Archive for the ‘Uncategorized’ Category

Quick rough notes

August 27, 2013
1)  Strawberries probably have xanthosine biosynthesis pathway, but I need to double check that they do.
2)  Need to verify the NCBI ascension numbers i have for the caffeine biosynthesis pathway are correct.
After 1+2 then I need to make some primers.
NOTES:
 Xanthosine biosynthesis:
guanine
[e] guanine deaminase
xanthosine
or
hypoxanthine
[e]xanthine oxidoreductase
xanthosine
Caffeine synthase pathway:
XANTHOSINE
[e1] xanthosine methyltransferase (XMT)
7-METHYLXANTHOSINE
[e2] 7-methylxanthosine nucleosidase
7-METHYLXANTHINE
[e3] 7-methylxanthine methyltransferase (MXMT or theobromine synthase)
3,7-dimethylxanthine (theobromine)
[e4] 3,7-dimethylxanthine methyltransferase (caffeine synthase)
1,3,7-trimethylxanthine (caffeine)
Xanthosine biosynthesis:
guanine
[e] guanine deaminase
xanthosine
or
hypoxanthine
[e]xanthine oxidoreductase
xanthosine
Caffeine synthase pathway:
XANTHOSINE
[e1] xanthosine methyltransferase (XMT)
7-METHYLXANTHOSINE
[e2] 7-methylxanthosine nucleosidase
7-METHYLXANTHINE
[e3] 7-methylxanthine methyltransferase (MXMT or theobromine synthase)
3,7-dimethylxanthine (theobromine)
[e4] 3,7-dimethylxanthine methyltransferase (caffeine synthase)
1,3,7-trimethylxanthine (caffeine)
Source:
Uefuji H, Ogita S, Yamaguchi Y, Koizumi N, Sano H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 2003;132:372–380.
Uefuji H, Ogita S, Yamaguchi Y, Koizumi N, Sano H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 2003;132:372–380.
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Hangout is live

February 2, 2013

Hangout is live

https://plus.google.com/111857545829837898782

Google+ hangout

February 2, 2013

There will be a Google Plus hangout tonight about anything DIYbio or bio related.  A link will follow.

Science Hack Day 2012

October 16, 2012

I am going to the annual Science Hack Day in San Francisco again this year (November 3-4).  For those of you not familiar with it, its a 2 day event (overnight if you like) where a bunch of like minded citizen science folks get together and work on projects.  Some hacks relate to space and others to biology.

http://sf.sciencehackday.com/

 I’ll be working on two biology projects ( I think).  I am going to try to make a sterile hood out of home depot and target supplies and I am going to work on some PCR related stuff.

 

Dont live near SF?  There are other affiliated science hack days that occur world-wide!  So check it out.

Isolate and drink your DNA with bacardi.

June 28, 2012

DNA tendrils floating between a sandwich of banana puree and booze.

This instructable was based off  a ScienceHackDay SanFrancisco team that I was part of along with Patrik D’haeseleer, Bonnie Barrilleaux, Lily Lew, Joseph Elsbernd, and Michelle Peters.  It is really easy to do and a fun way to incorporate molecular biology into your social life!

http://www.instructables.com/id/DNAquiri-the-delicious-DNA-extraction/?ALLSTEPS

Lab grade vs. home grade electrophoresis buffers

June 8, 2012

(note:  wordpress sucks so it screwed up my images some.)

I wanted to find a cheap way to make electrophoresis buffer from easily accessible ingredients and there were two pieces of knowledge that led me to this experiment.  First I had read about some labs using sodium borate (SB) buffer because it gave great results.  Secondly, I knew that borate and boric acid were easy to find at stores in the forms of roach poison (boric acid) and borax (sodium tetraborate).

Originally I had intended to compare a large number of buffers; TAE, TBE, SB (molecular biology grade), and SB (home grade).  Due to my own personal shortages of lab-grade materials I had reduce down to a comparison between TBE, SB (home grade), and SB with EDTA (home grade).

