WEEK 13 LEARNING JOURNAL

Please try to address these questions to the best of your abilities. Please post on your blog by the end of Sunday of week 13 (April 12th).

Congratulations on completing the course (and, if applicable, your degree!)

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.

• I learnt a lot of information about planarian regeneration because of the research project
• I learnt more about different techniques that can be used for genetic analysis
• Hox genes and their role in segment identity

1. 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).

• Information about planarian regeneration is mostly factual knowledge
• Information about different techniques could be procedural knowledge and also some factual knowledge
• Hox genes is conceptual knowledge

1. What makes “things” stand out for you

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

• I really love learning about planarians, so any information in this matter stands out to me
• I also like knowing about different laboratory techniques , so this stood out for me having this kind of knowledge will be very useful
• Hox genes stood out for me because they just show how complex genetics and development can be, and how much of it we still don’t know about

1. Relevance/use

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

• It will be helpful if I chose to do any research with planarians ! 🙂
• I think having as much knowledge as possible about different techniques and being able to use them in the appropriate situation will be very important in doing any kind of research, and can reduce research costs/time significantly
• I think Hox genes show us how important transcription factors can be during development. Also the internal regulation of Hox genes by themselves can be used to explain other complicated pathways and patterns.

1. 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?

• Time management – I think this is something that my undergraduate education allowed me to work on, this will be important for me in anything that I do in the future, whether it is working in a company or studying some more – being able to stay on top of things will always be helpful!
• I learned about my skills, interests, strengths, weaknesses. I have gained more confidence in myself and my skills in solving problems. I was also able to discover my interests in the field of biology. These are important because I can use my interests to pursue future career goals and use my problem solving skills when questions arise.
• Biology is messy – unlike math, physics and other areas of study that there is clear formulas to solve problems, there can be many “solutions” in biology as long as they are supported by evidence (ie. no one really knows what’s exactly happening) . I find this important because when I am doing research for example, I am motivated to always question previous findings/conclusions.

WEEK 11 LEARNING JOURNAL

 By now you have seen examples of (almost) all mechanisms for transcriptional gene regulation. You have experienced the complexity of the hox genes, the weirdness of some unruly enhancers, the “wow” factor of genomic imprinting, the messiness of chromatin and the mysteries of XCI. You have read and dissected papers, developed your project, taken midterms and (most of you) presented in front of your peers.

For a moment, try to focus on what you learned since the last learning journal.

 Please try to address these questions to the best of your abilities.

 Factual knowledge

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

       Xist is a non coding RNA that is expressed on the inactive chromosome and causes              the inactivation of that chromosome.

     Tsix is another non coding RNA that inhibits the actions of Xist

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.

One model for XCI is that ­Xist inactivates one chromosome in cis and Tsix prevents the accumulation of Xist on the other X chromosome and therefore prevents one of the chromosomes from getting inactivated. The balance between these two RNAs will lead to proper XCI in females.

The two pieces of knowledge described in A are connected to each other because they are both part of the process of XCI and can present a small detail in the general model.

 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.

I read over the article and found the parts of the article that described each figure and made notes of them beside the image. Then tried to connect the figures  together as a whole while also considering the points that they mentioned in the discussion.

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

Finding the main question that the article was trying to answer, because they tested many different things and did not seem to specify how they all connect together in the discussion.

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?

The figures were described well and they were clear, I think I had a good understanding of most of the individual figures because I was able to look at each figure and describe for myself what it was showing.  

WEEK 8 LEARNING JOURNAL

Please try to address these questions to the best of your abilities. If nothing really comes to mind, it is OK to leave one or two questions blank, but please indicate that you are deliberately leaving them blank (so that I can tell that you did not just forget to answer). Please post on your blog by the end of Saturday of week 8 (March 7th).

For simplicity, you can fill in your responses/thoughts in the table below. But first, read the questions carefully (they are different from previous formsJ)

1. Three things that stood out

Please describe, briefly, three things that you learned so far in BIOL463 and that really stood out to you (either because you enjoyed them, found them surprising, found them difficult – any reason).

1. Imprinting was a strange and new concept
2. Insulators and their blocking effects, this is also a new and difficult concept to grasp because we didn’t discuss the details of the mechanism.
3. Hox genes and their regulation by ncRNAs, the mechanism can become very confusing but also interesting.

1. 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 knowledge, because it is a model
2. Conceptual knowledge, because it is a model
3. Conceptual knowledge, because it is a model

1. What makes “things” stand out for you

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

1. It is strange that one copy of the same gene is turned off depending on the parental origin, and it shows me that genetics can become very complex and many things other than the genetics of the offspring can affect it’s phenotype.
2. It is really strange that insulators can “block” parts of the genome from enhancer activity, heterochromatins and position effects. I am curious to learn more about the details of this mechanism because I imagine that they have to somehow bind specific DNA sequences to prevent other molecules from binding that sequence. Previously I was only aware of heterochromatin and its role in turning off certain parts of the genome.
3. This concept stood out because I realized the importance of transcription factors. It is strange that Hox proteins are simply transcription factors, however they can be vital in determining segment identity during development by affecting other genes. Their regulation by ncRNAs, which are simply RNA molecules, is also a very new topic.

