April 22, 2008

More to do...

Other things I need to fix in my proposal:

PCR- Polymerase Chain Reaction: allows millions of copies of a specific DNA sequence to be produced in usually two hours. It bypasses the need for the use of bacteria.

Nuclear DNA content: the DNA located in the nucleus

“Purified” DNA: Means DNA samples that do not contain any other materials labeled “Junk” such as RNA and any other substances not pertaining to direct genetic mapping ( I need to ask Dr. Cullis more about this)

Variation in the Termination step: A thermocycler is used to vary the temperature in the solution so the ddNTP can bind to the template strand at different points. Each point in the strand represents a “letter” in a genetic sequence. Different ddNTP’s bind at different temperatures, so varying the temperature, allows them to bind in many places, therefore reducing the number of DNA templates needed for a complete and successful sequencing reaction.

The electropharigram shows the different wavelengths of color detected by the photocell , the peaks are seen and each peak represents a different letter (ACGT)

April 21, 2008

You said what?

One of the questions I talk about in my proposal involves the idea that part of this project is to develop new techniques for DNA purification. It was commented on my rough draft that I need to explain more about that key idea and develop it more.

“Also missing is a clear discussion of the data gained and how it will help address the fundamental questions in the proposed project.” So I figured the best way to tackle this is to free write, so here I go...

Here are the questions asked by Professor Hauck that need to be answered:
How will the data feedback into developing purification techniques?
As of now I am using a couple of techniques to purify the DNA and get rid of excess large pieces of RNA that cloud the sample.
We are using experimental amounts of Ribonuclease enzyme to help eat at the RNA and purify the sample. (Experimental means that a set amount of enzyme to add has not yet been determined as optimum). We also are using column filtration, to get rid of large pieces (Will this work? only trying will tell). And another technique is PCR through buffer solutions that will filter the DNA, that can be eluded, or removed from the filter through another solution. Optimum amounts for these solutions are still experimental and how much DNA that can be purified effectively at one time is still unknown.

2. What steps can be altered in response to new data?
We using gel electrophoresis to determine how pure a DNA sample is, or how clean it is. If bands corresponding to RNA show, then we have to continue, i.e., try same technique with different amount, or try another. That is what will be done in this experiment, to determine using trail and error what are the best amounts of solution to use for each technique for this kind of DNA.

okay now...to get this in my paper, and so that it makes sense...

April 20, 2008

Significance?

My rough draft is complete, all turned in but there is a lot I want to work on and fix.
It seems from my feedback, I need to relay more specifically the significance that sequencing the flax genome will have on the future of not only genomics in general. I want to emphasize the following:
-Studying that plant more closely and future implications that genetically modified (gm) flax crops could have in the future.
-A genetic sequence will allow us to see what makes up the genome and allow us to compare that genome with other sequenced plants, as well as allow us to discover if the flax genome really is as unique as we think it is, i.e.. does it really have low copy number sequences as we predicted
-Also this sequenced genome will allow us to see what makes makes flax oil polyunsaturated, i.e. study the composition and the implications of what makes it up with what it actually becomes, etc.
-Studying the genome will also allow us to get a better idea of how flax evolved, etc.

Just some ideas. Now to get them in my paper.

March 29, 2008

Introduction

So I’m working on my outline and I want to brainstorm some information that I will include in my introduction for the outline due monday.

--define genome
--define DNA sequence, what is it? how does it work? etc.
--Talk about complete sequences already mapped and how long they took
--Why is flax unique, what are the interesting properties
--Technology used to sequence genome
--How has this technology changed in the past years
--How this has changed what kind of questions can be asked in research

These are some ideas that I will add to my outline. Hopefully it will be enough for a well-thought out introduction.

March 28, 2008

Starting the outline

Working on the annotated bibliography allowed me to fully dive into the readings and try to not only determine why they are significant, but also how they relate to my research. Some of the papers have proved more difficult to muddle through than others.

Sometimes I found it difficult to get through the theory, I am only really familiar with the basics of DNA and genome research and theory. I have learned a lot however through the readings and my advisor was instrumental in helping me understand the key concepts.

Being able to connect what I was reading with my research was the key in understanding why I was given the paper and how it could help me write my grant proposal.

Meeting with my advisor, I have a got a better idea of how I am going to carry out my experiment, which involves classifying how much DNA is present in each sample prepared throughout the years and working to purify them, so they in turn can later on be sequenced.

Here is a rough draft of procedure:

Preparing samples for a gel electrophoresis to determine quantity of DNA present.

Looking at the most concentrated samples and purifying them to get rid of excess RNA etc

Running another gel to determine if sample has been successfully purified

Doing PCR to determine contents

Start over with new samples about 50 each time

More detail of course will be added but this is the very rough stuff to prepare for the outline.

March 11, 2008

Question Time!

I finally got my question together with Professor Cullis and I am really excited to finally know what I will be doing. I have to say I am really happy about this project not only because it is interesting but because it will allow me to explore techniques that, despite previous experience in the lab, I have never undertaken before. So now I can start going through the 7 articles given to me...LOL that should be fun. I have already been thorough some, and so far everything I have read has been helpful.

Here is my question:

Many plant genomes have been sequenced recently, and this project will involve working towards sequencing parts of the flax seen genome by fractionating the total nuclear DNA (flax genome) in order to determine the organization of the genome and how the genes in the flax are related to genes in other plants. In essence, two questions will be asked and answered in this project:

1. What is the characterization of the interspersion pattern of flax DNA? Interspersion refers to how repeated and low copy number sequences are arranged relative to one another
2.Are there recognizable retrotransposable elements in the flax genome?

March 04, 2008

I Need My Question!

So I met with my advisor, Dr. Cullis, about my senior project during the week that we did not have class. He spoke to me about two different possible projects that he thinks might be good for me to work on, including the one I am working on now.

The first involves something he is working on relating to the Biology class he teaches involving a plant from Africa, and looking at its genetic makeup and relating that to its ability to flourish in certain areas.

The second involves mapping of the Flax seed genome sequence. Which I am helping Dr. Cullis going through different samples taken years ago and running gels to determine how much DNA is present to determine which samples are best to undergo experimentation.

I am working hard with him to try and get a question formulated, he is just so busy since he has many graduate students under him and he teaches so many classes. I feel bad I was unable to turn in my question on Monday, but I do know when I turn one in, it will be complete and well thought out.

But other than the stress of getting my question together, things in the lab are going good.