Context for cheap bio lab tools / materials

[Jason Morrison]

The following might be interesting for learning what kinds of supplies/labs/equipment should be cheaper to help promote biology research in schools, and I think high schools' budgets are interesting to consider, when we are considering DIY budgetary constraints.

http://www.donorschoose.org/donors/search.html?sourceid=qs&keywords=biology&zone=0&x=0&y=0

"DonorsChoose.org is a simple way to provide students in need with resources that our public schools often lack. At this not-for-profit web site, teachers submit project proposals for materials or experiences their students need to learn. These ideas become classroom reality when concerned individuals, whom we call Citizen Philanthropists, choose projects to fund."

Example:  http://www.donorschoose.org/donors/proposal.html?id=195775&zone=0
$284 for 4 DNA extraction kits?  Not sure what's included, perhaps www.carolina.com/text/teacherresources/instructions/biotech/dna_necklace_kit.pdf ?

I think we can do better!

-Jason

--
Jason Morrison
jason.p....@gmail.com
http://jayunit.net
(585) 216-5657

[Mackenzie Cowell]

Great link, Jason.

I did a quick search for proposals that included the word "DNA".  The average donation requested was something like $400.  This usually was for a thermocycler and and some kind of PCR reagents or DNA extraction kit.

I agree wholeheartedly that we could do way better than $400.

Additionally, many of the teachers cited the physical, hands-on experience that hardware provides as the main reason for wanting it for their class.  But think about how cool it would be for kids to be *building* their own tools and then using them to do PCR.  Man, I for one felt like I got a better understanding of gel electrophoresis when we tried to do it for $20 with tupperware and agar-agar.

So I think there is a huge potential for us to develop a robust, diy biotech lesson plans for high school biology classes.

We could start with the gel electrophoresis protocol.

Mac

[Meredith L. Patterson]

The University of Utah's gel box is quite easy to build (well, to be
fair, I did get the plastic supplier to cut the pieces for me) and
cost about $30 in parts all told.

http://learn.genetics.utah.edu/content/labs/gel/gelchamber/

--mlp

[Jason Kelly]

that's neat. gel boxes are a complete rip off.

Meredith, which plastic supplier did you use - and can you post the
specifications you sent them?

thanks,
jason

p.s. apologies for the several emails to follow in a row --
apparently, i wasnt properly registered for the list so was just
sending mail into the ether for last week or two.

[Meredith L. Patterson]

I went to TAP Plastics in San Francisco and gave them the sizes
specified in the PDF linked below. They cut the acrylic exactly to
size (even the half-inch pegs), and the total came to just over $20.
They will do mail-order. Putting the pieces together with acrylic
cement took about an hour and a half. Do make sure to seal the seams
on both sides -- the box needs to be watertight! The PDF shows a
syringe with a curved plastic tip for the cement applicator. TAP has
these, though I used a syringe with a blunt metal needle and that
worked very well.

If you spill some cement, just let it dry -- it will smear if you try
to wipe it off.

You could probably get away with just making the gel carrier from
acrylic, and using a Tupperware and some terminal posts to seat the
electrodes. If you go that route, you'll probably want to seal the
holes for the electrode posts with hot glue or epoxy.

They didn't have the Teflon, but it sounds like Mackenzie et al did
pretty well with a used Charlie Card. You could also cut the comb from
a Blockbuster Video card or any other smooth plastic wallet-sized
card.

Radio Shack's banana plugs aren't quite the right size, but I got it
to fit together okay with a pair of stackable banana plugs and a pair
of screw-in posts. I'll see if I can find my camera's battery and take
a picture.

Do use steel wire, as copper will stain the gel blue.

--mlp

[Peter Olson]

Source of monel wire:

http://www.shopwiki.com/detail/d=20Lb_14%22_Monel_Wire_(30pc_per_tube)/jumpToFirst=t/

On Oct 22, 10:09 pm, "Meredith L. Patterson" <clonea...@gmail.com>
wrote:

> >> On Tue, Oct 21, 2008 at 12:22 PM, Mackenzie Cowell <macow...@gmail.com> wrote:
> >>> Great link, Jason.
>
> >>> I did a quick search for proposals that included the word "DNA".  The
> >>> average donation requested was something like $400.  This usually was for a
> >>> thermocycler and and some kind of PCR reagents or DNA extraction kit.
>
> >>> I agree wholeheartedly that we could do way better than $400.
>
> >>> Additionally, many of the teachers cited the physical, hands-on experience
> >>> that hardware provides as the main reason for wanting it for their class.
> >>> But think about how cool it would be for kids to be *building* their own
> >>> tools and then using them to do PCR.  Man, I for one felt like I got a
> >>> better understanding of gel electrophoresis when we tried to do it for $20
> >>> with tupperware and agar-agar.
>
> >>> So I think there is a huge potential for us to develop a robust, diy biotech
> >>> lesson plans for high school biology classes.
>
> >>> We could start with the gel electrophoresis protocol.
>
> >>> Mac
>

> >>> On Mon, Oct 20, 2008 at 3:08 PM, Jason Morrison <jason.p.morri...@gmail.com>

> >>> wrote:
>
> >>>> The following might be interesting for learning what kinds of
> >>>> supplies/labs/equipment should be cheaper to help promote biology research
> >>>> in schools, and I think high schools' budgets are interesting to consider,
> >>>> when we are considering DIY budgetary constraints.
>

> >>>>http://www.donorschoose.org/donors/search.html?sourceid=qs&keywords=b...

