The cultivation of aquatic organisms, including fish, mollusks, crustaceans and aquatic plants.
Aquatic organisms (for the purposes of this site) includes organisms covered by the Fisheries Act including finfishes, molluscs, crustaceans, marine plants and marine mammals and related organisms constituting their habitats (including freshwater plants). (The Fisheries Act explicitly includes eggs, sperm, spat, etc.)
To test or evaluate. The procedure for measuring the quantity of a given substance in a sample (chemically or by other means).
The science and study of bacteria, a specialized branch of microbiology. The bacteria constitute a useful and essential group in the biological community. Although some bacteria prey on higher forms of life, relatively few are pathogens (disease-causing organisms). Life on earth depends on the activity of bacteria to mineralize organic compounds and to capture the free nitrogen molecules in the air for use by plants. Also, bacteria are important industrially for the conversion of raw materials into products such as organic chemicals, antibiotics, cheeses, etc. Genetically engineered bacteria are starting to be used to produce high value added pharmaceuticals and specialty chemicals.
Bacterial Artificial Chromosome (BAC) is a DNA construct, based on a fertility plasmid, used for transforming and cloning in bacteria, usually E. coli. Its usual insert size is 150 kbp, with a range from 100 to 300 kbp. BACs are often used to sequence the genetic code of organisms in genome projects, for example the Human Genome Project. A short piece of the organism's DNA is amplified as an insert in BACs, and then sequenced. Finally, the sequenced parts are rearranged in silico, resulting in the genomic sequence of the organism.
One of the components of nucleosides, nucleotides and nucleic acids. Four different bases are found in naturally occurring DNA – the purines A (adenine) and G (guanine); and the pyrimidines C (cytosine) and T (thymine, the common name for 5-methyluracil). In RNA, T is replaced by U (uracil).
The two separate strands of a nucleic acid double helix are held together by specific hydrogen bonding between a purine and a pyrimidine, one from each strand. The base A pairs with T in DNA (with U in RNA); while G pairs with C in both DNA and RNA. The length of a nucleic acid molecule is often given in terms of the number of base pairs it contains.
Involves the direct addition of the microorganisms that can break down contaminants and accelerate their destruction.
The study of the chemistry of living organisms, especially focusing on metabolism.
Biodegradation is the decomposition of organic material by microorganisms. The term biodegradation is often used in relation to sewage treatment, environmental remediation (bioremediation) and to plastic materials. Organic material can be degraded with oxygen (aerobically) or without oxygen using other electron acceptors such as nitrate, ferric iron or sulphate. A term closely related to biodegradation is mineralisation, in which organic matter is converted to into CO2 , H2O, (+ CH4 in anaerobic conditions) through microbial action.
- A broad term referring to the variety of life in a given area. It includes ecosystem diversity, species diversity and genetic diversity. It also involves the countless, complex ways in which living things function and interact.
- The variability among living organisms from all sources, including, inter alia, terrestrial, marine and other ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems.
The use and organization of information of biological interest. In particular, concerned with organizing bio-molecular databases (particularly DNA sequences), utilizing computers for analyzing this information, and integrating information from disparate biological sources.
From the two Greek words bios (life) and logos (word), it is the field of science encompassing the "study of life".
'Bioremediation involves enriching the environment by adding substances that boost the capability of naturally-occurring microbes to break down toxic substances.
Biomarkers are a characteristic that can be measured and evaluated as an indicator of normal biologic processes, pathologic processes or pharmacologic responses to therapeutic intervention.
A collection of measurable molecular signals that are a surrogate or representation of a complex biological process.
involves the modification of the environment to stimulate existing bacteria capable of bioremediation. This can be done by addition of various forms of limiting nutrients, such as phosphorus, nitrogen, or carbon (e.g. in the form of molasses). Additives are usually added to the subsurface through injection wells, although injection well technology for biostimulation purposes is still emerging. Removal of the contaminated material is also an option, albeit and expensive one. Biostimulation is an alternative to bioaugmentation.
