Costs ($$$) for gene knockout experiments

[SysBio]

Hi all,

 

Question: how would you start to approximate the costs of gene knockout experiments?

 

I am doing a class project where I am writing a research grant proposal. My proposal involves using gene knockouts to validate malarial drug targets. (The steps include: take plasmid vectors, insert stuff using restriction enzymes, transfect into malaria, screen using southern blotting)

 

The problem is that I am actually mostly a computational researcher.

So I have no idea about how people practically buy and use these experimental items.

 

For example, I assume there are gene knockout kits???....how do you choose which kit to buy???....how many kits do you need???....how do you plan for mistakes/repeats????.....where do you find prices for experimental equipment???

 

As you can see I am completely lost in this....so if anyone has any idea about buying materials for gene knockout experiments....PLEASE HELP ME!

 

Thanks

[CharonY]

I assume this is just a "training" proposal?

 

Usually you first to have to make sure that basic equipment for handling is present P. falciparum, as well as labspace (e.g. you need at least a BS2 lab). Most project grants do not cover basic equipments.

 

Before I comment on the consumables I would advise you to look at existing protocols for the manipulation and maintenance of Plasmodium cells, though. You need to know this before you can write the grant.

Check the malaria journal (it is open access) as well as some of the parasitology journals for this. I recall a paper about the assessment of different deletion protocols for P. falciparum around last year or so in the malaria journal.

 

For standard cloning techniques check out "Molecular cloning" (Sambrook and Russell). There are tons of information in it and I recommend it to everyone. If you got a basic idea of the experiments you want to do, you can start checking out prices.

 

Mutagensis kits are, btw. not essential. What they do is creating a mutated insert. Most of the time you can do it just with the right primers for less money.

In order to get an idea how much the kits cost, I'd advise you to browse at least to Promega, Qiagen, Invitrogen, as well as general lab equipment vendors (e.g. VWR and Fisher).

[SysBio]

Wow....thanks a lot for the great information

 

I knew of the general molecular cloning procedure from class lectures, and I pieced together a procedure pertaining to malaria from a research paper that detailed its experimental techniques. But I'll remember the malaria journals for next time.....

 

I am still confused about the consumables though...it just seems overwhelming. How am I supposed to know HOW MUCH primers, plasmid vectors, etc to buy?

 

And thanks for tips regarding labspace and equipment. Its just a hypothetical grant application, so I will say that I have access to all necessary equipment and labspace through colaborators....can you explain what a BS2 lab space is though?

[ecoli]

http://en.wikipedia.org/wiki/Biosafety_level

[CharonY]

Right, it is short for Biosafety 2 Lab. The details how the setup has to be is likely differ from country to country, though. This includes e.g. restricted access, biosafety benches, available autoclave etc.

 

Anyhow, getting the exact amount for consumables is tricky, if not impossible. The best you can do are rough estimates and then add a chunk more, as usually during the grant review process a big chunk will be slashed off again.

Also you cannot know beforehand what will work and what has to be repeated how often. E.g. you may design four primer that looks perfect on paper only to find out that one (or both) pairs do not amplify.

What you can do is to identify every component you need, take down the price, and then add 25% or so for replicates. It is going to be an estimate, anyway.