BIOL398-01/S11:Class Journal Week 9

Formating

 * 1) Link to your journal entry from your user page.
 * 2) Link back from the journal entry to your user page.
 * 3) Sign your portion of the journal with the standard wiki signature shortcut.

Reflection
Critically evaluate the Schade et al. (2004) paper.
 * 1) Overall, do you think this paper was clearly written?  Why or why not?
 * 2) Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
 * 3) What else would you like to know about their methods, results, and future directions?

Sarah Carratt's Journal Entry

 * 1) Once I started to look up the unfamiliar terms and work through the pictures, the paper became really clear. It was well written and the authors made great comparisons between their study and the traditionally accepted Gasch study. Their whole paper is designed to be clear so that there are no future problems with comparing papers.
 * 2) If I was given the supplies, this would be a very easy experiment to replicate (aside from human error issues). This paper is very detailed and includes precise times, measurements and even specific descriptions of strains.
 * 3) I would like to know if current studies and researchers have set a standard for what can be defined as a cold shock.

Sarah Carratt 23:54, 23 March 2011 (EDT)

Carmen E. Castaneda's Journal Entry
--Carmen E. Castaneda 04:29, 24 March 2011 (EDT)
 * 1) Overall i think the paper was clearly written for someon with a biology background, but I know I had to constantly look up terms and look at class notes in order to understand what was going on.
 * 2) I feel like with the proper guidance I could possibly reproduce the experiment, but I'm not 100% sure on the outcome or if I'd succeed.
 * 3) I would like to see the process actually happen, I feel like the whole experiment still has an abstract feel to it that I would have to overcome in order to understand what is happening.

James C. Clements' Journal Entry
James C. Clements 01:34, 24 March 2011 (EDT)
 * 1) Overall, I believe that the paper was clearly written. I tried reading it before reading the background material and I had no idea what was going on, but after familiarizing myself with the terms and concepts I was able to understand what was happening. The background papers were completely key, however without them, I don't think the full significance of the paper can be understood.
 * 2) Based on what is written in the methods section, I think I could reproduce the experiment (after learning my way around the bio lab a bit better!!). The paper clearly wrote all the parameters necessary to reproduce the experiment. I found it particularly helpful (and necessary) that the paper included which phase the yeast was grown in. It would be interesting to redo this experiment in a slightly different phase and see what happens. Perhaps some correlation between growth rate and adaptability could be determined by such an experiment.
 * 3) I was intrigued at the relationship of the transcriptional response of different environmental stresses to cold exposure (figure 3). Perhaps the relationship between cold stress and other environmental factors could be observed.

Nicholas A. Rohacz's Journal Entry
Nicholas A. Rohacz 03:17, 24 March 2011 (EDT)
 * 1) I feel that this paper was written very clearly, however, some of the figures, such as figure 4, where hard to understand because they state a comparison between the different temperatures or strands, but do not clearly state the control.
 * 2) I would need to go into the cited papers from this paper to get more detail on the procedures, but overall, yes, I do believe that I could replicate this experiment based on whats written in the methods.
 * 3) I would like to know if they continued their experimentation and were able to isolate the cold stress transcription mechanism.

Alondra Vega's Journal Entry
Alondra Vega 21:18, 23 March 2011 (EDT)
 * 1) I personally believe that this paper was clearly written. I feel that I was able to understand most of it and the figures were easy to understand.  They had a lot of description and if they did lack something they told us where we could find the details.
 * 2) This has been the best scientific paper in the methodology section that I have read. The subsections help the reader understand what is going on and what tools were used.  They told us the specific strains and where they got them from.  Also, they told us what kits they used and the number of replicates.  They made it very clear, so we could replicate the experiment.  It makes sense too, since in their discussion they talk about the problem with comparing data sets, thus they wanted to make it easier for the people who would compare it to theirs next.
 * 3) I would like to know if any new mechanism was found that respond to cold stress. Also, if any new genes in the trehalose and glycogen were found to help with the accumulation in the ECR, if there has been any found.