My small step for science-kind

Well this week has been a little better then the last but I still have not gotten the results that I had initially hoped for, but the is the definition of science, right??
Actually, the definition of science, according to Webster, is "the intellectual and practical activity encompassing the systematic study of the structure and behavior of the physical and natural world through observation and experiment.". 

www.npr.org

 I've been doing a ton of experimentation but if nothing else, I'm fine tuning my DNA extraction skills, and in my field, that is never a bad thing. 

So this week there really isn't a whole lot of new progress but I have altered my protocol a bit.  I have increased my original DNA in salt solution sample.  Thanks to Anil, who gave me some valuable advice, I took 1.5 uL of each sample, spun it down, then I added another 1.5 uL of solution and spun in down again to maximize the amount of DNA. 

I think that my problem this week is that my samples are not longer viable, they may be too old.  So today, I'm hoping to start some new solutions with samples from my fellow students.  But I did make some progress, I got one really bright band from a member of our Bioscience staff, I was able to reproduce it twice so I know that I am on the right track.  Below are a few photos of my some-what-successful electrophoresis gels.

The bright orange band is the best sample that I have gotten so far

This is my desired results. 

The STEMamiga's

Yea!!  There are signs of new life....in the form of new STEM students and I'm excited.  Not that I'm complaining about the old blood that's been flowing around here for the past few months, (actually semesters) but the new gang seems like they are going to all fit right in, ESPECIALLY my new girls!!  I've racked my brain for this one (so hold on...its a real knee slapper....if you were born in the '70's or early 80's) but seeing as we are females are an uncommon species this time around in STEM, I unofficially named us The Three STEMamigas!

craveonline.com

BUT like so many things in my life this week, this didn't work out.  On the bright side, I've been told that there are 5 lovely ladies this semester, I can't wait to meet you all :o)

The other thing that didn't go well this week was my DNA extraction.  I tried using a new protocol that Gilbert and Matt had been working on.  To tell you the truth, I was really excited to use some advanced techniques to extract my DNA as my rudimentary soap extraction was not that high-tech.  I had my victims wash out their mouths out with a intense salt rinse for about 45 seconds and politely split the solution into a cup.

Me and my salt rinse

With the help of a kit from Promega called the "Wizzard DNA Clean-Up System" I added a resin that helps separate the DNA from the rest of the materials (frosted flakes, muffins...breakfast).  I added 1ml of the resin to Micro centrifuge tubes and added 50 uL of DNA solution, inverted the tube a few times to let the resin bind to the DNA.  Then I attached a lure lock syringe to a minicolum (which as a filter to catch the DNA.  The solution was pushed through the filter then I added 2mL of 80% isopropanol alcohol to the syringe and pushed that through the filter to clean the DNA and spun it in the centrifuge for 2 minutes on high.  I added 50uL of warm DI water and tel that soak into the filter for about 2 minutes then spun it again.  I was left with about 60 uL of a "pure" DNA solution...or was I???  I had my electrophoresis gel all ready to go and added my control sample and volunteer samples into the gel wells with the correct amount of orange loading dye and saber green.  I ran it at 120volts for 45 minutes while I was in class.  I was pumped when I got back to see what kind of bands were on my gel, but it was a bust!  I looked at my gel under the UV light box and only saw my control band.  Sigh....all that work for naught :o(

But I will try again tomorrow...so I'll be coming for all of you with salt water in hand!!!

I wanted to end this weeks blog with a great quote:

Remember that guy that gave up? Neither does no one else.

– Unknown

Looking for volunteers....You should probably inquire first before you say yes!!

“Three things you cannot recover in life: the WORD after it’s said, the MOMENT after it’s missed and the TIME after it’s gone. Be Careful!” – Unknown

I think that this quote is fitting seeing as we are all hitting midterms and we are really into the "meat and taters" of the semester...that said, putting the time and effort into S-STEM sometimes seems like the cherry on top of the cake that is on top of the pile of books, the mountain of papers, which is on the TI-84 calculator, on the beaker full of acetone, which is balancing on the broom.  But it can be done....trust me.

