Rosalie's Biol 463 blog

This reflection was submitted at the end of the term. As you can see I have come a long way

I think imprinting the one thing I learnt that stands out to me. Before this course, my understanding of imprinting was limited to imprinting via DNA methylation. In learning imprinting in X-inactivation, I discovered imprinting to be a more complex and interesting topic. It can invovle complex interactions between methylated sequences, histone modification and lncRNAs. As mentioned in one of my R&R previously, I came into this course with the impression that a lot of biological mechanisms may be rather rigid, which is why this stood out to me. In a sense, biological processes are tightly regulated and are rigid in some developmental processes. However, most mechanisms are dynamic as they can involve many factors and components. I have realized most of what I learnt as classical examples of regulation are really oversimplification of complex systems. Therefore, I was under the impression that most biological mechanisms are unchanging, and rigid processes. This course has made me realized, contrary to my previous impression, most biological processes are very dynamic, involves many components and can be flexible to accommodate mistakes. While mutations, misregulation could result in observable phenotypes as we have learnt throughout our undergraduate courses, it is possible that mistakes in development were compensated or does not cause any phenotypes.
I was not very confident in my paper reading skills in the beginning of the term. I have become more confident in reading papers because I have learnt to read figures critically with all the practise we have in class and in assignment.
I have learnt that I am rather impatient as a learner. This is important because it affects my reading and learning efficacy. While a lot of things may capture my interest, I get easily sidetracked/distracted, so reading papers become difficult when the papers are more than 20 pages long and I’m too impatient to carefully read it in one sitting. This is something I think I should work on to help myself learn better.

This is a reflection on my exam question response strategies.

1. On an exam I try to word my answers as clear as possible. When I am answering a question in an inconsequential situation, I may get lazy and may not be as specific.

On an exam, I already attempt to think about the full answer before I start to write to minimize the errors and the need to cross out words. When answering questions in inconsequential situations, I tend to write or say the words as they come to me. Sometimes this results in grammatical error and poor sentence structures.

Now that I am writing this reflection, perhaps my way to answer inconsequential questions is the best, However, if the question is asked verbally in conversation, it would be difficult to pause mid-conversation for an extended period of time to carefully phrase it then verbalize my response. I find myself often give a response verbally the first time but my audience would not understand it so I would then rephrase it better since I have had thought about the entire response during my first attempt at explaining myself

2. I ensure I think carefully and plan my sentences before I write, I often use the margin of the exam paper to jot down some key elements and words that I would like to include in my response. Sometimes I would make myself a short outline or one worded outline so my response flows logically.

In situations where my response is inconsequential, i tend to look at body language and facial expression of my audience to see if my response made sense. If they look rather confused, I would immediately rephrase my response. In settings where my response is written, sometimes I would send my response to a friend to read it over to see if it made sense to him/her.

3. The biggest challenge for me is to really understand the paper’s techniques and the logic behind doing all the experiments in the preparation phase. When I encounter difficulties in understanding a paper, I often google for simpler explanations for a new technique or a review for that paper. I expect myself to have difficulty with time and writing a good response in the exam because it is something I have always struggled with. To overcome that struggle, I find it best for myself to be as prepared as possible so I can spend less time thinking about the response and more time organizing how to phrase my response.

This is my R&R in the middle of the term.
Here you will read about my reflection on my progress.
If you are curious about in my progress at the end of the term, please check out R&R 5!

My view on gene regulation

1. How would you describe your progress so far?

I have progressed much more in understanding various mechanism and critically thinking about different gene regulation system than I expected from the beginning of the course. I think this is due to having discussions in class and reading a lot of papers to experience the advances in our understanding of gene regulation directly from recent research.

2. Are you satisfied with your progress so far?

I am satisfied with my progress.

3. What evidence/pieces of evidence did you use to determine whether you have made progress?

In the beginning of the course, I thought everything in gene regulation is rather rigid and absolute ,which is only accurate in some cases. For instance, conservation of Hox gene expression is important for body plan development, however not all Hox genes expression is necessary for survival. I have never thought such variation in the effect of gene expression in this conserved pathway is possible. Moreover, I have come to realize that as in everything in biology, gene expression is very dynamic and can be rather plastic. In some regulatory pathway, many components are necessary for proper gene expression. In other pathways, some components come to interact with gene of interest and is sufficient in producing a different morph( as in caste differentiation in queen bee) but they are not necessary for proper development into adults.

I have also come to read papers with ease and critically think about what the take home message is from primary literature. I have also noticed as I understand the material more, I generate better questions to challenge my knowledge in gene expression.

(Thanks, Pam! It has been amazing to be part of your class because it really pushes my brain to think more)

You may either record your answers in your portfolio and provide the url link here, or type tour answers here and then copy-paste them in your portfolio.

In Biol 463, we do not have finals, instead we have a final project. Our final project is writing a research proposal on a research question we want to answer.
In my directed studies at the Auld lab, I study what proteins affect the localization of Gliotactin at the epithelial tricellular junction. I have stumbled upon literary on an interesting protein which is associated indirectly with Gliotactin–Disc large.
Here is my R&R as I was developing my research question on disc large.
FYI: Disc large mutants are found to have enlarged wing imaginal disc, that is why the protein is named disc large.

1. In developing the draft research question, I have learnt to utilize Blast and NCBI extensively. I was expecting to learn to use these databases extensively because I was aware how much information was available through NCBI. I have also learnt how to prioritize which research articles and journals to read while consulting peer reviews. I was expecting to learn how to properly read articles and journals as I was coming up with a research question for the first time.

2. I expected I would have trouble finding the proper candidate proteins to test to answer my research question. This expectation was contrary to the outcome. I ended up with close to 100 candidate proteins to choose from after blasting for related proteins from a known system. Systematically organizing information helped prioritize which proteins to test as some homologs of candidate proteins have been tested in other systems.

3. The best strategy I have developed to prioritize the testing of proteins by evaluating how many of the following criteria they fulfil.

-Proteins with high percent identity with human proteins known to be involved with DiscLarge1

-Proteins with highly conserved domains which are known to interact with DiscLarge

-Proteins with multiple isoforms can be tested with one RNAi which carries consensus sequences among all the isoforms.

The research question for the final project is also one of the questions that are currently investigated by the lab which is sponsoring my directed studies (Biol 448). To answer this question, one would need to hypothesize a complex signals transduction pathway which would be challenging as not much is known about the mechanism that places Gliotactin onto the barkbeetle(anachonda) of tri-cellular junctions in Drosophila. The instructor is likely looking for a thorough, falsifiable research question which can be tested with current molecular biology technologies. A top-level draft research question would not be too broad and should be specific enough to be tested.

Hello, visitor!

You have stumbled onto my blog/portfolio. This blog is part of an assignment of the Biology 463 course at UBC. It is a really fun and interactive course in which the curriculum is based on research papers.

If you are perspective student of this course, I highly recommend this course if you would like to improve your skills in critically evaluating primary literature, learn more about the dynamic interactions in developmental gene regulation.

Rosalie