>
> >>>> "DonorsChoose.org is a simple way to provide students in need with
> >>>> resources that our public schools often lack. At this not-for-profit web
> >>>> site, teachers submit project proposals for materials or experiences their
> >>>> students need to learn. These ideas become classroom reality when concerned
> >>>> individuals, whom we call Citizen Philanthropists, choose projects to fund."
>
> >>>> Example:
> >>>>http://www.donorschoose.org/donors/proposal.html?id=195775&zone=0
> >>>> $284 for 4 DNA extraction kits?  Not sure what's included, perhaps

> >>>>www.carolina.com/text/teacherresources/instructions/biotech/dna_neckl...

> >>>> ?
>
> >>>> I think we can do better!
>
> >>>> -Jason
>
> >>>> --
> >>>> Jason Morrison

> >>>> jason.p.morri...@gmail.com
> >>>>http://jayunit.net
> >>>> (585) 216-5657

[Mackenzie Cowell]

This thread is awesome :)  Let's build one like Meredith's and blog it at DIYbio.org

[John Cumbers]

Mac,
You'd mentioned a DIYBio cookery show, how about you start it with 'how to make a gel box' we could offer to pay Ben Howard to film and edit the video,  perhaps you could mass order the $20 kits of plastic from TAP and then sell/redistribute the kits from the DIYBIO website along with the video showing you how to make it.

I guess that Ben would produce a decent video for $300 - $400, like the nanodrop one we paid him to make before (http://www.youtube.com/watch?v=aUZD8sj5c4w), or perhaps another DIYBIO'er would offer to make the video for free?   I offer $20 towards the cost of producing such a video, Mac would you be the host?  would anyone else chip in to see this happen? 

Cheers,
John







John Cumbers, Graduate Student
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.  
cell +1 (401) 523 8190, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA

[Jason Morrison]

On Thu, Oct 23, 2008 at 12:52 PM, John Cumbers <johnc...@gmail.com> wrote:

would anyone else chip in to see this happen? 

Definitely!

[Tito Jankowski]

I'll put in $50 towards a DIYbio video starring Mac, filmed by Ben Howard.
Tito

[Mackenzie Cowell]

Excellent!  I will contribute $100.

I think the idea of getting the resources together and offering them to the public at large on our site / wherever is a great idea, and one that the NUBs and their goal of "Angel Engineering" might be interested in helping us with.

What other episodes might we be able to develop quickly?  What other tutorials would be immediately useful?

Mac

[Jim H]

Do you think it's something we could ask the JoVE guys to do? I don't
know if they'd want to or not, but a thought.

On Oct 23, 3:40 pm, "Mackenzie Cowell" <m...@diybio.org> wrote:
> Excellent!  I will contribute $100.
>
> I think the idea of getting the resources together and offering them to the
> public at large on our site / wherever is a great idea, and one that the
> NUBs and their goal of "Angel Engineering" might be interested in helping us
> with.
>
> What other episodes might we be able to develop quickly?  What other
> tutorials would be immediately useful?
>
> Mac
>

> On Thu, Oct 23, 2008 at 1:41 PM, Tito Jankowski <titojankow...@gmail.com>wrote:
>
>
>
> > I'll put in $50 towards a DIYbio video starring Mac, filmed by Ben Howard.
> > Tito
>
> > On Thu, Oct 23, 2008 at 10:08 AM, Jason Morrison

> > <jason.p.morri...@gmail.com> wrote:
> > > On Thu, Oct 23, 2008 at 12:52 PM, John Cumbers <johncumb...@gmail.com>

> > > wrote:
>
> > >> would anyone else chip in to see this happen?
>
> > > Definitely!
>
> > > --
> > > Jason Morrison

[Tom Knight]

If we're doing this, it would be good to do a version with a set of
blue LEDs for under-gel illumination and an amber plastic cover for
viewing the gel. Both ethidium bromide and the sybr-safe and
sybr-green gel bands would be very visible with this illumination.
Done correctly, the illuminator and amber cover could be used to cut
out bands as well, without the gel box being present. We should
experiment with LED and plexiglass color to determine which ones work.
We might be able to arrange to use either the lab laser cutter or the
water jet cutter to fabricate these in reasonable volumes. Does anyone
know the stability of the monel wire? The pro boxes use platinum wire
electrodes, which are essential indestructible, though a little pricey.

