Musings of a BIOL463 Student

A. Three main things in BIOL463

Please describe, briefly, the three things that you learned in BIOL463 and that you consider to be the “most important” ones.

1) Loss of function experiments tells you necessity; gain of function experiments tell you sufficiency.

2) In different cells, enhancer sequences are not always enhancers; it depends on what binds to the enhancer sequence to cause activation or repression of a gene. It is better to call these regions regulatory elements.

3) Making direct conclusions from figures in an article and then using them to construct a model to explain how things work.

B. Identify types of knowledge

For each of your three “things”, please try to identify what type of knowledge it represents (Factual, Conceptual, Procedural/Skills, Metacognitive).

1) Conceptual

2) Conceptual

3) Skill

C. What makes “things” stand out for you

For each of your three “things”, please indicate what made it stand out for you.

1) This concept resonated throughout the whole course including the midterms and quizzes we wrote. This is the biggest take home message of this course. Many of the examples we looked at in class are GOF or LOF experiments.

2) Before this course, I thought that enhancers are named so because it was their sequence that determined their control over genes. However, I know understand that it depends on what proteins in the cell bind to the sequence that determines the control of the genes.

3) Throughout this course, it is very important to distinguish between direct conclusions and models. We got to practice this skill throughout the entire course.

D. Relevance/use

Please describe, briefly, what you expect each of these three “things” to be useful or relevant for.

1) It is important to distinguish between LOF and GOF experiments since they tell you different things. Different conclusions will result in different possible models so it is important to not confuse these conclusions.

2) This means that it is important to check whether your enhancer sequence actually increase the expression of a gene in a specific cell. You cannot assume that an enhancer will increase the expression of all genes in all cell types. There may also be position-dependent effects.

3) This skill will be useful in the future when I will be interpreting papers for research. Having this framework of determining what the figure shows and concludes and what you can take away from it will help understanding the paper better.

E. Three main things in your undergraduate education

Please describe, briefly, the three things that you learned during your undergraduate education and that you consider to be the “most important” ones. Why do you find them so important?

1) To reflect on what you have learned (using Learning Journals is a great choice) to reinforce what you have learned in a class. This also shows how much knowledge you have gained over a four month time period of classes. You would get a greater appreciation of the class after reflecting on how much you can take away from the class.

2) It is important to make connections with many people around you. Networking is the key to many opportunities in the future. There are many times when you can ask people for help or to collaborate with in the future. Additionally, people may ask you for help and this allows you to be a better person.

3) It is important to take a wide range of courses. It opens your eye to the world around you that you may not know existed. Knowledge is quite open with the age of the Internet. However, taking these classes allows you to be more critical about what you are learning in class. Additionally, it may help increase the understanding of other topics because you may be able to make some connections with what you already know.

A. Factual knowledge

Please describe, briefly, two new, distinct pieces of factual knowledge that you acquired or developed since the last learning journal

I learned that XIST and Xist is responsible for X chromosome inactivation (XCI) in humans and mice, respectively. This long noncoding RNA coats the X chromosome to inactivate it.

 I learned that there are certain histone modifications that are involved with activating genes (H4ac) and inactivating genes (H3K9me3).

 B. Conceptual knowledge

Since connections and models make for conceptual knowledge… please describe any connections (direct or indirect) that you can see between the two pieces of knowledge described in A.

Histone modifications involved in inactivating genes are important for XCI. H3K9me3 is found on the promoter of Xist in mice in order to prevent the expression of Xist, which will inactivate an X chromosome. The modifications are lost during development in order to allow XCI.

 C. Metacognitive knowledge (no skills this time!)

If you are like most students in the class, you probably spent a significant amount of time reading, studying, and dissecting the article assigned for MT2.

1. Please describe, briefly, the strategy that you employed to complete the task.

First, I quickly read through the paper once to get a feel of the paper. The second time I look at each figure and try to annotate what they observed and concluded. I also underline the results and the conclusion

2. Thinking about your experience with reading and dissecting this article, what was the hardest part?

There was a lot to keep track of since there were so many experiments and figures. It’s sometimes hard to see the overall picture of the entire paper.

3. Thinking about your experience with reading and dissecting this article this article, what did you feel most comfortable with/confident about? Why do you think that is?

I was most comfortable with understanding the difference between inner cell mass and the trophectoderm cells because it was something discussed it in class and I actually understood the difference in XCI between these two types of cells.

A. Factual knowledge

1. Please describe, briefly, one new piece of factual knowledge that you acquired or developed so far in the BIOL463.
   I learned that a morphogen is a diffusible substance (ligand, mRNA, protein) that changes the fate of cells in a concentration dependent manner.

2. Please describe how you know that you have acquired or developed this piece of factual knowledge, and provide some evidence for it.
   I can now identify what a morphogen is when given a scenario. For an example, in the terminal system in Drosophila, active trunk is a morphogen. Trunk is activated by torsolike, protein localized at the terminals of the embryo, which means there will be a gradient of active trunk with a higher concentration at the ends of the embryo and little to none in the middle of the embryo. This gradient of active trunk will allow for asymmetrical development of the embryo.

 B. Conceptual knowledge

1. Please describe, briefly, one new piece of conceptual knowledge that you acquired or developed so far in BIOL463.
   I learned about maternal effect genes are which are genes that are expressed by the mother in her nurse cell and passed on as mRNA to the oocyte. This means for these set of genes, the mother’s genotype will be the offspring’s phenotype.
2. Please describe how you know that you have acquired or developed this piece of conceptual knowledge, and provide some evidence for it.
   I now understand the mechanism for how some flies that are homozygous for a recessive lethal gene can still survive; however, her offspring’s will not survive. I can now apply this knowledge for genetic screening of flies.

 C. Skills

1. Please describe, briefly, one skill that you acquired or developed/are developing so far in BIOL463.
   I am continuing to develop my abilities to develop a novel and interesting research question. This is for the final project of this class and that assignment gave me an opportunity to further develop this skill. In my other classes and in the lab, I rarely get an opportunity to develop a research question I would like to answer. In this class, I can finally exercise this skill so in the future, I will be easier for me in graduate school.

2. Please describe how you know that you have acquired or developed this skill, and provide some evidence for it.
   It took me a very long time to read many articles to come up with my research question for my final project. From the articles, I have to piece together what is already known in the field and find the missing piece that I can use to develop my research question. I was able to find a few articles that were somewhat related; however, direct links were not made. From these articles, I came up with my question to see if there is a true link between the findings of these related paper. Perhaps in the future, it will not take me as long to develop a novel and interesting research question.

D. What is factual knowledge useful for?

1.  Think about a piece of factual knowledge that you developed/acquired. Briefly describe what you think it is useful for.
   I learned that eve has different enhancers that cause it to be expressed in different segments. For an example, there is an enhancer just for the expression in stripe 2 (eve2). This is useful in understanding how the expression of eve results in the pattern seen in the embryo. Then we can apply it to other genes with a similar expression pattern. By knowing these facts, we are able to come up with models on how other things work.