Archives for the Month of March 2008 on Christina Cajigas's Online Journal
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.
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.
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?
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.
Getting used to It
This is my second week in the lab and I have spoken to Dr. Cullis about preparations for my final project. I am working this week on getting used to certain things in the lab, and looking toward possible questions I may want to answer. I figure I can continue to work on the project that he has be working on now. We are trying to map the DNA genome of Flax seed, working towards making genetic maps. Of course that is a very rough definition of what we are doing but until I know more, that will suffice :)
As of now we are looking at all the DNA samples he has collected and developed over time and running gels to determine how much DNA and RNA is present. He is working to getting a lot of what he worked on in the past published today because many other labs are working on flax seed genome and he wants to publish what he already discovered before it gets too hard to publish.
Hopefully I can be some help there.