User talk:Carmen E. Castaneda

Week 12 Journal Feedback

• I see that you had a little trouble with interpreting your GO terms; hopefully it helped when we went over it in class.
• Also, you should look up the individual transcription factors that you added to the model at SGD to see if there is any further connection with these transcription factors and cold stress.
• I did not receive the PowerPoint file that was supposed to be turned in with this assignment, but I was at least able to see some of your figures in class when we went over your cluster, so that's OK. Remember that these figures are going to be included in your final paper.

— Kam D. Dahlquist 00:13, 28 April 2011 (EDT)

Week 11 Journal Feedback

• Thank you for turning in your assignment on time.
• As we discussed in class, the equations for the T statistic in your spreadsheet were incorrect because they were referencing the wrong ranges of cells and had the wrong number of replicates. I believe you have fixed this, but you didn't give me a copy of the corrected spreadsheet. Would you please post the corrected Excel file on Lionshare and send me the link so that I can double-check it for you?
  • Because the T statistics were incorrect, the answers to the subsequent questions (e.g., how many genes have p value < 0.05, etc.) are also incorrect. You will need to re-do this to include in your final paper. I can double-check this for you when I look at your spreadsheet, if you want.
• In answer to the question about why we use the "$" when referring to the cells containing the chip average and standard deviation, your answer is correct. It is important for us to keep the reference cell the same because we need to scale and center each log fold change on the chip with the same average and standard deviation; otherwise we will have mistakes in our data.
• You didn't answer the question about what Schade et al. considered a significant gene expression change. In the paper it says "To ensure significant data quality, we selected genes with at least twofold variation and a Student’s t test p value of < 0.03." How does this compare to what we are considering significant?
• Although the most significant gene will likely change once your equations are corrected, I will comment on your interpretation of YML038C. The word "putative" in the gene description means that the gene has only a predicted function based on the similarity of its sequence to other genes that have that function, but it has not yet been verified in the lab. You next need to look at the average log fold change to see if the expression is increased or decreased. The interpretation will be different whether the gene is increased or decreased in expression.
  • If the average log fold change is increased, it means that there is more mRNA (and thus more protein) being produced than before the cold shock started.
  • If the average log fold change is decreased, it means that there is less mRNA (and probably less protein) being produced than before the cold shock started.
    • So, to interpret, if this gene is increased in expression, maybe that means that the cell needs more sugars so it is increasing the number of transporters to let the sugars into the cell.
    • If this gene is decreased in expression, maybe the cell is not growing (as you suggest) and doesn't need more sugar at that time.
    • In the Schade paper, they verified that glucose (sugar) in the growth medium was not limiting, so the explanation has to be internal to the cell.
• The electronic lab notebook part of your assignment is extremely brief. Ideally, an electronic lab notebook would describe the steps you took in enough detail so that you or someone else could reproduce what you did.
• You did not complete question 4 of the shared journal assignment.
• Please let me know if you need further assistance with this part of the project.

— Kam D. Dahlquist 20:22, 25 April 2011 (EDT)

Announcement Concerning Matlab

The computers (24 iMacs) on the first floor of Hannon Library have matlab installed. You should be able to access them most of the weekend (hannon hours). Ben G. Fitzpatrick 20:46, 4 February 2011 (EST)

Week 5 Journal Feedback

• You're pushing it, timewise. Your work is a little late. You should consider starting sooner.
• The work is somewhat vague. Since you did not provide any plots or quantitative results, it is difficult for me to judge exactly what you did. Statements like "each parameter reaches this curve in a slightly different manner" beg for fuller description. Different in what way? I would encourage you to come see me so that you can show me more of what you did here. I would also welcome a more complete posting.

Ben G. Fitzpatrick 14:31, 16 February 2011 (EST)

Week 4 Journal Feedback

• Sorry the feedback is delayed so.
• The terminology section is a little vague. There are some missing points of importance that you should clarify. After we've discussed the chemostat, and you've read the notes, perhaps you could add some more detail to that one. Exponential growth is something pretty specific, as well. You might want to reflect on that too. The Lineweaver-Burk experiment requires measurement of the substrate concentration and what else, at different times or levels?
• Your matlab plots are good.
• Your Lineweaver-Burk computation is correct.
• I appreciate your candor on the matlab challenges. I understand the difficulty of learning new biology/chemistry/mathematics and computing all together. Please come to see me or ask questions during class time.
• The Michaelis-Menten equation is a model of an enzyme reaction that assumes a certain component of the model is in equilibrium. The model involves certain constants (rate parameters) that you have to know in order to use the model to simulate a reaction. The Lineweaver-Burk technique is a way to use experimental data to find values for those parameters. Does that help?

