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Category Archives: Learning Journals

A reflection of what I have learned in this course.

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

  1. 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.

  1. 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.

 Three things that stood out  Type of knowledge  What makes these things stand out for you Evidence/how you would test someone on this (select one “thing” only!)
1 GOF experiment shows sufficiency while LOF experiment shows necessity Conceptual This is the biggest take home message of this course! This is the basis of all the examples we look at in class. Most experiments in developmental biology are either GOF or LOF and it is important to know what can be concluded from these experiments. Give a list of a short description of different experiments and ask the students what can be concluded from each experiment.
2 Homeotic genes are usually expressed collinearly in terms of location and time that it is expressed Conceptual I found this to be very interesting how homeotic genes can be expressed according to their position on the chromosome. There are many interesting and complicated regulation in Hox genes which also makes this “thing” stand out.
3 Transcription of a particular gene can affect the expression of nearby genes; the gene product may not necessarily be responsible for the effect. Conceptual I never thought of this concept before but after learning about it in class, it blew my mind. At first, I was confused how this could work but when I realized that the transcription complex for one gene may block the binding of another transcription complex for a nearby gene.

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.
  1. 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.
  1. 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.

A. Factual knowledge

  1. Please describe, briefly, one new piece of factual knowledge that you acquired or developed so far in the course.I learned that cleavage is a stage of development where cells of an embryo divide but they do not grow in size. This means that there will be many more cells but the total size will remain the same.

 

 

  1. Please describe how you know that you have acquired or developed this piece of factual knowledge, and provide some evidence for it.I have heard of this term before and I knew it was a stage in development of an embryo. From a previous class, I only remembered this term as the division of cells. I did not however remember that cleavage had a more specific meaning. I learned that the cells divide but I did not know that the cells did not grow which means the embryo stays about the same size throughout this stage. Now I am more aware that cleavage means more than just a division of cells.

 B. Conceptual knowledge

  1. Please describe, briefly, one new piece of conceptual knowledge that you acquired or developed so far in the course.I learned that enhancers and silencers cannot be determined by the DNA sequence alone; they may have different effects depending on the protein that bind to these regions of the DNA. In one cell, a protein that binds to this region may increase gene expression (enhancer), while in another cell, a different protein that binds to this same region may decrease gene expression (silencer).

 

 

 

  1. 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 that I cannot say an enhancer is an enhancer for across all cells. A method of classifying these regulatory regions is through experiments. You must test if this region increases or decreases gene expression in order classify them as enhancers or silencers. A better term for these parts of the DNA is regulatory regions since this is a more neutral term. I am now aware that I cannot just assume that an enhancer would act like an enhancer in a different cell type.

C. Skills

  1. Please describe, briefly, one skill that you acquired or developed/are developing so far in the course.Although it is not in this course, I have learned how to make concept sketches in my EOSC 112 course. By drawing and annotating, you can connect key points together visually in order to make a concept map of things learned in class. There is an emphasis on finding and drawing relationships between different points taught in class.

 

 

  1. Please describe how you know that you have acquired or developed this skill, and provide some evidence for it.At the beginning, I was struggling to grasp what I am asked to draw for a concept sketch. I found it difficult to identify key points to include in my sketch. When I saw what concepts could be included, I started to see how to map things together. I usually do this in my head just when I am studying. However, this is the first time where I have physically drawn this map out. I found this to be an interesting way to lay out my ideas and also to reinforce relationship between points. I believe that it helps remember facts and concept when I have tied two together through a connection. I believe I can apply this to my other classes and I will continue to develop my skills to draw out a concept sketch.

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