The primary advantage of biostimulation is that bioremediation will be undertaken by already present native mocroorganisms that are well suited to the subsurface environment, and are well disributed spatially within the subsurface. The primary disadvantage is that the delivery of additives in a manner that allows the additives to be readily available to subsurface microorganisms is based on the local geology of the subsurface. Tight, impearmeable subsurface lithology (tight clays or other fine-grained material) make it difficult to spread additives throughout the affected area. Fractures in the subsurface create preferential pathways in the subsurface which additivies preferentially follow, preventing even distribution of additives
Synthesis of compounds by living cells, which is the essential feature of anabolism.
- In its broadest sense, biotechnology refers to the use of biologically based technologies including processes like fermentation to produce wine
- In its narrowest sense it is sometimes equated to genetic engineering or genetic modification
- The OECD definition is the application of scientific and engineering principles to the processing of materials by biological agents to provide goods and services
- The Government of Canada, through the Canadian Environmental Protection Act (CEPA) has adopted the following definition: the application of science and engineering in the direct or indirect use of living organisms or parts or products of living organisms in their natural or modified forms.
The group of males and females from which fish are bred for aquaculture.
A substance that promotes a chemical reaction by lowering the activation energy of a chemical reaction, without itself undergoing any permanent chemical change.
Abbreviation for complementary DNA
The fundamental level of structural organization in complex organisms. Eukaryotic cells contain a nucleus (with chromosomes) and cytoplasm with the protein synthesis machinery, bounded by a membrane. Prokaryotic cells have no nucleus.
The transition of cells (by the programmed activation and de-activation of the necessary genes) from a tissue-unspecific type, in which daughter cells are similarly undifferentiated, to a committed type in which the cell line specializes to become a recognizable tissue or organ.
A chromosomal location where foreign DNA can be integrated, often without impairing any essential function in the host organism.
- In eukaryotic cells, chromosomes are the nuclear bodies containing most of the genes largely responsible for the differentiation and activity of the cell. Chromosomes are mot easily studied in their contracted state, which occurs around the metaphase of mitosis or meiosis; they contain most of the cell's DNA in the form of chromatin. Each eukaryotic species has a characteristic number of chromosomes. Bacterial and viral cells contain only one chromosome, which consists of a single or double strand of DNA or, in some viruses, RNA, without histones.
- The threadlike structures found in the nucleus of plant and animal cells. They are composed of genes which carry the genetic information of living organisms.
- A group of cells or individuals that are genetically identical as a result of asexual reproduction, breeding of completely inbred organisms, or forming genetically identical organisms by nuclear transplantation.
- Group of plants genetically identical in which all are derived from one selected individual by vegetative propagation.
- Verb: To clone. To insert a DNA segment into a vector or host chromosome.
A DNA strand synthesized in vitro from a mature RNA template using reverse transcriptase. DNA polymerase is then used to create a double-stranded molecule. Differs from genomic DNA by the absence of introns.
Complementary RNA (called nuclear RNA) is made when cells are making proteins from genes. It is made from the single-stranded DNA code and eventually changed into messenger RNA (mRNA). The mRNA carries its coded message to another part of the cell where it is translated into proteins. Complementary DNA (cDNA) is an artificial DNA made in the lab from mRNA strands, and is often used as probes.
Measures and protocols applied to limit contact of genetically modified organisms or pathogens with the external environment.
Refers to methodologies such as netting fish and clipping or tagging their fin.
The annealing of a single-stranded DNA sequence to a single-stranded target DNA to which it is only partially complementary. Often, this refers to the use of a DNA probe to detect homologous sequences in species other than the origin of the probe.
Mating between members of different populations (lines, breeds, races or species).
To spell-out the sequences of DNA and proteins into their basic units.
Refers to the sharing of technology with other organizations to encourage their uptake of new tools that could benefit the wild fishery, aquaculture and/or aquatic ecosystems.
The status of having two complete sets of chromosomes, most commonly one set of paternal origin and the other of maternal origin. Somatic tissues of higher plants and animals are ordinarily diploid in chromosome constitution, in contrast with the haploid gametes.