Ben G. Fitzpatrick 14:31, 16 February 2011 (EST)

Week 3 Journal Feedback

• Sorry the feedback is delayed so.
• Thank you for providing personal interpretations along with quoted definitions.
• Mass action is pretty specific: the rate of change (or the "intensity" of the reaction from your quote) is proportional to the products of the concentrations of the reactants. Your definition is a little fuzzy there.
• The mass action ODEs need some work. For example, in the first problem, the rate of gain of C has to be the same as the rate of loss of A, which is also the same as the rate of loss of B. The other three problems had similar oversights. Please see my worked assignment 3 for more.
• Your matlab graphs look good.
• Equilibrium and homeostatis are not quite the same thing. I have provided some discussion in the worked assignment 3.

Ben G. Fitzpatrick 14:31, 16 February 2011 (EST)

Week 2 Journal Feedback

• Thank you for making the requested changes to your template.
• Thank you for submitting your week 2 assignment on time.
• Your definitions and outline are complete.
• Be careful of the formatting you use for external hyperlinks. For an external hyperlink, there is no "|" symbol between the URL and the label, the "|" is only used when the link is to a site within the wiki. Because of the extra "|" symbol, the hyperlinks you made to the online dictionary are not working. When you code your wiki, you should try the links to make sure they work as expected and you should look over your page to make sure it did what you wanted it to do.
• ACT1 and H2A-H2B are not actually biosynthetic genes (they do not code for enzymes that carry out biosynthesis reactions). Instead, ACT1 codes for actin which is a component of the cytoskeleton (literally cell's skeleton, providing structure support). H2A-H2B are histone proteins, which the DNA winds around in the nucleus to keep it compact and organized. These are controls for which the gene expression should remain constant in the experiment. If they had shown the blots, we should have been able to see that.
• For the figure you are presenting in class, you could have had a little more detail analyzing the plots.
• You did not need to copy the references from the paper into your outline. References should only be included if you personally read the paper. For your outline, the only reference should be the ter Schure paper itself (unless you did read one or more of those other papers.)

Week 1 Journal Feedback

• Thank you for submitting your assignment on time. The content and all of the skills are complete except for your template.
  • You did create your template page at Template:Carmen E Castaneda. However, the next step is to invoke your template in your use page. To do this you use the syntax {{Template:Carmen E Castaneda}}. Wherever you put that code, the content of your template will appear automatically.
  • To make your template more useful to you, you could take the table of assignment links that you made and put it in your template instead of on your user page. That way, each time you create a new page, you can just invoke your template and all of the links will be made for you automatically. I also suggest that you put the course category on your template page so that can be done automatically as well.
• You can delete the text that OpenWetWare put on your talk page below if you want.

— Kam D. Dahlquist 19:20, 17 January 2011 (EST)

Responses to Instructor Questions

You asked: "Hello Dr. Fitzpatrick! I was wondering what was your hardest math class as an undergrad? Carmen E. Castaneda 08:38, 16 January 2011 (EST)"

• I answered: Ben G. Fitzpatrick 13:53, 16 January 2011 (EST). Math 520 at Auburn, Real Analysis, like our 321, was the hardest, at least for the first 4 weeks. The course was taught by Professor Ed Moise in the R. L. Moore style, so that the teacher provided definitions, problems, and theorem statements ONLY. Students had to work out the proofs, detect incorrect theorems and provide counterexamples, and solve the problems. The library was off-limits. I had taken a year of modern algebra before this course, so I have some sense of proof (we didn't have a 248 equivalent). It took me a while to get the hang of it, but after taking two years of (undergrad and grad) real analysis this way, I found it very helpful in my future work.

You asked: "Hello there Dr. Dahlquist! After reading Janovy, I was wondering if you can recall your earliest memory that might have lead you to the career path you have chosen? Carmen E. Castaneda 08:36, 16 January 2011 (EST)"

I don't know how old I was (sometime early in elementary school), but my parents bought me a book called something like Charlie Brown's Big Book of Questions. In that book, I learned that all life was made of cells and that a human had trillions of cells in his or her body. The book also talked about matter being made of atoms and I wondering about the relationship between atoms and cells, like which was bigger or smaller. My parents were good about fostering my interest in science and in junior high school I participated in a summer CTY program in Biology at a local high school. Biology was one of my favorite classes in high school, so in college I continued along that track, most interested in how cells work. — Kam D. Dahlquist 19:28, 17 January 2011 (EST)