[Meredith L. Patterson]

FYI, TAP sells translucent amber-coloured acrylic, in 1/8" and 1/4" thicknesses.

http://www.tapplastics.com/shop/product.php?pid=341&

I like the blue LEDs idea too. I was just going to take an animator's
lightbox (a friend is getting rid of one) and replace the bulb with a
UV bulb, but LEDs are certainly cheaper.

--mlp

[Michael Katsevman]

I took many photos of the gel boxes used at Brandeis University, which
look identical to those Meredith linked to.

I will convert those photos to a set of SVGs that are suitable for
using with a laser cutter (easily convertible to DXF in Inkscape) such
as available at TechShop <http://techshop.ws/> and the FabLab@SETC
<http://bostonfablab.mit.edu/blog/>.

These will be available by Monday.

Mike.

[Norman]

Tom,

I've done quite a bit of trial & error experiment with building a DYI
illuminator since I didn't want to pay Invitrogen for a $1090
SafeImager (pretty much a bunch of LEDs and a light filter). It's a
complete ripoff!

To use the blue LEDs you will need a correct excitation wavelength
filter, otherwise there is a lot of background glow when exciting SYBR
Safe dyes. Here are pictures with filter (http://picasaweb.google.com/
analogAI/GelElectrophoresis#5260883718409650418) vs without (http://
picasaweb.google.com/analogAI/GelElectrophoresis#5260883714098620786).
For EtBr there's less interference because the emission is more into
the orange/red wavelengths (away from the blue excitation peak) as
supposed to SYBR green/safe. I purchased 4x4 blue Tiffen glass
filters about $130, but you can get away with sandwiching Kodak
Wratten gel filters ($30-60) between two slabs of acrylic or glass
since the light source won't be hot. I also purchased pre-assembled
linear arrays of blue LEDs for about $80 on eBay. Put all that into
an existing light box (picture: http://picasaweb.google.com/analogAI/GelElectrophoresis#)
and you got a home made illuminator. I plan on building another
that's more compact so it fits in our lab's dark imaging box.

I still don't have a good place to cut acrylic so our lab went for the
premade Owl gel boxes for $300. The Owl gel boxes works but could be
much improved with a built-in light source... Gel electrophoresis box
and illumination of DNA are like cd players and speakers in a boombox,
I don't see why most setups are two separate devices for a such
commonly practiced task (or at least make them modules that fit better
together).

For gel cutting, a pair of amber glasses is about $34, but I think it
can be made much cheaper.

For a voltage source with timer, the eGel base is hackable (although
only at ~70V)... (does anyone have any old eGel bases to give away?)
for higher voltages to run SB gels, a commercial powersource might be
needed to do this safely.

Light Filtering Diagram:

--- User or Camera ---
=== Emission Filter (amber) ===
--- DNA Gel w/ SYBR dyes ---
=== Excitation Filter (blue) ===
--- LED Light Source ---

I'll be in Boston for iGEM in early November... we can work on any
details then, and get this DIY gel box started. (or contact me via
email)

Norman

P.S. I'll put in $40 for the video too, starring Mac, filmed by Ben
Howard. (awesome video btw! can't wait till the day we can build a
DIY nanodrop... )

[John Cumbers]

Could the gel box (now on steroids) also include a top mount for a USB camera, or maybe it's just a trivial thing to photograph it with a regular camera? ... just throwing out another suggestion.
great to see the extra donations coming in...

John


John Cumbers, Graduate Student
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.  
cell +1 (401) 523 8190, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA

[Kay Aull]

On Oct 25, 3:07 pm, "John Cumbers" <johncumb...@gmail.com> wrote:
> Could the gel box (now on steroids) also include a top mount for a USB
> camera, or maybe it's just a trivial thing to photograph it with a regular
> camera? ... just throwing out another suggestion.

When the gel camera died on me at work last year, I rigged one up
using a regular, entry-level digital camera and a cardboard box.

I cut a hole in the top of the box, just big enough to fit the lens
through. Then, when I needed a picture, I put the box-camera assembly
on top of the usual lightbox-gel-filter assembly. The box keeps out
ambient light and stabilizes the camera during longer exposures. It
should be tall enough so that the camera can focus properly, and
sturdy enough to not break, but that's not rocket science. And it
worked...maybe 70-80% as well as the commercial one, since mine had a
really cheap camera.

Hope that's useful.
- Kay

[Mario Raya]

I used to use a flower pot with an old 28mm prime lens (i have a
Pentax K110d), i also added an orange filter and used B&W for
development. We have a GelDoc XRS in the lab now, it is better, faster
and more sensitive but my $7.50 prototype worked very well for me. On
your average gel anything will do, i had some students who used
cellphone cameras to get close to decent pictures.
The GelDoc can deal with tough gels and playing with the settings can
help you see things that would escape a regular camera or would trick
your eyes, it is great but that doesn't mean you can only use that.
The software that BioRad provides with the system (Quantity One) helps
a lot but most of its functions can be accessed under the basic
(free!) version of it.

Mario