
2014- present Professor, Institute of Biological and Environmental Sciences (IBES)
2012-2014 Reader, IBES, University of Aberdeen
2010-2012 Senior lecturer, IBES, University of Aberdeen
2007-2010 Lecturer IBES, University of Aberdeen
1999- 2007 Research Fellow, School of Biological Sciences, University of Aberdeen
1996-1999 Senior Research Officer, National Diagnostics Centre, NUI, Galway, Ireland
1993-1996 Postdoctoral RA, Department of Veterinary Parasitology, University of Glasgow
PhD Queens University Belfast 1993
BSc (Hons) Queens University Belfast 1989
Other links
Scottish Fish Immunology Research Centre:
International Centre for aquaculture Research and Development (ICARD)
Aquaculture Research Hub-UK (ARCH-UK)
Sam discusses his research interms of climate chaange and COP26, November 2021
Memberships and Affiliations
- Internal Memberships
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Director Scottish Fish Immunology Research Centre
Aquaculture Research Hub UK (ARCH-UK) Co lead
Mentor for new lecturer staff members
Degree program coordinator MSci Biology
Teaching Committee (SBS)
- External Memberships
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Aquaculture Research Hub UK (ARCH-UK) Co Lead
Scottish Excetutive Ministerial Advisory Group for Aquaculture
MASTS: Productive seas/ aquaculture forum member
Coordinator for "New technologies in fish nutrition" European Aquaculture Technology Implementation Platform
Editorial Board Member : Journal of Aquaculture Research and Development
Board of Directors, River Don Trust
- Research
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Research Overview
LIVE: PhD opportunity in gill health;
Closing date 27th November 2023
Seminar delivered to School of Biological Sciences 27th January 2022
1. Genomics in Aquaculture
2. Atlantic salmon transcriptomics
3. Nutrigenomics in farmed fish
4. Fish health and immunology
5. Life history stratagies and evolutionary adaptations in salmonMy research focuses on fish health and how this is impacted by other physiological processes. The fish immune system regulates the animals response to pathogens and other stressors, as such it is central fish performance at many levels. My research includes how nutrition- especially novel diets and functional feeds impact intestinal and systemic immune function. We have several programs that are focussed on vaacacination, which includes developemnt of cells lines using gene editing (crispr/cas9) in both salmon and carp.
Much of my research is related to aquaculture which is one of the fastest growing global food producing industries, but often this grwoth is retarted due to health management. Within Scotland the Atlantic salmon industry is worth >£1.3 Billion to the Scottish economy producing ~200,000 tons of salmon per annum, however there targets for increased production. Globally now ~50% all consumed fish is reared in aquaculture. My group uses a variety of genomcs approaches to address key traits relating to improving the performance of fish in culture.
For wild salmonids I have a long term interest in the parr smolt transformation and the underlying regulation that controls this physiological process that controls both the migratory behaviour and the ability to osmoregulate in the marine environment.
Research Areas
Accepting PhDs
I am currently accepting PhDs in Biological and Environmental Sciences.
Please get in touch if you would like to discuss your research ideas further.
Research Specialisms
- Aquaculture
- Bioinformatics
- Genomics
- Immunology
- Molecular Biology
Our research specialisms are based on the Higher Education Classification of Subjects (HECoS) which is HESA open data, published under the Creative Commons Attribution 4.0 International licence.
Funding and Grants
2022-2025 Immune cellular dynamics predictive of vaccine protection in Atlantic salmon. With Roslin Institute, University of Edinburgh. BBSRC Responsive mode BB/W008564/1
2020-2024 Development of cell culture tools to study fish virus interactions with a focus on fastidious carp viruses. Phd with CEFAS
2021-2024. Knowledge Transfer Partnership between Innovate UK and Vertebrate Antibodies Ltd. KTP
2021-2022. Artificial intelligence approaches to improve diagnosis of gill disease in Atlantic salmon (AIGD). Scottish Aquaculture Innovation Centre (SAIC)
2021-2022 Evaluation & Optimisation of thermal delicing in Scottish salmonid aquaculture SAIC
2020-2023 NucNanoFish: Nucleic Nanovaccines for fish. BBSRC (ICRAD) BB/V019902/1
2020-2022 Spatial and Temporal Drivers of Gill Pathology in Atlantic Salmon (STGP). SAIC
2019-2023 NOSIFISH: Novel Omega-3 Sources in Feeds and Impacts on Salmon Health BBSRC Responsive mode BB/S005919/1
2019-2022 NUTRIPROG (IPA). Investigating the potential of nutritional programming to improve the utilisation of sustainable feeds in aquaculture. With University of Strirling BBSRC Responsive mode BB/R018812/1
2019-2022: Feed Additives for Improved Physiological and Health Parameters in Fish. PhD studentship Newton-Mosharafa Fund (UK- Egypt)
2019-2023: Photoperiod and immune function, how critical life cycle events in salmon impact on disease response and post smolt performance. PhD studentship funded by SAIC (industrial partner Scottish Sea Farms)
2019-2023 ROBUST-SMOLT: Impact of early life history in freshwater Recirculation Aquaculture Systems on Atlantic salmon robustness and susceptibility to disease at sea. Consortium grant lead by University of Stirling BBSRC BB/S004270/1
2019-2023 Advancing European Aquaculture by Genome Functional Annotation. H2020 Coordinated NMBU Oslo.