All gels were 1% agarose.  Gel images were made with Foto/Phoresis I transilluminator and gel images were recorded with an iPhone 3GS camera.

Tris-Borate-EDTA (TBE)

Purchased from the “Online Science Mall” as a 5X concentrate.  Without a doubt this worked better than the buffers I cobbled together.

 

SB Buffer (home-grade)

SB buffer made by adding 1.91g of Sodium borate decahydrate (Borax by 20-mule team) to ~800mL distilled H2O (Target), pH was adjusted with 0.4M Boric Acid (Roach Away by Enoz) and then diluted to final volume with more distilled water.

SB Buffer with EDTA (home-grade)

Image

A 600 mL aliquot of the SB buffer, made previously, had 1.2 mL of 0.5 M EDTA (molecular grade) added to reach 2mM final concentration.

I decided to test the SB buffer with EDTA to see if there were any nuclease related problems occurring.  2/3rds of the way through the project it occurred to me I was using Target brand distilled water instead of nuclease free water when mixing the 2-log DNA.  It just simply slipped my mind.  So this third gel buffer test was done with EDTA and nuclease free water to see if the results would be drastically different or not and they were not.  I believe any differences in the images is due to my lack of a proper gel documenting system.

Given the choice between the three buffers, TBE is the superior.  I do not mean to say that one could not use the SB home grade buffers and get usable results, but rather they just are not as good.  Being that store bought TBE and TAE are not crazy-expensive and buffers can be reused a couple of times, there is not a lot of impetus to use home-grade SB buffers.

My results for the SB buffer tests do not even come close to mirroring the results from the Brody paper I linked earlier, I suspect that my preparation or formulation of SB may be flawed.

While unfortunate that I couldn’t test more buffers, I was happy to figure out that TBE will likely work for my PCR projects in the future and if I am ever mismanage my supply of TBE I now know I can make up some SB buffer to get by.

Democratized science instrumentation

May 30, 2012

Arield Waldman was commissioned to and wrote a guidebook about a bunch of DIY science projects that have gone on.  I was interviewed for background and my gel box was included in the paper!  Really cool!

You can check out the actual paper from a link on her blog.

 http://arielwaldman.com/2012/05/29/democratized-science-instrumentation/

My (finished) master’s project or this is why I haven’t posted much.

May 10, 2012

I finished my master’s project two weeks ago and it was accepted by the committee, and the school administration!  If anyone feels like checking it out, follow the link below.

Investigation of the role of fragile x mental retardation protein in embryonic neocortex using RNA interference.

What I did, in brief, was attempt to recreate a fragile-x-syndrome-related disease in neural stem cells by reducing fragile x mental retardation protein (FMRP) experimentally in normal mice.  I was able to get some aspects of the disease state to manifest but I did not completely recreate it.

The write-up and final touches really sucked up all my free-time (but was totally worth it).  So now I should have more time for cheapass science.

My project was supported by the California Insitute for Regenerative Medicine (CIRM), California State University Sacramento, and the Noctor Lab at the UC Davis MIND Institute.

 

Human cheek cells with methylene blue

April 16, 2012

I have not done much home lab work on account of finishing up my master’s.  But toady I squeezed in some time for microscopy.  Below is a link to some photos of my cheek cells stained with methylene blue.

 

http://www.flickr.com/photos/codonaug/sets/72157629826384173/

I used “aquarium grade” methylene blue for the staining – obviously because it was cheap.

Tekla Labs – Promising website

January 12, 2012

I was recently linked this website through a forum and thought it was worth sharing.  So far they have two guides, one for a stirplate and the other a sample rotator.

 

http://www.teklalabs.org/

Tekla Labs is a community effort to build, document and teach the construction of high quality, self made laboratory equipment. Our initial focus is on biological research.

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