BIOL398-03/S13:Class Journal Week 11

Reflection

Laura Terada Week 3 Journal

Laura Terada

Reflection

1. Overall, do you think this paper was clearly written? Why or why not?
   • I thought the paper was overall clear. I was able to understand the introduction and the materials methods section easily. The subheadings in the results section also helped, and it served as a general outline of the paper. The only confusing part was that the paper discussed many different genes from different studies; however, the figures and tables helped to clarify the comparisons between the different datasets.
2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
   • Yes- the authors gave a very detailed description of their culture parameters and which programs they used for data analysis.
3. What else would you like to know about their methods, results, and future directions?
   • I would like to know how this study could be used to analyze posttranscriptional modes of cellular regulation and what changes would need to be made or what other factors would need to be considered. Moreover, what exactly accounts for the differences in results between the batch cultures versus chemostat cultures? Is the only difference the fact that one is a more controlled environment? Also, are there different phases of long-term low temperature exposure/acclimation? Lastly, I would like to know how can these results on acclimation for yeast relate to more complex organisms.

Laura Terada 23:11, 29 March 2013 (EDT)

Kevin McKay Week 11 Journal

Kevin McKay

1. I thought it was clearly written, as clearly as it could be. There was so much in this paper including 4 separate experiments that they referred too and lots of genes and transcription factors so I thought it was clear for how much work they did although overall I found it messy as a whole.
2. If I knew what they were talking about through most of the analyzation methods I could probably reproduce the experiment.
3. I would like to know what lead them to choose the specific growth rate of 0.03/h in the batch culture experiments they based theirs off of. I would like to know more about the programs they used or analyzation. Also more about the function of the 259 genes that were consistently differentiated in regulation during adaptation in the three batch studies would be good. Maybe some more on how they plan to combat the effects of changing cultivation parameters without impacting others.

Kevin Matthew McKay 00:15, 2 April 2013 (EDT)

James P. McDonald Week 11 Journal

James P. McDonald

1. Overall, do you think this paper was clearly written? Why or why not?
   • I think the paper was written fairly clearly. The paper contains some complicated methods of data collection and analyses but it was as clear as it could have been in dealing with such topics.
2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
   • The paper contained a somewhat in depth methods section so I do think I could recreate the experiment but maybe not to great accuracy. I have not performed experiments like this before, especially from the data analysis perspective so it would not be easy at first. But since it was explained rather clearly I think I may be able to do it with their guidance.
3. What else would you like to know about their methods, results, and future directions?
   • I know that they wanted to eliminate a specific growth rate in their study to compare it to batch cultures but I was wondering if they had to make it anaerobic to do this. It seems that the lack of oxygen in their study caused discrepancies in their comparison to the batch cultures. Is their a way to make a closer comparison and eliminate this factor? Another thing I would like to know is what would happen at even lower temperatures than were tested. Would the same trend continue or would something else happen to its transcriptional regulation? Due to the difference between a gradual temperature decline and a cold shock I would be interested to see what would happen if the temperature continued to decline slowly. Would the yeast eventually enter a state that would correlate with the cold shock effect? This could be a possible future direction to take the study.

James P. McDonald 01:44, 4 April 2013 (EDT)

Matthew E. Jurek Week 11

Matthew E. Jurek

1. Overall, do you think this paper was clearly written? Why or why not?
   • In terms of clarity, I thought this paper was OK. The results section was rather large and the subheadings helped. However, I felt things could have been better organized. Also, the discussion of various genes became confusing. Sometimes examples of certain genes were stated and other times not. The large number of genes paired with inconsistent examples was somewhat confusing.
2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
   • The methods section is straight forward. However, at the end of the growth conditions section it is mentioned that several factors were constant for at least 3 volume changes before sampling. These volume changes were never stated. It would still be possible to recreate, but maybe not identically. I also don't know if I could work through the statistical testing even thought the equation is provided.
3. What else would you like to know about their methods, results, and future directions?
   • By the end of the paper it was clear that batch cultures were not appropriate for studies like these. However, in the discussion it is stated that the batch culture results are needed for comparison in order to fully understand which genes are impacted by the cold temp. I would assume previously published batch results will be used for as long as possible. If these results ever do not address specific genes, would they perform a batch culture experiment followed by a chemostat experiment for comparison purposes? This was a thought I had regarding future directions.