The chemical that forms the basis of the genetic material in virtually all living organisms. A long chain polymer of deoxyribonucleotides. A molecule that forms the basis for encoding the genetic information of most organisms; composed of two complementary strands of nucleotides organized in a double helix and capable of self-replication. In cells of higher life forms, DNA is organized into chromosomes in the nucleus and is found in a circular form in organelles such as mitochondria and chloroplasts. The sequence of nucleotides provides the information that is passed on to offspring.
The process of creating exact copies of a DNA strand using various technologies.
The derivation of unique patterns of DNA fragments obtained using a number of marker techniques; they are generally polymerase chain reaction based.
Is a collection of cloned DNA fragments. There are two types of library, the genomic library which contains DNA fragments representing the entire genome of the organism; and the cDNA library which contains only complementary DNA molecules synthesized mRNA molecules in a cell.
Strands of DNA used to search for, and highlight, specific sequences of DNA in a sample. They can contain complementary strands of DNA and/or radioactive markers. Also see Complementary strands of DNA/RNA.
Humans and other organisms can be uniquely identified based on their DNA sequences. DNA is composed of two single strands attached together to form a double helix. Based on a known sequence of DNA, scientists can create a synthetic copy of the matching double helix strand, called a DNA probe that is constructed so that the sequence of its nucleotides is complementary to a specific region of a DNA target. If the target sequence is present in the sample being tested, the DNA probe binds to the target. The subsequent signal from the DNA probe establishes the presence of the target. The unique properties of the gold nanoparticle probes allow detection through optical, electrical or magnetic processes.
A biological tool which allows the scientist to compare samples of DNA material.
The order of nucleotides that make up a given segment of a DNA molecule. Also see DNA
A local biological community and its pattern of interaction with its environment.
Multiple biomolecular signatures that when examined together present a unique pattern of molecular change in an organism and identify an exposure or response to a specific environmental stressor.
The process of identifying and quantifying the risks of the release or escape of transgenic aquatic organisms having an impact on the natural environment, including other organisms and their habitats.
Describes the process that converts the gene's coded information into the structures present and operating in the cell.
A short (200-500 base pairs) cDNA sequence from mRNA derived from a specific cell population and used for cloning a large number of genes that are expressed in that population.
The relative constancy of the phenotype of individuals of a given genotype. Mutations said to have variable expressivity show a relatively large amount of phenotypic variation among individuals having the same genotype.
The survival value and the reproductive capability of an individual, compared to that of competitor individuals of the same or other species within a population or an environment.
A natural unit of hereditary material. It is the physical basis for the transmission of characteristics of living organisms from one generation to another. The basic genetic material consists of chain-like molecules of nucleic acids – deoxyribonucleic acid (DNA) in most organisms and ribonucleic acid (RNA) in certain viruses.
- The process by which a gene produces mRNA and protein, and hence exerts its effect on the phenotype of an organism.
- Transcriptional activity of a gene resulting in one or more RNA products and, usually following translation, one or more protein products.
Determination of specifically which genes are "switched on" (e.g., in a cell); thereby enabling precise definition of the phenotypic condition of that cell (i.e., the phenotype of that cell at that moment).
Chemicals that inhibit or induce gene expression; for instance, a gene off-switch would be a regulator protein that inhibits the action of any gene under its control, while the on-switch would be an inducer chemical that turns the gene-inhibiting regulator protein into a gene-activating protein.
The branch of biology concerned with heredity. It is the study of how genes operate and are passed on from parents to offspring.
The correspondence between the set of 64 possible nucleotide triplets and the animo acids and stop codons that they specify.
Any mechanism, either a physical treatment or a genetic trait, that renders and organism incapable of transferring genetic traits to other organisms or incapable of producing viable organisms if such transfer takes place.
