BIOL388/S19:Class Journal Week 9

Ava Lekander's Reflection

1. What aspect of this assignment came most easily to you?
   • Writing the outline was easier for me with this paper because while reading it I already had some idea of what I was looking for and what aspects needed to be addressed.
2. What aspect of this assignment was the most challenging for you?
   • Although I stated this was the easier part for the last journal club I feel that the most difficult part was defining the terms. It was frustrating because definitions were not popping up as easily as previously and I included some of the actual laboratory techniques used in my list which made it challenging to find good definitions that were not from the manufacturer simply explaining why the tool/machine works great.
3. What (yet) do you not understand?
   • I am definitely still confused about some of the methods and techniques in this paper. Also, a few of the statistical test done I had never heard of.
4. Compared to the Schade et al. (2004) paper that you read for the first journal club, which paper do you think is stronger and why?
   • I believe that this paper is stronger as there are more details included and the actual data is actually accessible rather than an unavailable hyperlink as the Schade paper included. However, the time points were not included which really detracted and also this study seemed to be more of a meta-study with a lot of comparisons/contrasting between the previous three papers and this 'new, improved' chemostat methodology.

Avalekander (talk) 20:00, 9 May 2019 (PDT)

Brianna N. Samuels's Reflection

1. The easiest aspect of the assignment was defining the terms
2. The most difficult was describing the figures and tables assigned to me
3. I still am not 100% confident in my abilities to read some of the figures, specifically heat maps
4. I think this paper was better than the last because it had more details and was a little bit easier to follow compared to the Schade et al. (2004) paper.

Briannansamuels (talk) 22:59, 27 March 2019 (PDT)

Angela's Reflection

1. The easiest part of this assignment was understanding the main purpose of the study conducted in the article. Even though it was a lengthy paper, the writing was clear and easy to understand. The authors' conclusion was clear and well-defended.
2. The most challenging part was interpreting the table I was assigned. It had a lot of different variables that took a while for me to define.
3. I still don't understand the protocol of the statistical analysis. Even after reading the methods section a few times, the exact steps to analyzing microarray data are still confusing.
4. I think this paper was stronger because it was more clear and included extensive references to other studies. It didn't seem like it was missing anything significant that would make it questionable.

Angela C Abarquez (talk) 22:05, 27 March 2019 (PDT)

Austin Dias Reflection

1. The easiest aspect of the assignment was choosing 10 terms from the research paper and defining them.
2. The most difficult part of this assignment was determining what the main findings of the paper were. Many results were presented and conclusions were made, so it was hard to combine all of the small specific details to determine the overall messages the authors were trying to convey.
3. Table 3 is a part of the research paper that I still do not fully understand. I am confused about the importance of the inclusion of this table, as well as how they came to find which regulatory motifs and transcription factor binding targets were overrepresented.
4. In comparison to the Schade et al. (2004) paper, I believe this study is weaker. This is mostly attributed to the exclusion of time references in their research paper. I understand the messages they are trying to convey and for the most part they support it with their data. However, when it comes to comparing their data with other batch culture research experiments, it is difficult to be convinced of their reasoning because I have no concept of time and at what point genes are changing expression behavior.

Austindias (talk) 18:32, 27 March 2019 (PDT)

Desiree's Reflection

1. What aspect of this assignment came most easily to you?
   • The definition aspect of this assignment came most easily to me, since we just have to find and properly site where we are getting the definition from.
2. What aspect of this assignment was the most challenging for you?
   • The interpretation of the tables and figures was most challenging for me since I was still trying to grasp the differences between the experimental types (i.e. chemostat versus batch).
3. What (yet) do you not understand?
   • I am still having a bit of difficulty understanding why the chemostat experiment is deemed to be more "flexible" and "better" for measuring gene regulation changes over time.
4. Compared to the Schade et al. (2004) paper that you read for the first journal club, which paper do you think is stronger and why?
   • I personally believe that this paper was stronger than the one that we read for the first journal club since it actually showed some of its data in figures, and even compared its experimental outcomes to previous research on the same topic.
   • The Schade et al. (2004) paper did not release any of its data and only referenced outside sources for "proof."

