Archive for the ‘unfinished’ Category

Altoids tins are autoclavable

July 11, 2012

Last night I decided to autoclave (sterilization process that uses 125 C steam) the tin container that Altoids mints come in in order to see if they would survive the temperature/pressure.   The tins looked the exact same inside and outside after autoclaving.

It is not a huge surprize the tins survived – they are metal after all.  My actual intent in doing this was to use the tins as petri-dishes – which is why I needed to sterilize them in an autoclave.  But while the autoclaving of the tins went flawlessly, my media preparation failed miserably.  I tried to make some growth media with red wine, body-builder amino-acid supplements, sugar, and agar-agar (edit: FYI I boiled off most of the alcohol).  For whatever reason the media would not harden.  I will try again sometime after this week because I will be going to the TAM conference in Vegas this year!

Altoids (before)

Altoids (before)

Altoids inside (before)

Altoids inside (before)

As far as using these containers as petri-dishes goes – my only concern is the hinge.  It appears that when closed, the lid covers the hinge hole and should keep the innards sterile.  Until I get the media to harden I will not know if that is a problem or not.

Even if the tins fail to work as petri-dishes (metal could have unforeseen issues for micro-organisms), they may work out as containers for auto-claving parts or components.

Altoids (after)

Altoids (after)

Some preliminary results – electrophoresis buffer comparison

May 12, 2012

I did a quick test of four differnt electrophoresis buffers last night.  The buffers were 1X TAE (Molecular-grade), 1X TBE (Purchased), SB buffer (Home-grade), SB buffer (Molecular-grade).

I will run the test again on a better gel rig (that I dislike using because it uses 3x as much agarose and gel stain as 1 mini gel I used below).

All gels were run at 100V for 1 hour.

Image

SB Home Grade (left).  SB Molecular Grade (center).  1 TBE (right).

Image

1x TAE (left).  1x TBE (right).

You can see that the TAE buffer led to gel deformation whereas TBE did not have that problem.

Image

From left to right.  TAE, SB Home-grade, SB Molecular-grade, TBE.

The two SB buffers were noticeably cooler than the TBE and TAE buffers (27C for SB and 33C for TBE and TAE) and the DNA migrated slower.

I think most of the smearing is due to the high voltage used.  The crappy 2-log ladder (that I have had issues with before) also doesn’t help.

Another problem is my power supply doesn’t handle four simultaneous gels very well, the mA jump up super high in order to generate the needed voltage.  I will be running them individuals on the next test.

Buffer preparation.

May 10, 2012

I just made the last of the buffers I needed for my electrophoresis testing. Hopefully next week, after my final, I will start posting the comparison results.  For fun, here are a couple of pictures of my reagent preparation set-up in my apartment.

pH adjustment

pH adjustment

Filtering

Filtering

Not there yet, but I am getting close.

September 26, 2011

I bought a Dremel today and my first attempt at cutting gel comb with my new toy is worlds better than when I tried with a knife (see image below).

I need to practice a bit more to get the gel comb the way I want, but I am really happy with what I made.

Progression

Progression

Update: Microscope incubator

September 21, 2011

After putting the DIY microscope incubator I recently built through its paces it has come time to revise and improve (evolve?) it.  Aside from enlarging the chamber just a tad I have figured out how to more elegantly integrate the hair-dryer into the incubator.  There should be a significant reduction in waste heat now.

Ahhh yea. (Top view of the incubator)

LEGO electrophoresis box update.

September 19, 2011

I spent some time this weekend on improving the LEGO electrophoresis box.  Below are two images.  I should be done with the whole thing and testing it some time this week.

One thing holding me back is that I have been having a lot of problems soldering cables.  I have never soldered before and I think the iron I bought is defective.  Eventually I will work my way through the problem.

Box with cover.

