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  1. Article ; Online: Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding.

    Houston, R D / Macqueen, D J

    Animal genetics

    2018  Volume 50, Issue 1, Page(s) 3–14

    Abstract: Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high-quality reference genome assembly published. Advances in genomics have become increasingly central to ... ...

    Abstract Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high-quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole-genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome-wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.
    MeSH term(s) Animals ; Aquaculture ; Biological Evolution ; Breeding ; Chromosome Mapping ; Conservation of Natural Resources ; Gene Editing ; Genome ; Genomics ; Phylogeny ; Quantitative Trait Loci ; Salmo salar/genetics
    Language English
    Publishing date 2018-11-14
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 632766-7
    ISSN 1365-2052 ; 0268-9146 ; 0268-9154
    ISSN (online) 1365-2052
    ISSN 0268-9146 ; 0268-9154
    DOI 10.1111/age.12748
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  2. Article ; Online: Commentary on Galindo et Al. [Dev. Comp. Immunol. 33(4) (2009) 612-617].

    Macqueen, Daniel

    Developmental and comparative immunology

    2009  Volume 33, Issue 7, Page(s) 877; author reply 878–9

    MeSH term(s) Animals ; Evolution, Molecular ; Phylogeny ; Proteins/chemistry ; Proteins/classification ; Proteins/immunology ; Ticks/immunology ; Zebrafish/immunology ; Zebrafish Proteins/chemistry ; Zebrafish Proteins/classification ; Zebrafish Proteins/immunology
    Chemical Substances Proteins ; Zebrafish Proteins
    Language English
    Publishing date 2009-07
    Publishing country United States
    Document type Comment ; Letter
    ZDB-ID 752411-0
    ISSN 1879-0089 ; 0145-305X
    ISSN (online) 1879-0089
    ISSN 0145-305X
    DOI 10.1016/j.dci.2009.02.011
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  3. Article ; Online: Community forestry

    Macqueen, Duncan / Grouwels, Sophie

    ICT Update

    A social alliance

    2019  

    Abstract: Forest Connect works in 12 countries to link small-scale forestry enterprises to each other and to national institutions, and helps them to gather and deliver information using ICTs. ...

    Abstract Forest Connect works in 12 countries to link small-scale forestry enterprises to each other and to national institutions, and helps them to gather and deliver information using ICTs.
    Language English
    Publishing date 2019-08-14T10:12:59Z
    Publisher Technical Centre for Agricultural and Rural Cooperation
    Publishing country fr
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Foresterie communautaire

    Macqueen, Duncan / Grouwels, Sophie

    ICT Update

    Une alliance sociale

    2019  

    Abstract: Forest Connect aide les petites entreprises forestières de 12 pays à collecter des informations et à communiquer entre elles et avec des institutions nationales grâce aux TIC. ...

    Abstract Forest Connect aide les petites entreprises forestières de 12 pays à collecter des informations et à communiquer entre elles et avec des institutions nationales grâce aux TIC.
    Language French
    Publishing date 2019-08-14T10:12:57Z
    Publisher Technical Centre for Agricultural and Rural Cooperation
    Publishing country fr
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

    Houston, R. D / Macqueen, D. J

    Animal genetics. 2019 Feb., v. 50, no. 1

    2019  

    Abstract: Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high‐quality reference genome assembly published. Advances in genomics have become increasingly central to ... ...

    Abstract Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high‐quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole‐genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome‐wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.
    Keywords Salmo salar ; ecology ; evolution ; farmed fish ; fish culture ; gene editing ; genetic improvement ; genome ; genome assembly ; genomics ; physiology ; salmon ; technology
    Language English
    Dates of publication 2019-02
    Size p. 3-14.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note REVIEW
    ZDB-ID 632766-7
    ISSN 1365-2052 ; 0268-9146 ; 0268-9154
    ISSN (online) 1365-2052
    ISSN 0268-9146 ; 0268-9154
    DOI 10.1111/age.12748
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  6. Article: Enabling Conditions for Successful Community Forest Enterprises

    Macqueen, Duncan

    Small-scale forestry. 2013 Mar., v. 12, no. 1

    2013  

    Abstract: In search of sustainable forest landscapes that reduce poverty and mitigate climate change, many countries have adopted a forest policy model that encourages community forest enterprise (CFE). This paper draws on international experience from the Forest ... ...

