BIOL398-01/S10:Class Journal Week 11

Kristoffer Chin

1. The purpose of this assignment was to introduce the class into the application of DNA microarray. The journal was used in order to understand more of its application as an example rather than just describing. It gave insight of what kind of research question we can establish and how to go about answering it
2. I learned that microarray is efficient finding genes and its expression but there are still errors that can occur. I also learned that zinc is actually very important to the growth of a plant and growing it without a sufficient amount of minerals can cause a decrease in growth. I also learned that there are certain plants that are able to take in more zinc than others which may have occurred from evolution due to its environment

• There were many proteins that were identified in the paper but not thoroughly explained. I was wondering if when we do the research portion of the microarray, if we would have to only identify them or explain each protein found.

--Kristoffer T. Chin 23:23, 11 April 2010 (EDT)

Kristoffer Chin: Week 11

BIOL398-01/S10:Week 11

Salomon Garcia

1. The purpose of this assignment was to begin the preparations needed for our final project which involves DNA microarrays. And in order to begin this task we began by reading the article we were given by Dr. Dahlquist on Arabidopsis. While doing this we were to define words that we did not understood for a total of 10 words.
2. I learned from this assignment that there is a lot of data to be covered that will in turn be useful when it comes to time using programs such as GenMAPP and MAPPfinder. I also learned from the article that Zinc in plants in high amounts is not as toxic as it is in others.
3. So far there are no questions, but it does seem that there is a tough road ahead when it comes to this the final project.

(Salomon Garcia Valencia 15:04, 6 April 2010 (EDT))

Angela Garibaldi

1. The purpose of this assignment was to read a paper that utilized DNA microarray to thoroughly understand the process. In this we were meant to understand how samples were generated, the number of replicates, what the results meant, and how this was important in the experiment.
2. I learned that it can be really frustrating reading a short paper because authors tend to pack as much into every paragraph as possible and it may not always be clear as to what came first or what was done. However, when I accessed the data related to the paper through the accession number given at the end of the paper, I found that some aspects were better covered in regards to experimental set up and development of samples. I will definitely be sure to look up any accession numbers to microarray data in the future.
3. I am still not 100% clear on all of the samples and how many chips were used. I looked up the sample chip and how they plotted the samples and didn't understand. It didn't look like a DNA Microarray with the green, yellow, and red dots. Angela A. Garibaldi 00:14, 12 April 2010 (EDT)

• Week 11 Assignment

• Week 11 Journal

Alex George

1. The purpose of this assignment was to read to relevant article to our project topic and begin outlining it for our journal club presentation. This topic covers using Microarray data in order to notice patterns in the transcriptome activity of organisms
2. From this class period and assignment, I learned the reason why DNA Microarray analysis is performed and why RNA is used for analysis instead of proteins. Also, from the paper I learned the different techniques of Microarray data and how it can be used to analyze the response of yeast to cold environments
3. I have no questions regarding the idea of the project. Some of the aspects of the paper are hard to work with. One question I have is, Do I have to look at the other paper's techniques in order to figure out the methods used by Tai et al.?

J'aime Moehlman

1. The purpose of this assignment was to read the article that was related to our project topic and then create an outline for our journal club. The paper talks about the use of microarray data in order to analyze the bacterium V. cholerae.
2. I learned more about what exactly microarray data is used for and how to interpret it. I also think that this is one of the more interesting topics we've been working on and am excited to create a research project based off of the microarray data.
3. At this point I dont have any specific questions, I'm not positive that I know what all the microarray data can be used for, but I think that will be cleared up in this weeks work session.

J'aime C. Moehlman 03:18, 12 April 2010 (EDT)

• Week 11 Assignment

KP Ramirez

1. The purpose of this assignment was to begin working on our DNA microarray project. It began by getting our research paper centered on Prostate cancer in human beings. After reading through the paper, I analyzed 10 terms as definitions and proceeded to begin an outline of the paper to being my journal club presentation for next week.
2. This week allowed me to begin looking over my raw data in excel form to prepare getting it ready for GenMAPP and MAPPfinder.
3. Currently I don't have any questions yet, however, I'm already beginning to prepare as to how i'm going to analyze and prepare the data. Since it was done using an earlier form of DNA microarray data I realize that it will be a little bit of work to classify everything.

KP Ramirez 10:54 am April 6 Individual week 11

Michael Piña

1. The purpose of the assignment this week was to familiarize ourselves with our organism and the research done on it order to carry out our own projects. Once we are able to input the data from the study into GenMAPP, we will take a look at the biological pathways involved and compare them to what was covered in the article.
2. This week I learned how Zinc can affect organisms such as A. thaliana. I am becoming increasing comfortable reading articles that used to seem daunting not too long ago. Also, I am getting more comfortable creating professional style presentations.
3. There wasn't much I didn't understand besides some of the vocabulary. The article was fairly straightforward. I expect some questions may arise as we begin our project.