2019-2023 AQUALEAP: Innovation in Genetics and Breeding to Advance UK Aquaculture Production. Consortium grant lead by Edinburgh. BBSRC BB/S004181/1
2018-2022: Functional feeds and gill health. PhD studentship with BioMar
2018-2022 Improving resistance to infectious salmon anaemia using genome editing: Novel approaches to tackling viral disease in aquaculture (PI Prof Ross Houston, Roslin Institute) BBSRC BB/R008612/1 responsive mode
2017-2019 Clinical nutrition and the treatment of Atlantic salmon gill diseases. SAIC
2017-2019 Vaccines for chronic viral pathogens in salmon- generation of interferon attenuated cell lines. NERC NE/P010946/1
2017-2020 Functional annotation of the Atlantic salmon genome, translation to improved health and performance for Aquaculture (Partnering award with Canada) BBSRC BB/P02582X/1
2017-2021 Gut leucocytes as a screen for the health impact of functional feeds. PhD studentship with Skretting
2017 Innovation for Health and Robustness in Aquculture in NE India. NERC_BBSRC Innovation ODA scoping award
2017-2021 UK Aquaculture Initiative Network. Aquaculture Research Collaborative Hub -UK (ARCH-UK). NERC / BBSRC BB/P017223/1
2016-2018 Mucosal health and microbiota during sea lice parasitism: effect of oral delivery of immunomodulants. Newton Fund RCUK-CONICYT
2015-2017 Gut health and immune function: the emerging role of gut microbiota in sustainable aquaculture. BBSRC BB/M026604/1
2015-2017. Epigenetic management of stress and disease resistance in Atlantic salmon. BBSRC BB/M026469/1 (with Prof Carlos Garcia de Leaniz, University of Swansea)
2015-2019 Nutrigenomic approaches for development of sustainable fish feeds. PhD studentship. Ministry of Education, Malaysia.
2015-2019 The role of functional amino acids as regulators of metabolic pathways in Atlantic salmon (Salmo salar) and Rainbow trout (Oncorhynchus mykiss). (Industrial PhD studentship with BioMar).
2015-2019 Light & Salt – thyroid hormone deiodinase paralogs and the evolution of complex life-history strategy. Research Council of Norway (Prof. David Hazlerigg, University of Tromso).
2015–2019 Characterization & exploitation of copy number variation in Atlantic salmon. BBSRC industrial CASE PhD studentship, Lead Dr Dan Macqueen.
2013-2017 Gut health and nutrition in Atlantic salmon (Salmo salar). BBSRC EastBio PhD studentship
2013-2017 (Norwegian Research Council) Salmon health and immune function during parr smolt transformation. (Coordinated by Dr Sonal Patel, Bergen, Norway)
2013-2016 The Molecular Interactions between Growth and Health Status in Salmonid Fish. PhD studentship (Kuwait University sponsor)
2011-2016 Development of protein-rich and starch-rich fractions from faba beans for salmon and terrestrial animal production respectively. Technology Strategy Board, UK.
