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)

“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...

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

--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.

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.

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?

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.

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.

It is weird being in this position having to come up with my final project so early in the year, but this will allow me to get done quicker as well as let me work in the summer to lighten my load next year. Most biology majors I have spoken to haven’t even really considered their final projects. I guess Noha and I will be more than prepared now!Hopefully the project I undertake will be interesting and open for my interpretation.

I would love to mimic this in my own research. If not now, then definitely in the future. I have a passion for Biology yes, but I also find Sociology equally important with what I want to do with my future career. It would be nice to merge the two and find a way to study how group interactions can effect biology.

For the last sages class I took which was a class on studying Human Attention, I found a way to merge the subject of attention with my love for sociology. I wrote my final research paper on how Human attention is affected by an individual’s cultural background and upbringing. In this paper I talked about how individuals from Eastern countries focus attention very differently than those from Western countries. This is due to the fact that cultural morals and values differ based on a society’s standards. I was really happy to be able to put my love for sociology into my research of attention because it made me really invested in the topic and paper allowing me to do a really good paper.

I hope to merge my interest in Biology and Sociology in my future endeavors. I think the more you are interested in a subject the better you will do in working with it. It is really important that when doing research, you never limit yourself to whatever you can find, but that you work to find what interests you the most. I hope for my final project I can do just that. I would love to have a passion for what I am studying.

The first option is to find a lab and work on a project independently were you can solve a problem, present it, and work on a poster or paper. This would fall under Biology 388 course.

The second option is to take a SAGES Keystone course that has the final project requirements built into the course.

The third option is for those who are in a research lab outside of school. To complete a project here, one must find a Biology faculty member to sponsor their project and have a lab boss at the place they are working to supervise a presentation and project.

The last option is an almost last resort where a student can do research on a certain area of study or topic and write a thirty page report or monogram on the topic. This option is completely independent and the student must meet periodically with their advisor as the project is completed to try and keep on a writing schedule.

So yeah picking one of these should be very interesting. I am leaning towards option one since I recently got into a lab...hopefully it all works out.

Oh and a random option would be doing my SAGES final project in Sociology, since it is my other major. According to Dr. Drushel, as a Biology major I can do a project in either one.

Lots to think about.

This got me thinking about other ways that can help in understanding what a research paper actually means. I found both this week and last week, that reading and truly understanding the introduction was really helpful. If you can get a firm grasp of the definitions, and background information that is less complicated then the methods, you can kind of get an idea about why they studied a particular thing and what they found. It seems to me that it is more important to understand the introduction, and conclusion rather than the methods. This approach was really helpful for me. I found it more beneficial to focus on the theory and what they wanted to find and what they did find versus the complicated methods they used in conducting research.

It is important to recognize your limitations when reading research articles. If the paper is on a topic or field you are not familiar with you have to realize what it is you want to gain from the paper. Ask yourself why am I reading this paper? You may come to realize that you want to gain a firm grasp of the theory, purpose and conclusion of the paper. Don’t get me wrong it is important to understand how the researcher collected data and conducted research, but at times you must realize that your limited knowledge does not allow for a complete understanding of the methods. I guess my point here is, don’t get all caught up in the fact that you don’t know how to derive a certain equation or that you don’ t really know what a Monte Carlo Simulation is, it is more important to get to why the researcher was interested in the topic, the benefits the findings could have, and the final conclusions discovered.

Oh and having an encyclopedia or internets source nearby is really helpful... :)

In my Sociology classes, we have talked about how as sociologists, we will constantly need to defend sociology as a legitimate “science.” It is not like Biology and Chemistry where questions are answered with concrete answers based on experiments that can be retested and the same outcome will arise. Sociology is more open to interpretation, and the answers that come from social experiments are very much limited to the factors that make it up, such as a sample size. The nature of the experiments and the questions asked are subject to many variables and it is impossible to account for all.

I guess there will be debates all around on what makes a field an actual “science”. I think the important thing to remember is legitimacy. If what you are studying and the results found are credible, testable, and the conclusions legitimate, then it can be considered a science. What makes something legitimate is also open to interpretation. If it is safe to say that what is legitimate is something that is agreed upon by many educated in that specific field, and something that is of interest and important to many in that field of study, then such a subject that deals with the earth, and the solid matter that makes it up is important to many, and the discoveries make an impact, then Geology is a legitimate science. The same can be said for Sociology, the study of groups and how they shape the individual and society is something that is to a degree testable, a topic of interest for many in the field, and involves conclusions that benefit and make an impact. By this definition, many areas of study, can and are considered a “science”.