Is synonymous with genetic variability, intraspecific (bio)diversity and biological diversity on the gene level) represents the existence of variants (alleles) of individual genes resulting from alterations of the DNA sequence. The alleles of a particular gene may occur in different frequencies in different groups of interbreeding individuals (populations) and the genetic variation of a particular species is therefore distributed both within populations (expressed as different allele combinations between individuals) and between populations (differences in occurrence and frequency between populations). (Nordic Council of Ministers 2004 Report)
A variety of techniques used to intentionally change the genetic information in a living cell.
A map showing the position of genes or markers on a chromosome.
A DNA sequence used to identify a particular location on a particular chromosome.
A general term which refers to any intentional change to the heritable traits of an organism. This includes both traditional breeding and recombinant DNA techniques. Also see Recombinant DNA techniques and Breeding.
A DNA sequence or genetic sequence is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, with the capacity to carry information.
The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand - adenine, cytosine, guanine, thymine bases covalently linked to phospho-backbone. Typically the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, going from 5' to 3' from left to right. A succession of any number of nucleotides greater than four is liable to be called a sequence.
Implies a fishery that does not result in unacceptable loss of genetic diversity and/or unacceptable change of the genetic composition of distinct populations or population systems. It is currently not clear what levels of loss/change that may be regarded as acceptable. (Nordic Council of Ministers 2004 Report)
Genes of certain observable traits that are used as markers when introducing foreign genes into an organism. They are usually "tagged" onto the desired genes and indicate whether an organism has successfully incorporated those desired genes into its genome. The gene for antibiotic resistance is often used as a genetic tag. Also known as selectable markers.
This type of testing involves the examination of an individual's DNA. Also known as gene testing and DNA testing.
The entire hereditary material in each cell of an organism. It is composed of one or more chromosomes, depending on the complexity of the organism.
Broadly defined, encompasses numerous scientific disciplines and technologies, including efforts to: (i) determine the entire DNA sequence (the genome) of organisms; (ii) assign function to identified genes (functional genomics); (iii) study transcription patterns of genes (transcriptomics); (iv) determine which proteins are expressed (proteomics); and (v) investigate the flux patterns of metabolites (metabolomics). Genomics-based approaches to research in the life sciences are transforming our understanding of how complex biological systems as a whole function and respond to change. Within this area, environmental genomics is the application of genomics-based approaches to address environmental issues and problems.
All the genetic information inherited by an individual from its parents.
Various chemicals that play numerous roles in the promotion of cell growth and cell maintenance throughout the body.
Is a polypeptide hormone synthesised and secreted by the anterior pituitary gland which stimulates growth and cell reproduction in humans and other vertebrate animals.
Is a field of pathology which specialises in the histologic study of diseased tissue. It is an important tool of anatomical pathology and is used for accurate diagnosis of cancer and other diseases.
A type of chemical messenger in plants and animals which inhibits or excites metabolic activities (in that plant or animal) by binding to receptors on specific cells.
The offspring of two parents that are genetically different. A cross between two genetically unlike individuals.
A highly infectious disease of Atlantic salmon that was first reported within Norweigan aquaculture facilities.
- Immunohistochemistry is a technique for identifying cellular or tissue constituents (antigens) by means of antigen-antibody interactions, the site of antibody binding being identifiedeither by direct labelling of the antibody, or by use of a secondary labelling method
- Refers to the process of localizing proteins in cells of a tissue section exploiting the principle of antigens in tissue binding to their respective antibodies.
A gene of known function or known location, used for marker-assisted selection or genetic studies.
A technique for determining the composition of a molecule and its fragments.
Metabolomics is the "systematic study of the unique chemical fingerprintsthatspecificcellular processes leave behind" - specifically, the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological organism, which are the end products of its gene expression. Thus, while mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling can give an instantaneous 'snapshot' of the physiology of that cell.
Metagenomics (also Environmental Genomics or Community Genomics) is the study of genomes recovered from environmental samples as opposed to from clonal cultures. This relatively new field of genetic research allows the genomic study of organisms that are not easily cultured in a laboratory
- An array of hundreds or thousands of spots containing specific DNA sequences for the analysis of gene expression by hybridization. Microarrays are used to detect changes in gene expression by comparing radioactively – or chemically-labelled cDNA prepared from the total mRNA of an experimental sample to that of a control sample. The relative intensity of the signal reveals whether the expression of a particular gene is increased, decreased, or unchanged in the experimental mRNA sample compared to the control mRNA sample.