2013 Gene expression and health relating to organic feeds in aquaculture. MASTS visiting Fellow (Dr E Mente).
2011-2014 Nutritional requirements during viral induced muscle wasting in Atlantic salmon (Industrial PhD studentship with BioMar)
2011-2014 Selenium as an antiviral agent in farmed fish (Industrial PhD studentship with Alltech)
2010-2014 Application of nutrigenomics to develop new diets that reduce lice burden in Atlantic salmon. Industrial PhD studentship with BioMar
2010-2014 Farm animal proteomics. EU COST
2010-2014 The physiological and genomic basis to the timing of life history transitions in Atlantic salmon. BBSRC
2008-2011: Evolutionary dynamics of major histocompatibility genes in Arctic charr. NERC (with Prof Rene Stet and Dr W.C. Jordan, IOZ London)
2009-2013: LIFECYCLES: Building a biological knowledge-base on fish lifecycles for competitive, sustainable European aquaculture.
2009-2012: A systems biology based approach to functionally annotate and analyse the genome of the fish pathogenic oomycete Saprolegnia parasitica. BBSRC (with Dr P. Van West)
2008-2011: Molecular basis of improved feed quality for aquaculture. PhD studentship with BioMar
2009-2010: Modulation of muscle atrophy gene expression in Atlantic salmon following an inflammatory response. Royal Society
- Teaching
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Teaching Responsibilities
Lecturer:
1st year Introduction to Biological Sciences (BI1008)
1st year Diversity of life 1, (BI1012)
1st year Diversity of life 2, (BI1512, Course Coordinator)
3rd year Aquatic Biology, Conservation and Exploitation (ZO3809)
3rd year Skills, Bioinformatics unit (BI3010)
4th year Sustainable Aquaculture (ZO4811, Course Coordinator)
4th year Grant Writing for MSci degree programme (BI4015, Course coordinator)
MSc Applied Marine and Fisheries Ecology, Aquaculture (ZI5505, Unit Coordinator)
MSci Degree programme coordinator
Outreach to Schools: "Trout in the Classroom". I teach about ecology and fish in the river Don by growing fish from eggs to fry in the classroom. (Kemnay Academy 2008, Inverurie Academy 2009, Strathburn School 2010).
- Publications
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Page 2 of 4 Results 51 to 100 of 168
Four selenoprotein P genes exist in salmonids: Analysis of their origin and expression following Se supplementation and bacterial infection
PloS ONE, vol. 13, no. 12, e0209381Contributions to Journals: ArticlesContrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon
Epigenetics, vol. 13, no. 12, pp. 1191-1207Contributions to Journals: ArticlesHigh-throughput proteomic profiling of the fish liver following bacterial infection
BMC Genomics, vol. 19, 719Contributions to Journals: ArticlesGrowth hormone transgenesis in coho salmon disrupts muscle immune function impacting cross-talk with growth systems
Journal of Experimental Biology, vol. 221, no. 13, jeb173146Contributions to Journals: ArticlesCore vs. diet -associated and postprandial bacterial communities of the rainbow trout (Oncorhynchus mykiss) midgut and feaces
Open Biology, vol. 7, bio034397Contributions to Journals: ArticlesProteomics in fish and aquaculture research
Proteomics in Domestic Animals: from Farm to Systems Biology. de Almeida, A. M., Eckersall, D., Miller, I. (eds.). Springer International Publishing AG, pp. 311-338, 28 pagesChapters in Books, Reports and Conference Proceedings: Chapters- [ONLINE] DOI: https://doi.org/10.1007/978-3-319-69682-9_16
- [ONLINE] View publication in Scopus
The compositional and metabolic responses of gilthead seabream (Sparus aurata) to a gradient of dietary fish oil and associated n-3 long-chain PUFA content
British Journal of Nutrition, vol. 118, no. 12, pp. 1010-1022Contributions to Journals: ArticlesSeawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.)
