How to identify gene based on molecular weight? - (Jun/04/2015 )

Lets say I want to separate a specific gene that codes for something interesting. Lets say a plain - typical red rose, and I want to know which gene codes for the pigmentation for example, or thorns...

Is there an online library in which one can search up species of plants, mammals, insects, fish etc, with the molecular weight and gene expression listed?

Oh, and in case you didnt notice - I am pretty much clueless. :)

I am currently setting up a lab at home in order to do some exploration in this field as a hobby.

sincerely, Dr. N00b.

There are databases for this sort of thing. Try the databases at http://www.ncbi.nlm.nih.gov/, in particular the genome and nucleotide databases there. Note that you might need to learn a bit about the terminology associated with these databases before you can use them effectively, for which the tutorials page will help.

Genes are encoded by the DNA and as such don't have a molecular mass, rather they are a sequence within the chromosomes (or mobile genetic elements such as plasmids). As such, you can't separate based on size in particular (you can chop the DNA up and then separate on a gel), you need an additional method of identification, as there will be typically be many many fragments of genome that are of similar size, any one of which could contain the sequence you are looking for. On the other hand, you can extract RNA and get the messenger RNA (mRNA) and separate that based on size (to do it properly is relatively difficult, as RNA is easily degraded), but a similar situation to the above size problem still exists. You may want to check out Southern and northern blotting.

Note that many traits are coded by more than one gene, such that you often can't pinpoint any particular place and say "this is the single gene that causes this", though flower colour (at least in peas, like Mendel studied) is one where you can say this.

Thank you very much Thelymitra. :) This was incredibly informative.

With my limited knowledge I was counting on separating the DNA on a gel through electrophoresis, and then selecting parts of it based on the molecular weight. Seems it will not be that easy.

I shall have to try to extract the RNA and get the mRNA like you said, and separate that based on size. I still need to identify which piece I should extract from that though, but I guess the link you provided will be usefull for that. I will have to look into that and learn the terminology - or at first create a step-by-step protocol for searching. ;)

I am looking to borrow certain traits such as color from one plant and infuse it in another.

I was originally planning on doing this using biolistic (Bio-Rad Helios Gene Gun) method, but as I've come to understand - it can be accomplished using bacteria as well?..

No problem. You should be aware that the traits expressed for flower colour and the like are not necessarily transferable between different species, and traits are usually a result of levels of expression, determined by the relative expression of the dominant and recessive alleles, rather than just straight expression of the gene.

Note that the project you are undertaking is quite complex and will involve some pretty good technical skills, best learned in the lab from experienced people. Also note that you are aiming to do some genetic modification of higher plants (commercially valuable?)... which is illegal or requires some special permits in many countries.

Having said that, to get your desired gene into a plant, you will need to create an expression system, usually based off a plasmid (mobile genetic element found in many bacteria), which contains all the information for the plant to be able to express the gene. I haven't done anything with plant expression systems, so I can't giide you on which are best there, but it will need to contain at a minimum, a promoter sequence (plant specific), your gene, and a terminator sequence. Preferably you will also need some way to propagte this plasmid in the lab, which is usually done in bacteria such as E. coli, so you will also need a selection mechanism to kill off bacteria that don't contain the plasmid, and possibly one to select for the gene in your transgenic plants.

As for getting the gene in - be prepared for a lot of failure. I know that one method used is Agrobacterium tumefasciens, but a gene gun should also work. Note that for both methods your need to ensure that the gene is inserted into the part of the plant that you want the gene to express (not much use if you insert it into a leaf and you are looking at flower colour...), or into a seed making part, so that you can propagate it and get the desired result. How you would go about this, I have no idea.

Incidentally, my user name is Bob; Thelymitra pulchella is the species of orchid shown in my profile picture.

I am aware that my project is quite complex and that I would benefit unquantifyably (did I just invent a new word? :) ) much more in an actual lab environment with experienced people. However, I do not have that luxury - and must rely on instructional lab videos and forums such as this one. To <<rely on the kindness of strangers>> I guess one could say. :)

I shall create a new thread with an apropriate topic as to what kind of project I should undertake as a first-timer.

Once again - thank you so much for your corrections and pointers thus far - Bob.

Sincerely, N00b.