• Matthew E. Jurek 02:05, 4 April 2013 (EDT):

Anthony J. Wavrin Week 11 Journal

Anthony J. Wavrin

1. Overall, do you think this paper was clearly written? Why or why not?
   • I think the paper was very clear overall. The information that is described is very thorough and uses a lot of references. It is evident that they are doing a lot of work and comparisons. The only unclear part is that overall result. Instead, they come up with a lot of minute conclusions about a lot of things but, the y do not do a good job of wrapping it all up into 1 coherent message.
2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
   • Due to my lack of expertise in this field, I do not think I could reproduce their experiment and data analysis. I think the actual experiment could be replicated using the sources they cited in the materials and methods. I think the data analysis would be very difficult to try to replicate because they just cite programs and one equation.
3. What else would you like to know about their methods, results, and future directions?
   • I think the one thing I would like to know is their overall result. They concluded many things from this study, it seems it was much more work in analysis rather than actually conducting the experiment, but the ideas seemed very unorganized and all over the place. I am interested to see what direction they went into after this paper because, that would probably be a pretty good indicator of the most important finding in this study.

Anthony J. Wavrin 02:25, 4 April 2013 (EDT)

Helena M. OlivieriWeek 11

Helena M. Olivieri

1. Overall, do you think this paper was clearly written? Why or why not?
   • I thought that the intro and materials and methods was well written and clear. I thought, in places, that the results were confusing. There was a lot going on and the article was very dense.
2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
   • I think the methods section was clear and likely reproducible. Parts of the analytical and microarray methods seemed to make assumptions that we understood general procedures, but given prior papers the methods seem replicable.
3. What else would you like to know about their methods, results, and future directions?
   • I would like to know about the furthur relationships between the batch cultures and the chemostat cultures.

Helena M. Olivieri 02:38, 4 April 2013 (EDT)

Paul Magnano Week 11 Journal

Paul Magnano

1. Overall, do you think this paper was clearly written? Why or why not?
   • Yes for the most part it was clearly written especially the intor, I could very clearly understand what the overview of the study and its general purpose was. the results were somewhat confusing in places, but im not sure there was a way to break them up anymore than th epaper did.
2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
   • I think that one could reproduce the experiments and data analysis based on the materials and methods section, they listed every piece of software and background data they used, so assuming I knew how to use the software and had a solid understanding of how to perform the microarray methods it would be reproducible.
3. What else would you like to know about their methods, results, and future directions?
   • I would like to know their "take home result". The paper concluded many things that were all relevant but I would like to known what their main finding was, since it most likely was used to continue their research (assuming they continued research the topic)

Paul Magnano 02:46, 4 April 2013 (EDT)

Ashley Rhoades Week 11l

Ashley Rhoades

1. Overall, do you think this paper was clearly written? Why or why not?
   • Yes and no. I think it was well written but it could have been organized better to show that it was well written.
2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
   • I think we could because they were very specific about their methods but it would take a lot of work because they used a lot of outside sources.
3. What else would you like to know about their methods, results, and future directions?
   • I would like to better understand the specific implications of the results regarding specific genes.

Ashley Rhoades 03:05, 4 April 2013 (EDT)

Salman Ahmad Week 11 Journal

Salman Ahmad

1. I think the paper was written clearly, but it was hard to follow. The actual explanations of everything that was done was easy to read and to follow, but towards the end I felt like it started to lose focus. There were a lot of different pieces of data being talked about, but they were either not analyzed deeply enough, or they did not seem to be relevant to the thoughts brought up in the beginning of the paper.
2. The experimentation seemed a bit tedious, but it the methods were written out pretty clearly and I think with the right tools it would definitely be possible to follow what they did.
3. I would definitely like to know more about their future directives. It seems that the experiments they compared their papers to had completely different results from them and from each other. It would be interesting to see where they are thinking about going from there in order to get some data that is more consistent.

Salman Ahmad 15:45, 4 April 2013 (EDT)