<Ul> <Li> Loss of function experiments, such as in a gene knockout experiment, in which an organism is engineered to lack the activity of one or more genes . In a simple knockout a copy of the desired gene has been altered to make it non-functional . Embryonic stem cells incorporate the altered gene, which replaces the already present functional copy . These stem cells are injected into blastocysts, which are implanted into surrogate mothers . This allows the experimenter to analyse the defects caused by this mutation and thereby determine the role of particular genes . It is used especially frequently in developmental biology . When this is done by creating a library of genes with point mutations at every position in the area of interest, or even every position in the whole gene, this is called "scanning mutagenesis". The simplest method, and the first to be used, is "alanine scanning", where every position in turn is mutated to the unreactive amino acid alanine . </Li> <Li> Gain of function experiments, the logical counterpart of knockouts . These are sometimes performed in conjunction with knockout experiments to more finely establish the function of the desired gene . The process is much the same as that in knockout engineering, except that the construct is designed to increase the function of the gene, usually by providing extra copies of the gene or inducing synthesis of the protein more frequently . Gain of function is used to tell whether or not a protein is sufficient for a function, but does not always mean it's required, especially when dealing with genetic or functional redundancy . </Li> <Li> Tracking experiments, which seek to gain information about the localisation and interaction of the desired protein . One way to do this is to replace the wild - type gene with a' fusion' gene, which is a juxtaposition of the wild - type gene with a reporting element such as green fluorescent protein (GFP) that will allow easy visualisation of the products of the genetic modification . While this is a useful technique, the manipulation can destroy the function of the gene, creating secondary effects and possibly calling into question the results of the experiment . More sophisticated techniques are now in development that can track protein products without mitigating their function, such as the addition of small sequences that will serve as binding motifs to monoclonal antibodies . </Li> <Li> Expression studies aim to discover where and when specific proteins are produced . In these experiments, the DNA sequence before the DNA that codes for a protein, known as a gene's promoter, is reintroduced into an organism with the protein coding region replaced by a reporter gene such as GFP or an enzyme that catalyses the production of a dye . Thus the time and place where a particular protein is produced can be observed . Expression studies can be taken a step further by altering the promoter to find which pieces are crucial for the proper expression of the gene and are actually bound by transcription factor proteins; this process is known as promoter bashing . </Li> </Ul> <Li> Loss of function experiments, such as in a gene knockout experiment, in which an organism is engineered to lack the activity of one or more genes . In a simple knockout a copy of the desired gene has been altered to make it non-functional . Embryonic stem cells incorporate the altered gene, which replaces the already present functional copy . These stem cells are injected into blastocysts, which are implanted into surrogate mothers . This allows the experimenter to analyse the defects caused by this mutation and thereby determine the role of particular genes . It is used especially frequently in developmental biology . When this is done by creating a library of genes with point mutations at every position in the area of interest, or even every position in the whole gene, this is called "scanning mutagenesis". The simplest method, and the first to be used, is "alanine scanning", where every position in turn is mutated to the unreactive amino acid alanine . </Li> <Li> Gain of function experiments, the logical counterpart of knockouts . These are sometimes performed in conjunction with knockout experiments to more finely establish the function of the desired gene . The process is much the same as that in knockout engineering, except that the construct is designed to increase the function of the gene, usually by providing extra copies of the gene or inducing synthesis of the protein more frequently . Gain of function is used to tell whether or not a protein is sufficient for a function, but does not always mean it's required, especially when dealing with genetic or functional redundancy . </Li> <Li> Tracking experiments, which seek to gain information about the localisation and interaction of the desired protein . One way to do this is to replace the wild - type gene with a' fusion' gene, which is a juxtaposition of the wild - type gene with a reporting element such as green fluorescent protein (GFP) that will allow easy visualisation of the products of the genetic modification . While this is a useful technique, the manipulation can destroy the function of the gene, creating secondary effects and possibly calling into question the results of the experiment . More sophisticated techniques are now in development that can track protein products without mitigating their function, such as the addition of small sequences that will serve as binding motifs to monoclonal antibodies . </Li>

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