    Abstract In search of sustainable forest landscapes that reduce poverty and mitigate climate change, many countries have adopted a forest policy model that encourages community forest enterprise (CFE). This paper draws on international experience from the Forest Connect alliance, involving teams supporting small forest enterprises in 12 countries with more than 800 associate members from 60 countries. The hypothesis emerging from this alliance is that three main enabling conditions are required for successful CFEs: accessible commercial forest rights; processes of enterprise-oriented social organisation; and infusion of competitive business skills. Having established criteria and indicators of successful CFE, this paper critically examines a series of eight national and sub-national case studies (for Brazil, China, Ethiopia, Ghana, Guatemala, Laos, Mozambique and Nepal) to test this central hypothesis. Findings demonstrate a clear association between the implementation of these three enabling conditions and indicators of successful CFE. Examples from Dolakha and Sindhupalchowk (Nepal) and Monapo (Mozambique) illustrate the importance of ensuring these conditions. The paper concludes by drawing a number of policy implications about how to foster the enabling conditions necessary for successful CFE.
    Keywords case studies ; climate change ; forest communities ; forest policy ; forests ; landscapes ; models ; poverty ; small businesses ; social structure ; sustainable forestry ; teams ; Brazil ; China ; Ethiopia ; Ghana ; Guatemala ; Laos ; Mozambique ; Nepal
    Language English
    Dates of publication 2013-03
    Size p. 145-163.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2365256-1
    ISSN 1873-7854 ; 1873-7617
    ISSN (online) 1873-7854
    ISSN 1873-7617
    DOI 10.1007/s11842-011-9193-8
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  7. Article ; Online: Rainbow trout (Oncorhynchus mykiss) urea cycle and polyamine synthesis gene families show dynamic expression responses to inflammation.

    Clark, T C / Tinsley, J / Macqueen, D J / Martin, S A M

    Fish & shellfish immunology

    2019  Volume 89, Page(s) 290–300

    Abstract: The urea cycle is an endogenous source of arginine that also supports removal of nitrogenous waste following protein metabolism. This cycle is considered inefficient in salmonids, where only 10-15% of nitrogenous waste is excreted as urea. In rainbow ... ...

    Abstract The urea cycle is an endogenous source of arginine that also supports removal of nitrogenous waste following protein metabolism. This cycle is considered inefficient in salmonids, where only 10-15% of nitrogenous waste is excreted as urea. In rainbow trout, arginine is an essential amino acid that has attracted attention due to its many functional roles. These roles include the regulation of protein deposition, immune responses and polyamine synthesis; the latter is directly linked to the urea cycle and involved in tissue repair. The key enzymes used in the urea cycle, namely arginase, ornithine transcarbamylase, argininosuccinate synthase and argininosuccinate lyase, in addition to two rate limiting enzymes required for polyamine synthesis (ornithine decarboxylase and s-adenosylmethionine decarboxylase) are poorly studied in fishes, and their responses to inflammation remain unknown. To address this knowledge gap, we characterised these gene families using phylogenetics and comparative genomics, investigated their mRNA distribution among a panel of tissues and established their transcriptional responses to an acute inflammatory response caused by bacterial infection in liver and muscle. Gene duplicates (paralogues) were identified for arginase (ARG1a, 1b, 2a and 2b), ornithine decarboxylase (ODC1 and 2) and s-adenosylmethionine decarboxylase (SAMdc1 and 2), including paralogues retained from an ancestral salmonid-specific whole genome duplication. ARG2a and 2b were highly upregulated following bacterial infection in liver, whereas ARG1b was downregulated, while both paralogues of SAMdc and ODC were upregulated in liver and unchanged in muscle. Overall, these findings improve our understanding of the molecules supporting the urea cycle and polyamine synthesis in fish, highlighting major changes in the regulation of these systems during inflammation.
    MeSH term(s) Animals ; Fish Diseases/genetics ; Gene Expression ; Inflammation/genetics ; Inflammation/veterinary ; Multigene Family ; Oncorhynchus mykiss/genetics ; Phylogeny ; Polyamines/metabolism ; Urea/metabolism
    Chemical Substances Polyamines ; Urea (8W8T17847W)
    Language English
    Publishing date 2019-04-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 1067738-0
    ISSN 1095-9947 ; 1050-4648
    ISSN (online) 1095-9947
    ISSN 1050-4648
    DOI 10.1016/j.fsi.2019.03.075
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  8. Article ; Online: Arginine, ornithine and citrulline supplementation in rainbow trout: Free amino acid dynamics and gene expression responses to bacterial infection.

    Clark, T C / Tinsley, J / Sigholt, T / Macqueen, D J / Martin, S A M

    Fish & shellfish immunology

    2020  Volume 98, Page(s) 374–390

    Abstract: Supplementing the diet with functional ingredients is a key strategy to improve fish performance and health in aquaculture. The amino acids of the urea and nitric oxide (NO) cycles - arginine, ornithine and citrulline - perform crucial roles in the ... ...

