First ever project suggestions? - Starting genetic lab for hobby purposes. - (Jun/05/2015 )
Hello everyone!
I've over the course of the last couple of years picked up an interest in genetics, and I am currently setting up a lab so that I can do some experiements as a hobby.
I am a bit unsure as to where to start.
Alot of my equipment is on the way from various countries as I write this, and within three to four weeks I will have a fully equipped lab. I have access to a PCR Machine, microsentrifuges with RPM's ranging from almost nothing to 15000, incubators, micropipettes, electrophoresis equipment, microscopes ranging from low magnification to 2000x oil immersion, bright-field and dark-field. I've even gotten my hands on a 2nd hand Bio-Rad Helios Gene gun...
So - I need something relatively simple as a first project. I thought "why not bacteria" - since the incubation time is quite short.
I've seen some images of people making paintings or drawins in petri dishes using e coli. Would this be a fairly straight forward task?
Or perhaps there is something else that would be visually interesting that I could do - that would require less skilled hands?
I would appreciate any input on this matter. :)
Sincerely, N00b.
Dr. N00b on Fri Jun 5 07:53:56 2015 said:
Hello everyone!
I've over the course of the last couple of years picked up an interest in genetics, and I am currently setting up a lab so that I can do some experiements as a hobby.
I am a bit unsure as to where to start.
Alot of my equipment is on the way from various countries as I write this, and within three to four weeks I will have a fully equipped lab. I have access to a PCR Machine, microsentrifuges with RPM's ranging from almost nothing to 15000, incubators, micropipettes, electrophoresis equipment, microscopes ranging from low magnification to 2000x oil immersion, bright-field and dark-field. I've even gotten my hands on a 2nd hand Bio-Rad Helios Gene gun...
So - I need something relatively simple as a first project. I thought "why not bacteria" - since the incubation time is quite short.
I've seen some images of people making paintings or drawins in petri dishes using e coli. Would this be a fairly straight forward task?
Or perhaps there is something else that would be visually interesting that I could do - that would require less skilled hands?
I would appreciate any input on this matter.
Sincerely, N00b.
yeah, making those colored plates is fairly easy to do.
Al you need is some bacteria that are fluorescent... you can buy those or why not, make them yourself...
All you need is some save E.coli strain and some plasmids with the required genes.
See here for some information: http://14ilcatchicago.blogspot.be/2014_07_19_archive.html
pito on Fri Jun 5 12:54:38 2015 said:
...or why not, make them yourself...
All you need is some save E.coli strain and some plasmids with the required genes.
See here for some information: http://14ilcatchicago.blogspot.be/2014_07_19_archive.html
Very interesting!
I have been looking into this CHROmagar and briefly thought of ways to do it. From what I understand, with chromagar one makes a nuitricious agar using this substance, then grows the bacterial culture on it - and they will display the color chosen? If so - I guess I could make several agar plates, grow e-coli on them, then use the various e-coli colonies to create the final image?
About the E-coli strain and plasmids though.. I guess I need to make the plasmids myself? I mean, get a gene coding for fluorescense, create a plasmid vector, inject into E-coli and grow a culture? One for each color?
am I even slightly on the right track here? :)
Sincerely, N00b.
you do not need chromagar. Just regular medium will do.
You do need a blacklight to see the fluorescence!
And yes: all you need is a plasmid that expresses the GFP!
(and a regular E.coli to express the GFP/plasmid)
If you can find one with , eg, GFP you could use this plasmid for GFP and look around for other variations, like YFP and replace the GFP in your plasmid with YFP (or just use the YFP plasmid if thats possible)
And yes, you just grow each of them seperately and then you restreak them forming an image on a novel plate.
Dr. N00b on Fri Jun 5 15:09:27 2015 said:
pito on Fri Jun 5 12:54:38 2015 said:
...or why not, make them yourself...
All you need is some save E.coli strain and some plasmids with the required genes.
See here for some information: http://14ilcatchicago.blogspot.be/2014_07_19_archive.html
Very interesting!
I have been looking into this CHROmagar and briefly thought of ways to do it. From what I understand, with chromagar one makes a nuitricious agar using this substance, then grows the bacterial culture on it - and they will display the color chosen? If so - I guess I could make several agar plates, grow e-coli on them, then use the various e-coli colonies to create the final image?