- Microarrays form the basis of environmental genomics research designed to investigate the range of genetic responses in populations and species to environmental changes. A microarray is a set of short Expressed Sequence Tags (ESTs) (genes) made from a cDNA library of a set of known (or partially known) gene loci. The ESTs are dye, one red and one green, and spotted onto a cover-slip-sized glass plate. They are then put through a laser machine where the dye fluoresces proportional to the degree of hybridization that has occurred. Relative gene expression is measured as the ratio of the two fluorescences.
The organelles that generate energy in eukaryotic cells. Mitochondria have their own genome encoding, a subset of the proteins found in mitochondria; the mitocondiral genome uses an alternate genetic code.
The DNA within an organism's (e.g., human) cells that is located inside the mitchondria (organelles); not inside the cell nucleus. Mitochondrial DNA is only passed-down from mother to offspring; not from father to offspring, as nuclear DNA is.
The study of living processes at the molecular level.
The process of isolating a DNA sequence, and reproducing it in an organism, usually in a bacterium like E-coli.
The science dealing with the study of the nature and biochemistry of the genetic material. Includes the technologies of genetic engineering.
Messenger RNA. An RNA molecule that is the product of transcription of a gene, after that molecule has been spliced and polyadenylated, that can be translated into a protein product.
MSX (Multinucleated Sphere X) disease is caused by a single-celled Protozoan parasite, Haplosporidium nelsoni. MSX is lethal to the eastern oyster (Crassostrea virginica), but it is not known to be harmful to humans. The parasite is commonly present as a multinucleated cell (plasmodium) which ranges from 5 to 100 um in diameter. Occasionally it forms spores.
The CEPA 99 New Substances Notification Regulations (NSNR) have been in force since 1994 (for chemicals and polymers) and 1997 (for living biotechnology products). There are provisions in CEPA 99 which allow for exemption from the notification requirement for those new substances which are notified and assessed under another federal act in the manner envisaged in CEPA 99. Acts and Regulations that meet the criteria for this exemption may be listed in a CEPA 99 schedule.
At a very general level, means "new".
Refers to a characteristic of an aquatic organism that has been intentionally selected, created or introduced into an aquatic species through a specific genetic change.
The DNA that is contained within the nucleus of a cell.
The DNA or RNA found in the cells of all living organisms. It is responsible for protein synthesis and the cell's hereditary characteristics.
One of the building blocks of DNA or RNA consisting of one nitrogen base, one phosphate molecule, and one sugar molecule.
The structure within cells that contains DNA.
The observable properties of an organism, thought to be a result of the interaction of the organism's genetic constitution with its environment.
Refers to a virus, bacterium, parasitic protozoan, or other microorganism that causes infectious disease by invading the body of an organism (e.g., animal, plant, etc.) known as the host. It should be noted that infection is not synonymous with disease because infection does not always lead to injury of the host.
The genetically and environmentally determined appearance of an organism.
A branch of biology that deals with the functions and activities of life or of living matter (as organs, tissues, or cells) and of the physical and chemical phenomena involved; the organic processes and phenomena of an organism or any of its parts or of a particular bodily process.
A major challenge in genetics research is defining and dissecting the diversity of developmental and physiological pathways that lie between genes and traits. New functional genomics methods are transforming these studies by providing comprehensive and systematic approaches that complement traditional methods of formal genetics, biochemistry, and cell biology. Together, these complementary approaches will test whether reductionism can account for the complex web of interactions that lead from genetic variation to morphological, physiological, and behavioral traits in health and disease.
- A method of copying a DNA or RNA strand thousands of times, in a matter of minutes, by using the natural ability of an enzyme called polymerase to copy DNA or RNA.
- A method of amplifying specific DNA segments based on hybridization to a primer pair. A DNA sample is denatured by heating in the presence of a vast molar excess of short single-stranded DNA primers (around 20 nucleotides) whose sequence is chosen based on target sequence.