Box without cover

LEGO electrophoresis box and gel cast (prototype)

September 11, 2011
Completed casted gel

(visit the photo gallery for more pictures)

Gel boxes are ridiculously expensive, so much so that  I was able to buy a used electrophoresis machine off eBay for less than the cost of a gel box!
My first attempts in building a gel box involved scoring and sawing 1/4″ plastic boards in an attempt to cut square pieces for a gel box.  This method was too crude and I could not get a straight  line.  The only positive thing from this attempt was I found that PVC cement was able to join plastic pieces together to make a strong water-tight seal.
While brainstorming I reckoned  that LEGO’s would be perfect for a gel box.  After googling for a bit I found only one reference to LEGO’s and electrophoresis and it was at the journal of BioTechniques (link here).  It was frustrating to discovery that no digital copy of the article exists and so I decided I would fumble around in the dark on my own.

Casting a gel with LEGOs

The image above shows my prototype gel box and gel mold (with molten agarose).  The box itself is just a frame.  The gel mold is square so that the mold can be rotated once the agarose cools to make for easy gel casting.  The bottom of the mold is covered in those smooth LEGO planks without rivits (I suspect it may have worked even with the rivits, but the acetone treatment would be more difficult).

One of the big design challenges with using LEGO’s is waterproofing the construct.  LEGO’s are made from ABS plastic and from all of the reading about 3D printers I have done, I knew that acetone melts and melds ABS plastic together.  After constructing my gel mold I dipped a Kim-Wipe (lint free paper towel) into some acetone and rubbed it all over the sides and surfaces of the LEGO mold.  Immediately the colors began to smear and the cracks and grooves filled in.  Within minutes the whole thing was dry and ready for casting a gel.
Nearly all of the agarose stayed inside the mold (I added 40mL of 2% agarose) and the mold and gel both were removed and rotated nicely!
I ran into one issue.  The acetone was not completely dry and it seeped up from the base plate of LEGO’s and made a weird tiny plastic ridge (which I later removed with more acetone).  I only gave the LEGO’s about 5 minutes to dry so I am not surprised.  But what was surprising was the patriotic shape theplastic made in my gel!

Flag? Gel?

I am definitely going to pursue the LEGO gel box further and will post more if I have success.

 

Incubator update, 071911.

July 19, 2011

The company I ordered a temperature controller from sent me the wrong product.  Now I am waiting an exchange by snail mail.  So to pass the time I made some updates to the incubator.

I decided that the cardboard set-up I had was too crude along the edges and so I switched the material to foam-core board (bought from the dollar tree store for $1 a sheet).  I was able to make much straighter and cleaner lines – which is important for preventing air from escaping.

Picture 1 – The chamber.

It is clear from the picture that the middle does not align tightly.  This is mainly because the 6″ supports I used on each side were sized for cardboard which was thicker than the foam-core board.  Nevertheless I decided to test out how well the rig heats up.

Picture 2 – The heating unit.

I visited the local Home Depot and after dealing with a cashier who had no idea what a hose was, I returned to the lab.  I opted to ghetto rig the hose to the hair-dryer (I’ll need a better solution for long term).

The results?  Very promising!  Despite the presence of small gaps in the front, bottom left, bottom right and rear of the chamber the entire inside heated up very quickly.  Running the hair-dryer on medium settings I got both sides of the chamber to reach around 40-50C each.

What is left to be done:

  • Make new supports for each side of the chamber.
  • Find a way to properly connect the hose to the hair-dryer.
  • Hook up the thermal controller once it arrives.
  • Block off the few gaps in the incubator.
  • Decide if a circulated fan is needed to keep the inside homogenous.

Microscope Incubator, In-progress

June 26, 2011

Actual incubators for microscopes cost a hefty-sum and so I have taken it upon myself to build my own incubator for an Olympus Fluoview inverted confocal microscope.

My first step is to build a cardboard enclosure for the stage and lenses (I am currently at this step).  The second step will be to add doors and refine the box (maybe use a better material).  The third step is to hook up a thermal controller ($30) and a hair-dryer to the box and test out how evenly the inside warms up.

I ran into some difficulties with the left side (user error), so depicted below is the right half of the incubator box.