Scientific Reports, vol. 7, pp. 1-11Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/s41598-017-13249-8
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/9498/1/s41598_017_13249_8.pdf
Nutrigenomics and immune function in fish: new insights from omics technologies
Developmental and Comparative Immunology, vol. 75, pp. 86-89Contributions to Journals: ArticlesFunctional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture
BMC Genomics, vol. 18, 484Contributions to Journals: EditorialsLineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
Genome Biology, vol. 18, 111Contributions to Journals: ArticlesDivergent regulation of insulin-like growth factor binding protein genes in cultured Atlantic salmon myotubes under different models of catabolism and anabolism
General and Comparative Endocrinology, vol. 247, pp. 53-65Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.ygcen.2017.01.017
Phylogeny and expression analysis of C-reactive protein (CRP) and serum amyloid-P (SAP) like genes reveal two distinct groups in fish
Fish & Shellfish Immunology, vol. 65, pp. 42-51Contributions to Journals: ArticlesPostprandial hepatic protein expression in trout Oncorhynchus mykiss a proteomics examination
Biochemistry and Biophysics Reports , vol. 9, pp. 79-85Contributions to Journals: ArticlesNFAT5 genes are part of the osmotic regulatory system in Atlantic salmon (Salmo salar)
Marine Genomics, vol. 31, pp. 25–31Contributions to Journals: ArticlesEnvironmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)
Aquaculture, vol. 467, pp. 149-157Contributions to Journals: ArticlesDietary Yeast Cell Wall Extract Alters the Proteome of the Skin Mucous Barrier in Atlantic Salmon (Salmo salar): Increased Abundance and Expression of a Calreticulin-Like Protein
PloS ONE, vol. 12, no. 1, e0169075Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1371/journal.pone.0169075
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/7954/1/Plos_One.pdf
Influence of dietary inclusion of a wet processed faba bean protein isolate on post-smolt Atlantic salmon (Salmo salar)
Aquaculture, vol. 465, pp. 124-133Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.aquaculture.2016.09.008
- [ONLINE] View publication in Scopus
Genetic improvement of feed conversion ratio via indirect selection against lipid deposition in farmed rainbow trout (Oncorhynchus mykiss Walbaum)
British Journal of Nutrition, vol. 116, no. 9, pp. 1656-1665Contributions to Journals: ArticlesTranscriptomic responses in the fish intestine
Developmental and Comparative Immunology, vol. 64, pp. 103-117Contributions to Journals: ArticlesDevelopment of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line
Marine Biotechnology, vol. 18, no. 4, pp. 449-452Contributions to Journals: ArticlesDisparate developmental patterns of immune responses to bacterial and viral infections in fish
Fish & Shellfish Immunology, vol. 53, pp. 92Contributions to Journals: AbstractsGrowth and immunity cross-talk in rainbow trout: Suppression of the insulin-like growth factor system during infection
Fish & Shellfish Immunology, vol. 53, pp. 111Contributions to Journals: AbstractsGut health and integrity in atlantic salmon fed plant protein diets
Fish & Shellfish Immunology, vol. 53, pp. 69Contributions to Journals: AbstractsCross Talk Between Growth and Immunity: Coupling of the IGF Axis to Conserved Cytokine Pathways in Rainbow Trout
Endocrinology, vol. 157, no. 5, pp. 1942–1955Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1210/en.2015-2024
Interactions between Paramoeba perurans, the causative agent of amoebic gill disease, and the blue mussel, Mytilus edulis
Aquaculture, vol. 456, pp. 1-8Contributions to Journals: ArticlesDifferential responses of the gut transcriptome to plant protein diets in farmed Atlantic salmon
BMC Genomics, vol. 17, pp. 1-16Contributions to Journals: ArticlesImpact of selenium supplementation on fish antiviral responses: a whole transcriptomic analysis in rainbow trout (Oncorhynchus mykiss) fed supranutritional levels of Sel-Plex®
BMC Genomics, vol. 17, pp. 1-26Contributions to Journals: ArticlesAir-classified faba bean protein concentrate is efficiently utilized as a dietary protein source by post-smolt Atlantic salmon (Salmo salar)
Aquaculture, vol. 452, pp. 169-177Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.aquaculture.2015.10.035
- [ONLINE] View publication in Scopus
The complete salmonid IGF-IR gene repertoire and its transcriptional response to disease
Scientific Reports, vol. 6, 34806Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/srep34806
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/7964/1/srep34806.pdf
Regulatory factors controlling muscle mass: competition between innate immune function and anabolic signals in regulation of atrogin-1 in Atlantic salmon
Molecular Immunology, vol. 67, no. 2 Part B, pp. 341-349Contributions to Journals: ArticlesAtlantic salmon (Salmo salar) parr as a model to predict the optimum inclusion of air classified faba bean protein concentrate in feeds for seawater salmon