Individual Week 11

Janelle N. Ruiz

1. The purpose of this assignment was to learn about the methods used in our papers and begin to get comfortable with the data in preparation for beginning our microarray project.
2. I learned the purpose of DNA microarrays and how to look at the raw data.
3. I have no questions at the moment but I am sure I will be confused once we start our analysis next week.

Janelle N. Ruiz Assignment 11

Janelle N. Ruiz 13:37, 11 April 2010 (EDT)

Bobak Seddighzadeh

1. Purpose of this assignment was to have us do a journal club on the start of another paper and to familiarize ourselves with our organism that we will be doing our project on
2. I learned from this journal club the different effects of cold shock and acclimation in S Cerevisae yeast
3. I am still slightly unclear on a couple of the results in the paper. I want to come into office hours tomorrow to clarify them

• Electronic Journal

1. Bobak Seddighzadeh Week 2
2. Bobak Seddighzadeh Week 3
3. Bobak Seddighzadeh Week 4
4. Bobak Seddighzadeh Week 5
5. Bobak Seddighzadeh Week 6
6. Bobak Seddighzadeh Week 7
7. Bobak Seddighzadeh Week 8
8. Bobak Seddighzadeh Week 9
9. Bobak Seddighzadeh Week 10
10. Bobak Seddighzadeh Week 11
11. Bobak Seddighzadeh Week 12
12. Bobak Seddighzadeh Week 13

• Shared Journal

1. BIOL398-01/S10:Class Journal Week 2
2. BIOL398-01/S10:Class Journal Week 3
3. BIOL398-01/S10:Class Journal Week 4
4. BIOL398-01/S10:Class Journal Week 5
5. BIOL398-01/S10:Class Journal Week 6
6. BIOL398-01/S10:Class Journal Week 7
7. BIOL398-01/S10:Class Journal Week 8
8. BIOL398-01/S10:Class Journal Week 9
9. BIOL398-01/S10:Class Journal Week 10
10. BIOL398-01/S10:Class Journal Week 11
11. BIOL398-01/S10:Class Journal Week 12
12. BIOL398-01/S10:Class Journal Week 13

• Assignments

1. BIOL398-01/S10:Week 2
2. BIOL398-01/S10:Week 3
3. BIOL398-01/S10:Week 4
4. BIOL398-01/S10:Week 5
5. BIOL398-01/S10:Week 6
6. BIOL398-01/S10:Week 7
7. BIOL398-01/S10:Week 8
8. BIOL398-01/S10:Week 9
9. BIOL398-01/S10:Week 10
10. BIOL398-01/S10:Week 11
11. BIOL398-01/S10:Week 12
12. BIOL398-01/S10:Week 13

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Amanda Wavrin

• Amanda N. Wavrin Week 11
• Week 11 Assignment Page

1. What was the purpose of this assignment? The purpose of this assignment was to start working with DNA microarrays and to familiarize ourselves with our project topic, Vibrio cholerae. The journal gave us a more in depth understanding of the procedures used in DNA microarray.
2. What did I learn from this assignment (head, hands, heart)? From this assignment I learned the importance of DNA microarray. I also learned about all of the work that goes into preparing and performing microarrays and the importance of them relative to our topic.
3. What did I not understand (yet) about this assignment? So far I do not have any questions so far. However, it was frustrating using such a short article for our journal this week. There was a lot of information packed into little space and that made it difficult to umderstand at times.

Ryan Willhite

1. What was the purpose of this assignment? The purpose of the assignment was to learn about microarrays and how this method is used to see differences in gene expression in comparison to two different cells. Through color, it allows one to see whether or not gene regulations was increased or decreased or perhaps similar between the two cells. Along with this knowledge comes a better understanding about our papers and how it all connects. With the sample powerpoint there was a basis as to the steps of microarray as well as analysis steps. In our papers these steps were taken, however had different solutions used, tissues or cells sampled, etc. We had to make the correlations in this assignment.
2. What did I learn from this assignment (head, hands, heart)? I learned how important microarray is in experimenting and I also was able to see all the benefits. Along with benefits limitations were found as well that may hinder experimentation, however knowing these limitations allow for improvements. What was really interesting is doing my own reserach and finding how microarray can even be used in sampling tissues for cancer cells versus healthy cells. Once the samples are taken we can analyze and see what genes are turned off or on in cancer cells as well as what genes are particularly different and do further research.
3. What did I not understand (yet) about this assignment? I still have a hard time correlating or making much sense of the data we received in the excel document.

Ryan N. Willhite 20:40, 11 April 2010 (EDT)

• Week 11 Assignment Page

• Week 11 Journal