1. Evidence (of course, we are in a science course … we like evidence!)

Imagine that you need to test a group of students on one of your three “things”. Imagine that you need to determine, precisely, whether these students have acquired/developed the same knowledge that you have. How would you test them, and what would you consider as evidence that they have developed/acquired this knowledge?

Factual knowledge

1. Please describe, briefly, one new piece of factual knowledge that you acquired or developed so far in the BIOL463.

I have learnt the meaning of the term “morphogene”.  This term describes a                          substance that is diffusable,  and is invovled in patterning in a concentration                       dependent manner. This substance eventually affects structure formation during                 development.

2. Please describe how you know that you have acquired or developed this piece of factual knowledge, and provide some evidence for it.

        Because I can apply the term to other substances  involved in development, such as         bicoid which is a morphogene.

 Conceptual knowledge

1. Please describe, briefly, one new piece of conceptual knowledge that you acquired or developed so far in BIOL463.

I have learnt a great deal about maternal effect genes. This concept explains how               the mother’s genotype can determine the offsprings phenotype by inserting                         RNA/proteins into the egg. RNA molecules can be anchored to the cell wall                        and cause a concentration gradient in the egg. This  gradient will help the                            embryo to form an axis and activate other genes.

2. Please describe how you know that you have acquired or developed this piece of conceptual knowledge, and provide some evidence for it.

   I could explain it to someone who had no knowledge of biology!

 Skills

1. Please describe, briefly, one skill that you acquired or developed/are developing so far in BIOL463.

Now I can figure out the gene pathways (upstream/downstream) based on data from          the phenotype of double mutants. The gene that is more downstream in the pathway          causes the phenotype that is seen

2. Please describe how you know that you have acquired or developed this skill, and provide some evidence for it.

Because I was able to go through the dorsalized/ ventrilized pathway in drosophilla             again on my own! (from week 4)

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 think factual knowledge is useful to understand what everyone else is talking                    about. For   example, knowing that usually a gene’s name comes from the                          phenotype of the mutant, can be very helpful when reading articles/information                    about genes that are newly found or ones that I have no knowledge about.

Please try to address these questions to the best of your abilities. If nothing really comes to mind, it is OK to leave one or two questions blank, but please indicate that you are deliberately leaving them blank (so that I can tell that you did not just forget to answer).

(For Dr. Kalas – I emailed you this journal because my wordpress wasn’t working) 

A. Factual knowledge

1. Please describe, briefly, one new piece of factual knowledge that you acquired or developed so far in the course.

I have learnt how to read the graphs in week 2 of lecture slides, page 9.

2. Please describe how you know that you have acquired or developed this piece of factual knowledge, and provide some evidence for it.

These graphs can be used to see the location of a mutation when comparing to the wild  type sequence. If the curve does not match the normal sequence then we can tell that there is a mutation at that point. If two peaks can be seen at a certain location, then we can tell that the mutant is heterozygote for the mutation. The colors of each curve on this graph can also tell us what base pair change is causing that mutation. For example in the case of the graphs in the lecture slides, the mutation for family 1 was a base pair change of G to A in one of the alleles of the gene.

B. Conceptual knowledge

1. Please describe, briefly, one new piece of conceptual knowledge that you acquired or developed so far in the course.

I learnt knowledge about what it means for a cell to be specified or committed.

2. Please describe how you know that you have acquired or developed this piece of conceptual knowledge, and provide some evidence for it.

If a cell is determined, it means that its fate cannot be reversed. Therefore if you take a cell from one part of the body and transplant it into another part of the body, it will still continue its normal fate.  If a cell is specified, it’s fate can be reversed, therefore if you transplant it into another part of the body it may turn into another cell.

The frog experiment that was done previously, shows that chromosomes become more restricted and packed as time progresses in the development. Therefore, depending on the location the cells become more determined and their potency is reduced.

C. Skills

1. Please describe, briefly, one skill that you acquired or developed/are developing so far in the course.

I have obtained some skill in choosing a proper technique for doing an experiment.

2. Please describe how you know that you have acquired or developed this skill, and provide some evidence for it.

The staining technique can be used to obtain information about the location, distribution, structure  and expression patterns of genes. The strongest advantage for this technique is that it’s very visual.  However, it can be difficult to quantify your findings and many controls are needed.

We can also remove/knock out a gene from an organism’s genome, and this will help us conclude  whether that gene is necessary and required for the proper development of the organism. A  gene/DNA segment can be added to an organism,  and from this type of experiment we can  conclude whether the added segment is sufficient to cause a change in the development.