A class of high molecular weight polymer compounds composed of a variety of amino acids. Each protein is the ultimate expression product of a gene. Proteins are the "workhorses" of living systems and include enzymes, antibodies, receptors, peptide hormones, etc.
- The study of the structure and function of proteins, including the way they work and interact with each other inside cells.
- Systematic analysis of protein expression of normal and diseased tissues that involves the separation, identification and characterization of all of the proteins in an organism.
A region of DNA that is associated with a particular trait (e.g., plant height). Though not necessarily genes themselves, QTLs are stretches of DNA that are closely linked to the genes that underlie the trait in question. One use of QTLs is to identify candidate genes underlying a trait. Once a region of DNA is identified as contributing to a phenotype, it can be sequenced. The DNA sequence of any genes in this region can then be compared to a database of DNA for genes whose function is already known.
QTLs are essentially a statistical creation that identifies a particular region of the genome as containing a gene (or genes) that is associated with the phenotype being measured. They are shown as probability curves across a chromosome where the probability of association is plotted for each marker used in the mapping experiment.
Includes the placing into cages, ponds, land-based tanks etc., in or near natural bodies of water or wherever escape (acts of people or nature) could give access to the wild environment, and includes rearing outside of the laboratory.
A cell that receives a particular form of stimulation and produces a specific physiological response.
Molecules extracted from two or more different sources, and joined together to form a single molecule.
A combination of DNA molecules of different origin that are joined using recombinant DNA technologies - created by splicing together two or more different pieces of DNA.
The regrowth of tissues, organs or entire organisms from a small quantity of cells and/or tissue.
A gene whose function is to regulate the expression of a structural gene.
Found in the cells of organisms, where it plays an important role in protein synthesis; in some organisms, such as certain viruses, it is the carrier of genetic information.
Obtaining high quality, intact RNA is the first and often the most critical step in performing many fundamental molecular biology experiments, including Northern analysis, nuclease protection assays, RT-PCR, RNA mapping, in vitro translation and cDNA library construction.
Describes the process of finding the sequence of nucleotides in a fragment of DNA. Also known as gene sequencing.
Variations that occur when a single nucleotide in the DNA sequence of a genome is altered.
This disease is caused by a microscopic parasite – too small to see with the naked eye – with the scientific name Haplosporidium costale. SSO stands for "Seaside Organism" since it was first found in oysters on the ocean side of Virginia, unlike MSX (a closely related oyster disease) that is found in estuarine waters.
Standards are defined by the International Organization of Standardization (ISO) as "documented agreements containing technical specifications or other precise criteria to be used consistently as rules, guidelines or definitions of characteristics, to ensure that materials, products, processes and services are fit for their purpose."
Improving the quality of life within the ecological carrying capacity of supporting systems.
A characteristic of an organism, which manifests itself in the phenotype (physically). Many traits are the result of the expression of a single gene, but some are results from simultaneous expression of more than one gene (polygenic).
The synthesis of an RNA copy from a sequence of DNA (a gene); the first step in gene expression.
Proteins that regulate the activity of other genes.
A process by which the genetic material carried by an individual cell is altered by the incorporation of foreign DNA into its genome.
Cells which have successfully incorporated foreign DNA into their genomes.
Describes an organism whose genome has been altered by the inclusion of foreign genetic material (transgene). This foreign genetic material may be derived from other individuals of the same species or from wholly different species. Genetic material may also be of an artificial nature.
Aquatic organisms that have been genetically-modified through the integration and expression of a foreign gene
The status of having three complete sets of chromosomes. Triploidy typically renders the individual or organism sterile.
- An organism, usually an insect, that carries and transmits pathogens.
- A small DNA molecule (plasmid, virus, bacteriophage, artificial or cut DNA molecule) that can be used to deliver DNA into a cell. Vectors must be capable of being replicated and contain cloning sites for the introduction of foreign DNA.
The study of viruses and viral diseases.
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