About the E-coli strain and plasmids though.. I guess I need to make the plasmids myself? I mean, get a gene coding for fluorescense, create a plasmid vector, inject into E-coli and grow a culture? One for each color?
am I even slightly on the right track here?
Sincerely, N00b.
pito on Fri Jun 5 16:41:06 2015 said:
...And yes: all you need is a plasmid that expresses the GFP!(and a regular E.coli to express the GFP/plasmid)
If you can find one with , eg, GFP you could use this plasmid for GFP and look around for other variations, like YFP and replace the GFP in your plasmid with YFP (or just use the YFP plasmid if thats possible)
And yes, you just grow each of them seperately and then you restreak them forming an image on a novel plate.
Ok...
So now all I need to figure out is how to make a plasmid, and where to find a GFP / YFP and then making the plasmid into a vector. 
I saw a video on e-coli and vectors a while back, but the details escape me. 
I searched for GFP's and found a whole color pallet commercially available. They are complete vectors ready for use with a variety of bacteria. Among them ofc. e-coli.
However, these "kits" are expensive (225USD a piece).
I see Bio-Rad has a classroom kit for something similar. Perhaps it would be a good idea for me to go through one of these first. 
Yes, it can be expensive...
What you could do is ask for some plasmids by sending emails to certain labs.. Some labs just send them for free (sometimes) other labs just ask you to pay for the mailingcosts, some labs just ask you to pay a small fee for the work when they have to send/prepare the plasmids...
You can get it pretty cheap in the end if you look a bit!
The kit I do not know it...
But could work yes.
In the end its not that hard: all you need is an e.coli strain, not hard to get.
Some plasmids (vectors witht the right GFPs on it): you should be able to find them somewhere too..
And you are ready to start!
Of course: if you really want to alter the plasmids, do some genetic work, you need to buy restriction enzymes and stuff.. that can get pretty expensive in the end!
pito on Fri Jun 5 18:58:26 2015 said:
Of course: if you really want to alter the plasmids, do some genetic work, you need to buy restriction enzymes and stuff.. that can get pretty expensive in the end!
I kind of want to do most of the work myself. If not I can't really say "I've done this".. 
I found restriction enzymes though. The prices dont look half bad if you ask me. But then again, I dont know how many of them I will need for any one single operation.
Where does one ordinarily harvest e.coli? Just leave some raw chicken meat in room temperature, swab it, rub it in a petri dish, incubate and hope for the best?
It would be interesting to use several common bacteria for this so that it is not only e.coli.
What other easilly obtainable bacterias are there that I can harvest from say food, fecies, soil etc?
Dr. N00b on Fri Jun 5 20:19:15 2015 said:
pito on Fri Jun 5 18:58:26 2015 said:
Of course: if you really want to alter the plasmids, do some genetic work, you need to buy restriction enzymes and stuff.. that can get pretty expensive in the end!
I kind of want to do most of the work myself. If not I can't really say "I've done this"..
I found restriction enzymes though. The prices dont look half bad if you ask me. But then again, I dont know how many of them I will need for any one single operation.
Where does one ordinarily harvest e.coli? Just leave some raw chicken meat in room temperature, swab it, rub it in a petri dish, incubate and hope for the best?
It would be interesting to use several common bacteria for this so that it is not only e.coli.
What other easilly obtainable bacterias are there that I can harvest from say food, fecies, soil etc?
NONO!
You do not just take e.coli from "raw chicken"!
You need a non pathogenic labstrain!
For example: K12 strain or any other labstrain that is safe to use.
You can find other bacteria as well, labstrains that are safe to work with.
Just start with safe labstrains rather than trying to find your own strains somewhere.. like food or fecies...
Thats a bit dangerous...
pito on Fri Jun 5 20:48:50 2015 said:
NONO!
You do not just take e.coli from "raw chicken"!
You need a non pathogenic labstrain!
For example: K12 strain or any other labstrain that is safe to use.
You can find other bacteria as well, labstrains that are safe to work with.
Just start with safe labstrains rather than trying to find your own strains somewhere.. like food or fecies...
Thats a bit dangerous...
Allright... First mistake already avoided. 
Ok, there we go... I found the K12 strain for sale.
yes, its easy to find it and you only need to buy it (or request it somewhere) and you are good for ever! You can simply grow it and store it yourself later.