    Abstract Supplementing the diet with functional ingredients is a key strategy to improve fish performance and health in aquaculture. The amino acids of the urea and nitric oxide (NO) cycles - arginine, ornithine and citrulline - perform crucial roles in the immune response through the generation of NO and the synthesis of polyamine used for tissue repair. We previously found that citrulline supplementation improves and maintains circulating free arginine levels in rainbow trout more effectively than arginine supplementation. Here, to test whether supplementation of urea cycle amino acids modulates the immune response in rainbow trout (Oncorhynchus mykiss), we supplemented a commercial diet with high levels (2% of total diet) of either arginine, ornithine or citrulline during a 7-week feeding trial, before challenging fish with the bacterium Aeromonas salmonicida. We carried out two separate experiments to investigate fish survival and 24 h post-infection to investigate the immediate response of free amino acid levels, and transcriptional changes in genes encoding urea cycle, NO cycle and polyamine synthesis enzymes. There were no differences in percentage fish mortality between diets, however there were numerous highly significant changes in free amino acid levels and gene expression to both dietary supplementation and infection. Out of 26 amino acids detected in blood plasma, 8 were significantly changed by infection and 9 by dietary supplementation of either arginine, ornithine or citrulline. Taurine, glycine and aspartic acid displayed the largest decreases in circulating levels in infected fish, while ornithine and isoleucine were the only amino acids that increased in concentration. We investigated transcriptional responses of the enzymes involved in arginine metabolism in liver and head kidney; transcripts for polyamine synthesis enzymes showed highly significant increases in both tissues across all diets following infection. The paralogous arginase-encoding genes, Arg1a, Arg1b, Arg2a and Arg2b, displayed complex responses across tissues and also due to diet and infection. Overall, these findings improve our understanding of amino acid metabolism following infection and suggests new potential amino acid targets for improving the immune response in salmonids.
    MeSH term(s) Aeromonas salmonicida ; Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Arginine/administration & dosage ; Arginine/pharmacology ; Citrulline/administration & dosage ; Citrulline/pharmacology ; Diet/veterinary ; Dietary Supplements ; Gene Expression Regulation/drug effects ; Gene Expression Regulation/immunology ; Gram-Negative Bacterial Infections/immunology ; Gram-Negative Bacterial Infections/veterinary ; Oncorhynchus mykiss ; Ornithine/administration & dosage ; Ornithine/pharmacology
    Chemical Substances Citrulline (29VT07BGDA) ; Arginine (94ZLA3W45F) ; Ornithine (E524N2IXA3)
    Language English
    Publishing date 2020-01-20
    Publishing country England
    Document type Journal Article ; Randomized Controlled Trial, Veterinary
    ZDB-ID 1067738-0
    ISSN 1095-9947 ; 1050-4648
    ISSN (online) 1095-9947
    ISSN 1050-4648
    DOI 10.1016/j.fsi.2020.01.026
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  9. Article: Rainbow trout (Oncorhynchus mykiss) urea cycle and polyamine synthesis gene families show dynamic expression responses to inflammation

    Clark, T.C / Macqueen, D.J / Martin, S.A.M / Tinsley, J

    Fish & shellfish immunology. 2019 June, v. 89

    2019  

    Abstract: The urea cycle is an endogenous source of arginine that also supports removal of nitrogenous waste following protein metabolism. This cycle is considered inefficient in salmonids, where only 10–15% of nitrogenous waste is excreted as urea. In rainbow ... ...