Desireegonzalez (talk) 23:11, 27 March 2019 (PDT)

Edward's Reflection

1. The figures were very well done in terms of representing the comparisons amongst datasets, so this was easy to understand.
2. Because the discussion for each of the tables and figures were scattered around the discussion section, it was difficult to determine the main points of each.
3. I still do not really understand the chemostat method as different from the other studies, as well as why they compared these datasets if they had different methods and parameters for analysis.
4. This paper is stronger and more easy to understand. I remember the other paper being more confusing, and the figures were not easy to understand. Also, this paper spends a great portion into comparing the results to previous studies, which is a good thing; however, there were a lot of discrepancies that should be looked into for the future.

Alison's Reflection

1. What aspect of this assignment came most easily to you?
   • For me, outlining the article is easiest for me because the wiki syntax makes it extremely easy to create outlines. While reading the article and interpreting all the biological terms can be difficult, I enjoy breaking it down into a simple outline that I can follow.
2. What aspect of this assignment was the most challenging for you?
   • It is always hard for me to read scientific articles because of all the technical jargon they use. The most challenging part of this assignment was definitely working my way through the article and trying to interpret the information.
3. What (yet) do you not understand?
   • I am having a hard time understanding my table (Table 3). There are lots of number in there, and I do not quite understand what they all mean.
4. Compared to the Schade et al. (2004) paper that you read for the first journal club, which paper do you think is stronger and why?
   • I think this paper is the stronger one because the authors make it easier to follow their steps and they cite every article, resource, and reference that they used. Because of their strong documentation, I feel like I could follow their steps to recreate the experiment. In the Schade et al. paper I felt that I could not have followed their steps, especially because they did not give us the names of the programs they used to run their statistical analysis, etc. Also I think the labeling of figures was much clearer in this paper than Schade et al.

Alison S King (talk) 09:23, 28 March 2019 (PDT)

Fatimah F. Alghanem

• What aspect of this assignment came most easily to you?

interpreting the results

• What aspect of this assignment was the most challenging for you?

analyzing the figures/ tables. What (yet) do you not understand? I don't completely understand figure 4. Compared to the Schade et al. (2004) paper that you read for the first journal club, which paper do you think is stronger and why?

I think this paper is stronger because it was more inclusive of other people's work on the same subject. Also it was far more easier to read than the other paper.

Leanne's Reflection

1. Not much of this assignment came easily. Finding terms to define was easy, but defining them was challenging as most of the terms I did not recognize required further research into other studies. Additionally, this paper was much more difficult to understand than the Schade et al. (2004) paper, which made the outline challenging as well.
2. Interpreting the paper was the most challenging aspect of this assignment. Many of the tables and figures had unclear captions which made it difficult to connect them to the purpose of the paper.
3. I do not understand why they had a limiting nutrient. It seems that if there is not enough nutrients (for instance, a lack of glucose), then how can they attribute the transcriptional changes they saw to temperature as opposed to a nutrient deficiency? I also still do not understand what specific growth rate is and why it is important. When they refer to a change in specific growth rate with a decrease in temperature, does this mean that overall growth decreases in the culture?
4. I found the Schade et al. (2004) paper stronger in comparison to this study. The main issue with the Schade paper was that they did not explain their statistical analysis well enough to be reproduced, however I did not find that this paper did either. I found the Schade paper much easier to understand and their results were much more concise than the current study. A few issues I had with this paper were, first, I did not find that this study had any control group other than the cultures grown at 30C. I think to be more effective it would have been beneficial to also conduct a batch study for comparison. Second, this study never defines how long they subjected their cultures to cold-shock, or if they compared transcriptional changes during a recovery period. Third, this paper's methods sections seemed incomplete. While they did refer to previous studies for their protocol, it would have been easier to understand if they had a couple sentences of the general procedure as I had trouble accessing some of the other papers. In the very least, it would have been beneficial to have a supplementary section with a more detailed methods. Lastly, I do not understand why this group makes it seem like adaptation to CS and acclimation to CS are mutually exclusive. To my understanding, in order for acclimation to even occur, adaptation would have to occur first, thus there must be some connectino between the two.

Leanne Kuwahara (talk) 22:26, 27 March 2019 (PDT)

Sahil's Reflection

1. For me, the aspect of the assignment that came easiest was defining terms that I was not familiar with because this was very straightforward.
2. The most challenging part of the assignment was getting through the paper and creating the outline because since the article is pretty concise and comprehensive it is hard to omit things from the outline.
3. Some things that I am still unclear about was with the reference to previous studies and the methods utilized in different studies to acquire data were still compared to one another.
4. This paper is stronger because it has sources to support data referenced throughout the article; it also has a working accessible database online making the study able to be replicated.

Sahil Patel (talk) 05:03, 28 March 2019 (PDT)