Aquaculture, vol. 444, pp. 70-78Contributions to Journals: ArticlesSelenium Supplementation in Fish: A Combined Chemical and Biomolecular Study to Understand Sel-Plex Assimilation and Impact on Selenoproteome Expression in Rainbow Trout (Oncorhynchus mykiss)
PloS ONE, vol. 10, no. 5, e0127041Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1371/journal.pgen.1006500
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/4551/1/PLOSOne_e0127041.pdf
- [ONLINE] Correction: Selenium Supplementation in Fish: A Combined Chemical and Biomolecular Study to Understand Sel-Plex Assimilation and Impact on Selenoproteome Expression in Rainbow Trout (Oncorhynchus mykiss)
Functional characterisation of a TLR accessory protein, UNC93B1, in Atlantic salmon (Salmo salar)
Developmental and Comparative Immunology, vol. 50, no. 1, pp. 38-48Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.dci.2014.12.014
Functional Divergence of Type 2 Deiodinase Paralogs in the Atlantic Salmon
Current Biology, vol. 25, no. 7, pp. 936-941Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.cub.2015.01.074
Antiviral and metabolic gene expression responses to viral infection in Atlantic salmon (Salmo salar)
Fish & Shellfish Immunology, vol. 42, no. 2, pp. 297-305Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.fsi.2014.11.003
Disparate developmental patterns of immune responses to bacterial and viral infections in fish
Scientific Reports, vol. 5, 15458Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/srep18524
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/5130/1/srep15458.pdf
Identification and characterisation of TLR18-21 genes in Atlantic salmon (Salmo salar)
Fish & Shellfish Immunology, vol. 41, no. 2, pp. 549-559Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.fsi.2014.10.006
The vertebrate muscle-specific RING finger protein family includes MuRF4 – A novel, conserved E3-ubiquitin ligase
FEBS Letters, vol. 588, no. 23, pp. 4390-4397Contributions to Journals: ArticlesIdentification and characterisation of the IL-27 p28 subunits in fish: Cloning and comparative expression analysis of two p28 paralogues in Atlantic salmon Salmo salar
Fish & Shellfish Immunology, vol. 41, no. 1, pp. 102-112Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.fsi.2014.06.024
- [ONLINE] View publication in Scopus
Nasal immunity is an ancient arm of the mucosal immune system of vertebrates
Nature Communications, vol. 5, 5205Contributions to Journals: ArticlesCloning and characterisation of multiple ferritin isoforms in the Atlantic salmon (Salmo salar)
PloS ONE, vol. 9, no. 7, e103729Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1371/journal.pone.0103729
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/4773/1/journal.pone.0103729.pdf
- [ONLINE] View publication in Scopus
Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon
Genome biology and evolution, vol. 6, no. 7, pp. 1790-1805Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1093/gbe/evu131
- [ONLINE] View publication in Scopus
Insights into the fish thioredoxin system: Expression profile of thioredoxin and thioredoxin reductase in rainbow trout (Oncorhynchus mykiss) during infection and in vitro stimulation
Developmental and Comparative Immunology, vol. 42, no. 2, pp. 261-277Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.dci.2013.09.013
Inflammatory responses in primary muscle cell cultures in Atlantic salmon (Salmo salar)
BMC Genomics, vol. 14, 747Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1186/1471-2164-14-747
- [OPEN ACCESS] http://aura.abdn.ac.uk/bitstream/2164/3391/1/Pooley_BMC.pdf
Identification and characterization of TLR7, TLR8a2, TLR8b1 and TLR8b2 genes in Atlantic salmon (Salmo salar).
Developmental and Comparative Immunology, vol. 41, no. 2, pp. 295-305Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.dci.2013.05.013
Characterization of cytosolic glutathione peroxidase and phospholipid-hydroperoxide glutathione peroxidase genes in rainbow trout (Oncorhynchus mykiss) and their modulation by in vitro selenium exposure
Aquatic Toxicology, vol. 130-131, pp. 97-111Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.aquatox.2012.12.020
- [ONLINE] View publication in Scopus
Transforming growth factor-β1b: a second TGF-β1 paralogue in the rainbow trout (Oncorhynchus mykiss) that has a lower constitutive expression but is more responsive to immune stimulation
Fish & Shellfish Immunology, vol. 34, no. 2, pp. 420-432Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.fsi.2012.11.011
MULAN related gene (MRG): a potential novel ubiquitin ligase activator of NF-kB involved in immune response in Atlantic salmon (Salmo salar)
Developmental and Comparative Immunology, vol. 38, no. 4, pp. 545-553Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1016/j.dci.2012.08.004
- [ONLINE] View publication in Scopus
Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ
Marine Biotechnology, vol. 14, no. 5, pp. 559-569Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1007/s10126-012-9447-2