    Abstract The urea cycle is an endogenous source of arginine that also supports removal of nitrogenous waste following protein metabolism. This cycle is considered inefficient in salmonids, where only 10–15% of nitrogenous waste is excreted as urea. In rainbow trout, arginine is an essential amino acid that has attracted attention due to its many functional roles. These roles include the regulation of protein deposition, immune responses and polyamine synthesis; the latter is directly linked to the urea cycle and involved in tissue repair. The key enzymes used in the urea cycle, namely arginase, ornithine transcarbamylase, argininosuccinate synthase and argininosuccinate lyase, in addition to two rate limiting enzymes required for polyamine synthesis (ornithine decarboxylase and s-adenosylmethionine decarboxylase) are poorly studied in fishes, and their responses to inflammation remain unknown. To address this knowledge gap, we characterised these gene families using phylogenetics and comparative genomics, investigated their mRNA distribution among a panel of tissues and established their transcriptional responses to an acute inflammatory response caused by bacterial infection in liver and muscle. Gene duplicates (paralogues) were identified for arginase (ARG1a, 1b, 2a and 2b), ornithine decarboxylase (ODC1 and 2) and s-adenosylmethionine decarboxylase (SAMdc1 and 2), including paralogues retained from an ancestral salmonid-specific whole genome duplication. ARG2a and 2b were highly upregulated following bacterial infection in liver, whereas ARG1b was downregulated, while both paralogues of SAMdc and ODC were upregulated in liver and unchanged in muscle. Overall, these findings improve our understanding of the molecules supporting the urea cycle and polyamine synthesis in fish, highlighting major changes in the regulation of these systems during inflammation.
    Keywords adenosylmethionine decarboxylase ; arginase ; arginine ; argininosuccinate lyase ; argininosuccinate synthase ; bacterial infections ; essential amino acids ; fish ; genes ; genomics ; immune response ; inflammation ; liver ; liver diseases ; messenger RNA ; muscles ; Oncorhynchus mykiss ; ornithine carbamoyltransferase ; ornithine decarboxylase ; phylogeny ; polyamines ; protein deposition ; tissue repair ; tissues ; transcription (genetics) ; urea ; urea cycle ; wastes
    Language English
    Dates of publication 2019-06
    Size p. 290-300.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1067738-0
    ISSN 1095-9947 ; 1050-4648
    ISSN (online) 1095-9947
    ISSN 1050-4648
    DOI 10.1016/j.fsi.2019.03.075
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  10. Article ; Online: Supplementation of arginine, ornithine and citrulline in rainbow trout (Oncorhynchus mykiss): Effects on growth, amino acid levels in plasma and gene expression responses in liver tissue.

    Clark, T C / Tinsley, J / Sigholt, T / Macqueen, D J / Martin, S A M

    Comparative biochemistry and physiology. Part A, Molecular & integrative physiology

    2019  Volume 241, Page(s) 110632

    Abstract: Functional amino acids (FAA) regulate metabolic pathways directly linked to health, survival, growth and development. Arginine is a FAA with crucial roles in protein deposition and the immune response. In mammals, supplementation of arginine's precursor ... ...

    Abstract Functional amino acids (FAA) regulate metabolic pathways directly linked to health, survival, growth and development. Arginine is a FAA with crucial roles in protein deposition and the immune response. In mammals, supplementation of arginine's precursor amino acid, citrulline, is known to increase circulating arginine to levels beyond direct arginine supplementation, however, citrulline supplementation is poorly studied in fish. To address this knowledge gap, we supplemented the diet of rainbow trout with arginine and its precursor amino acids, ornithine and citrulline, at 3 levels (0.5%, 1% and 2% of the total diet) during a 14-week experiment. We sampled fish at 3 h and 24 h post-feeding to investigate immediate and steady-state effects, respectively. There were no differences in fish growth for any of the diets across a range of indicators. In blood plasma, out of 26 amino acids detected, 11 and 6 displayed significant changes 24 h and 3 h post-prandial, respectively. Arginine, ornithine and citrulline levels were all significantly increased by the citrulline supplemented diets. In muscle, 8 amino acids were significantly altered by supplemented diets, while there were no significant changes in liver. Arginine was increased by 2% citrulline supplementation in muscle tissue. We also investigated the transcriptional responses of urea cycle, nitric oxide cycle and rate-limiting polyamine synthesis enzymes, related to arginine's metabolism, in liver. At both time points, only 2 enzymes were significantly altered by the supplemented diets, however several significant changes were observed comparing 3 h and 24 h post-prandial expression levels. Of these, the paralogous polyamine synthesis enzyme encoding genes ODC1 and ODC2 displayed the largest increases in 3 h post-prandial fish. These findings demonstrate that endogenous synthesis of arginine is possible from a citrulline supplemented diet and improve our understanding of arginine metabolism in fish.
    MeSH term(s) Amino Acids/blood ; Animals ; Arginine/administration & dosage ; Citrulline/administration & dosage ; Dietary Supplements ; Liver/drug effects ; Liver/growth & development ; Liver/metabolism ; Oncorhynchus mykiss/blood ; Oncorhynchus mykiss/genetics ; Oncorhynchus mykiss/growth & development ; Oncorhynchus mykiss/metabolism ; Ornithine/administration & dosage
    Chemical Substances Amino Acids ; Citrulline (29VT07BGDA) ; Arginine (94ZLA3W45F) ; Ornithine (E524N2IXA3)
    Language English
    Publishing date 2019-12-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 121246-1
    ISSN 1531-4332 ; 0300-9629 ; 1095-6433
    ISSN (online) 1531-4332
    ISSN 0300-9629 ; 1095-6433
    DOI 10.1016/j.cbpa.2019.110632
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