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How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium).

I already cut some parts (NdeI-PciI) of the vector (pUC18) and wondering if it affects the integration procedure. Is there any recombination-like procedure same as gateway?

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What is your host in this case? For integration into the genome of a bacterium, you would need to use an "integration" vector. Most commercial vectors (such as pUC18) will be maintained without integrating into the host genome.

Here is a description of an integration vector from the Bacillus Genetic Stock Center to give you an idea of how foreign DNA would be integrated into a Bacillus genome:

Integration vectors are plasmids that feature conditional replication coupled with a selectable marker. If the plasmid is transformed into an appropriate host under conditions that select for the plasmid’s presence but restrict its replication, all transformants will have integrated the plasmid into their chromosome (or some other resident DNA capable of replicating under the selective conditions). In practice, the selectable marker usually specifies antibiotic resistance. Conditional replication usually means that the plasmid has replication functions that work in E. coli but not in gram-positive bacteria, such as B. subtilis. Sometimes a temperature-sensitive replication phenotype is employed instead. Integration is targeted to a particular locus on the chromosome by including identical sequences on the plasmid. If there is a single homologous sequence, a single crossover will integrate the entire chromosome into the target locus by a Campbell-type mechanism. If there are two homologous sequences, and they are relatively close together on the chromosome, then a double crossover will result in a cassette integrating between the chromosomal targets. (source)

For most routine molecular biology labwork, there is no need to integrate genes into the E. coli genome. Integration is usually used to generate "knockout" cell lines to study gene function in the bacteria of interest.

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Thanks for your time and consideration...but the host is microalgae (a eucaryote microorganism). –  Saeid Kadkhodaei Jan 23 '12 at 12:58
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