I am running another experiment this week in order to collect my DNA and run my PCR.  I am going to enlist the help of Anil to do so as he is the resident PC PCR expert (toot toot!!).   Once this is completed, I'd like to get one of my fellow STEM buddies to do a salt rinse so that I can collect their DNA.  I would really like to do a comparison to see what STR's that we may have in common.  STR stands for "Short Tandem Repeat", it is an analysis is a relatively new technology in the area of forensic science, which many of you may know is my major, and it is very up and comming. It has been recently identified as “genetic fingerprinting.” Results from this analysis are most often used in the identification of a suspect in a crime. These results are input into the Combined DNA Index System (CODIS) for matching purposes. CODIS is an FBI-funded computer database, which stores the DNA of convicted sex offenders, convicted murderers, certain felony offenders and other criminals.  So if my volunteer fits any of these categories....you may want to rethink giving me your DNA!!  Kidding, I'll be keeping it off the FBI database, I promise.

www.le.ac.uk

STRs are short sequences of DNA, normally of length 2-5 base pairs, that are repeated numerous times in a head-tail manner, i.e. the 16 bp sequence of "gatagatagatagata" would represent 4 head-tail copies of the tetramer "gata". The polymorphisms (variations in DNA sequence between individuals) in STRs are due to the different number of copies of the repeat element that can occur in a population of individuals. (Criminalistics: An Introduction to Forensic Science, R. Saferstein)

Any takers????

Viruses, alive or not alive....that is the question

Let’s first define life. According to the online Webster's dictionary, life is “an organismic state characterized by capacity for metabolism, growth, reaction to stimuli, and reproduction.”
Grrr....So I guess I was wrong, viruses are not living things. Viruses are complicated assemblies of molecules, including proteins, nucleic acids, lipids, and carbohydrates, but on their own they can do nothing until they enter a living cell. Without cells, viruses would not be able to multiply. Therefore, viruses are not living things.
But viruses are stilling of the fence of the definition of life. They lie somewhere between complex molecules and very simple biological units. Viruses contain some of the structures and exhibit some of the activities that are common to organic life, but they are missing many of the others. So in a nut-shell, viruses are entirely composed of a single strand of genetic information encased in a protein capsule. Viruses lack most of the internal structure which define 'life', including the organ structures that are necessary for reproduction. In order for a virus to replicate or multiply, it must first infect a suitable host cell.

So I stand corrected...or do I??

There is still a debate that flip flops in the scientific world, that viruses are thought of as being in a gray area between living and nonliving, so it really depends on who you ask!!!
Jeremy and I had a nice little conversation about this today so I thought it was fitting to address in this weeks blog.

And, for your viewing pleasure, here are two hand drawn (by me of course) examples of viruses.

I'm back baby...better late then never

Hello STEM family,

I know, I know..I've been away for the last week recovering from surgery but glad to report that I'm on the mend.

In my down time (only when the vale of pain meds had lifted), I read some really great articles on viral DNA in the human genome and what is actually does and how through Bioinformatics, viruses are being tracked .  I'll report on some of that later this week but today (better late then never) I wanted to give you a little bit of insight on viruses.

Viruses are actually the smallest living thing known to man.  We all know of and we have all has small and quite simple viruses like the cold or a flu, but viruses cause a wide range of disease, a lot of them being deadly.
When we think about it, viruses have been around for a long time, maybe even as long as the first humans inhabited the earth.  One can say that we, humans are all actually part virus.  The human genome contains more DNA from viruses then the DNA that makes up our own genes.  Scientists have identified thousands of segments of retroviruses (A retrovirus is a virus whose genes are encoded in RNA instead of DNA) DNA in our genes, which make up about 8% of the human genome.
Human genome DNA and viral DNA contain segments.  According to an article written by Carl Zimmer, three of these segments that are shares are gag - which is where virus genes or genetic make up are stored, env - the knobs that appear on the surface of the virus that allows the virus to attach itself to the non infected cell in order to invade said cell and pol which creates the enzyme that inserts the virus genes into the host cell DNA.  Together, these segments invade viable cells where they are replicated and multiply at alarming rates causing rapid decline in a number of hosts, such as cancer and aids patients. 

www.dna.org