BioMiha

As leelee said TBE causes less heating because borate ions have better mobility than acetate. The problem with using borate is if you want to excise your band out of the gel and purify it the borate ions form complexes with the DNA and the yield is much lower. Therefore people use TAE. There was a paper on this subject a while ago called "Not your father's buffer" and it said that the best is Li-borate or Na-borate and in my experience you can really speed things up with a different buffer.

If your multiplicity of infection (MOI) is low, you can be fairly certain according to the Poisson distribution that you will have only one phage per cell. If MOI is high then more phage can infect at once. Helper phage cannot replicate, but are added at a high MOI to ensure rescue of all displaying phage.

Because of the library preparation procedure. You have a phage vector to which you add your insert - which is very small. You then ligate and transform the host bacteria. If the vector ligates without the insert, you get insertless phage.
There is a very good paper on this subject that I recommend to anyone = Levitan - Stochastic modeling and optimization of phage display. Otherwise, I did a big part of my PhD with phage display, however the successes were few and far between.

Not that I am really an expert on this but I've had my share of frustrating moments especially at congresses feeling like a kindergarden child compared to the annoyingly witty professors with huge departments and annoyingly perfect publications. I think every language in the world has a version of the saying: "those that know do, those that don't know teach". In other words once you get your hands dirty, you will know exactly what you need to know. You will also know very well which papers to read and what to remember.
My 2c. Best of luck.

Hi,
Self vs. foreign is a gross oversimplification of the immune system. The fact is that the immune system only rejects certain autoreactive antibodies, that react to antigens expressed in the bone marrow. For the majority of other self antigens that are found in the periphery the immune system deletes autoreactive clones because there is an absence of additional activational signals associated with pathogens (which are for the purpose of immunisation usually provided by ajuvants). So in essence the immune system differentiates between self and non-self because self is not associated with danger signals. If however, a self antigen is associated with danger signals = immunisation in the presence of adjuvants (most often killed mycobacteria), it mounts an immune response. Therefore the rabbit makes antibodies to the antigen.
But even more importantly in your case I imagine that the rabbit was immunized with some sort of peptide. Even though this peptide might correspond to an amino acid sequence encountered in the rabbit itself, the conformation of the peptide is very different when it is bound to the carrier molecule as compared to when it is part of the protein. I myself think immunization using peptides is more often than not a waste of time, because the immune response is more often than not directed to the free ends of the peptides and the antibodies that are generated usually do not cross react with the intact antigen.

Of course they are transcribed and translated. The plasmids confer a selective advantage to the cells that carry it in a selective environment. If you leave a bacterial suspension carrying a plasmid to grow into stationary phase in a medium without antibiotic the bacteria will loose the plasmid, meaning the bacteria without plasmid will outgrow the bacteria with plasmid. Nothing in a bacterial cell is completely non-essential.

I don't think the problem is the agarose. I've had this problem myself. In my experience this happened because voltage was too high or because the salt content of the samples was too high. I am guessing that your loading buffer is too concentrated. Try a different loading buffer.
Just my two cents.
Best of luck.
Miha