Please see the email correspondence I had with a certain Tito
Jankowski, founder of Pearl Biotech at the bottom of this message for
more information. Sorry this is so jumbled, I'm still working out my
plan. Feel free to add to this
This can also tie in with the custom inkjet printer apparatus,
possibly in being a decent gene sequencer once modified properly:
http://www.physorg.com/news173950754.html
Justin (XiO2)
Also,
The International Genetically Engineered Machine competition (iGEM) is
the premiere undergraduate Synthetic Biology competition. Student
teams are given a kit of biological parts at the beginning of the
summer from the Registry of Standard Biological Parts. Working at
their own schools over the summer, they use these parts and new parts
of their own design to build biological systems and operate them in
living cells. This project design and competition format is an
exceptionally motivating and effective teaching method.
Justin (XiO2)
I am interested.
wow, this is really cool.
not sure how i can help, but you have my sword.
A few links to whole courses worth of video lectures I found. Amazing
what is available for free nowadays. If I'm not mistaken, a lot of
what goes on at Berkely is available online even if you don't take the
class.
http://www.learnerstv.com/course.php?cat=Biology
http://freescienceonline.blogspot.com/2006/08/chemistry-biology-and-life-sciences.html
http://webcast.berkeley.edu/courses.php
More updates as I come up w/ them
So will we be able to make glowing puppies?
(Reference: http://www.newscientist.com/article/dn17003-fluorescent-puppy-is-worlds-first-transgenic-dog.html)
hehe
Wow, really interesting stuff. Count me in. When are you getting the
Gel electrophoresis kit?
We could try to make this one that's up on thingiverse.com using the MakerBot:
http://www.thingiverse.com/thing:985
See also: http://www.shapeways.com/shops/labsfromfabs and
http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/
~Dave
That would be the win, definitely a sweet idea. But look at the shiny!
http://www.pearlbiotech.com/wp-content/uploads/2009/10/gel_box1.jpg
-Justin
P.S. Wonder if we could do that with this and other equipment? If only
temporarily :D. How big of an object can we make again?
Not sure when I plan on getting much equipment, I was hoping that if
enough people got interested we could take up a donations thing on
that one site (it is escaping me atm), at least until the next month
or so. It would of course then be property of the hive.
We need a lot of basic stuff too, like a nice microscope w/ camera
capability, and various other basic equipment (gloves, chemicals, pvr
thermal cycler, spectrometer). Not that we necessarily need it all to
begin working on something cool. Algae strains and various bacteria
would be cool to start working with. Maybe watching a few lectures on
the projector for those interested. I only recently started
accumulating data, maybe we should start a wiki w/ interested members
listed so we know who to keep in the circle?
-Justin
I have a cool looking microscope, it may need some work. I think we picked it up at a school auction some years ago… I can bring it into the hive.
This week and next are going to be pretty much hell for me, midterms, projects, homework and quizes all coming due in the same two weeks… I will see if I can take a picture of it and upload, I might ahve time tonight.
That would be excellent!
I should say from what I recall it might have some issues with the higher zoom lenses (maybe they need to be cleaned?) and the platform is set up to allow for X, Y panning, but it is missing the X part of the platform (could be replaced with some cut acrylic probably). I have not used or looked at it in years so it is also a bit dusty. In any case, it is something to look at and try. I just wanted everyone to be aware that it might not be the ideal option.
Hey, anything is helpful. Maybe this would be a good opportunity to
learn about how it operates, and fixing it might be fun. Maybe we
could use the makerbot to print missing pieces out?
-Justin
Updated Email correspondence:
Hi Tito and Justin -
I've got an idea for incorporating your gel box into a BioWeatherMap
protocol and for doing a distributed / collaborative research project
involving a few hackerspaces around the country.
One of my collaborators (professor at Univ. Colorado) has been
collecting a variety of environmental samples, ranging from swabs of
crosswalk buttons, doorknobs, handrails, ATM buttons, various surfaces
in public restrooms, etc...and seeing if he can get DNA to amplify in
the lab. So far, he has not been able to get DNA to amplify from
crosswalk buttons, meaning that the amounts of bacterial DNA are not
significant enough on the buttons in Boulder CO. Obviously, without
being able to amplify DNA from an environmental sample, we can't
perform DNA sequencing. So, this the "sniff test" for potential
BioWeatherMap samples.
My friend will continue to have the undergrads, grads, and post-docs
in his lab collect a diverse set of samples from different surfaces to
examine which ones will amplify, so we know what will work for the
BioWeatherMap. We're basically building a "hit list" for the
BioWeatherMap. It occurred to me that this might be an excellent
project to do on a distributed basis, leveraging hackerspaces et
cetera, and the results will be used in real life down-the-road to
help guide the BWM.
The protocol used by my collaborator is as follows: For each sample:
a. Extract DNA using the MoBio PowerSoil DNA sample extraction
kit
http://www.mobio.com/samples/powersoil-dna-isolation-kit-sample.html
b. Perform 4 independent PCRs and 1 negative control (no-
template, just water). The PCR will amplify a region (e.g. 27F-338R)
of the 16S rRNA gene
c. Combine the four replicate PCR products
d. Purify the combined PCR products with Ampure magnetic
purification beads (Agencourt)
http://www.agencourt.com/products/spri_reagents/ampure/
e. Quantify using Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and
a fluorospectrometer (NanoDrop ND3300)
http://products.invitrogen.com/ivgn/product/P11496?CID=Search-Product
http://www.nanodrop.com/Productnd3300overview.aspx
The cost of a nanodrop machine might put this particular protocol out-
of-range, but perhaps step e could be replaced with running the PCR on
a gel with a ladder. (Or, perhaps we could convince Thermo Scientific
to donate nanodrop instruments)
I think it would be useful to look through this protocol or a
variation of it, through a few lenses:
(1) Biosafety: Do any of these reagents call for special waste mgmt
practices? Are they safe to work with?
(2) Do-ability: How easily could this protocol, or one like it, be
implemented by hackerspaces
(3) Cost: What would the price be for each experiment, assuming
reagents are purchased at relatively low-volumes?
Thanks again,
Jason