Learning Journal 1

1.        Factual knowledge

Briefly describe one new piece of factual knowledge that you acquired or developed since the start of the course.

Cells maintain their potency in regulative development types at early stages of development.

2.        Making connections (conceptual knowledge!)

How does this new piece of knowledge fit into what you already knew? What other facts is it connected to, and how? Does it fit into any concepts? How?

Cells exposed to extracellular signals can reverse their determination to give rise to different structures or cells or lineages.

The four transcription factors cMYC, OCT4, KLF4 and SOX2 are able to reverse any cell into a stem cell.

We can take advantage of this knowledge to potentially grow entire organs out of a living person’s cell for medical treatments

 

Learning Journal 2

1.        One new (or ‘improved’) concept

Now that we have looked a variety of experiments and techniques (e.g. honeybee papers, techniques presentations), some epigenetics mechanisms, the effects and characteristics of boundaries/insulators, etc., identify and briefly describe one concept that is either new for you, or that you understand better or in a new way.

Role of methylation on gene expression. Even though, I’m very interested in genetics, I had not encountered DNA methylation before.

During the past few weeks, we’ve discussed transcriptional regulation through modifications such as DNA methylation. We first started talking about DNA methylation during our discussion on honey bees and the intracellular and extracellular factors that influence the development of worker and queen bees.

One of those factors were DNA methylation where Kucharski, 2008 compared the different levels of methylation between worker and queen bees on certain locuses and looked at the effect of expressing siRNA of Dnmt to get phenotypes of opposite proportions.

I’m excited for new findings on the effects of DNA methylation on gene expression as not much seems to be known at the moment except that DNA methylation seems to be suppressing gene expression.

2.        Thinking about your new or ‘improved’ concept

• How did you identify your new or ‘improved’ concept? How did you decide that it is a concept (and not, for example, a fact or a skill or a technique)?
• What made you realize/decide that you understand it better or in a new way?
• Do you think having a good understanding of this concept is important and/or useful? Why/how?

• We had been discussing differential gene expression and the mechanisms that control that through DNA modifications such as methylation. It is a concept because we have results from a series of studies and experiments that suggest DNA methylation decrease gene expression. This can be further studied to disprove or further support previous findings.
• I kept up (read everything this few days actually) with all the assigned and supplementary readings to understand it.
• Yes, of course! Genetics is love, genetics is life. I love genetics because it is the basis of everything (well, electrons, protons and neutrons are the basis of everything). I’m always enthusiastic and ready to learn more about everything there is to know about genetics. That why I registered for this class!

 

Learning Journal 3

One thing that stood out for you on the midterm or during your midterm preparation

This week you will write (or may already have written) your first midterm for the course. What is one thing that stood out to you either during your preparation for the midterm, or on/during the midterm itself? Is this something that had stood out to you before, or is it something new?

Briefly describe it and explain what made it stand out for you.

What amazes me about science is not the amount of facts we now know but rather the process by which researchers formulated hypotheses, designed experiments and obtained the raw data that were used to propose a model. Unfortunately, lower level courses are taught in the exact opposite way, where they present us with the final model and then show us the raw data.

In the preparation for this exam, I found that there was not much to study for except understanding concepts taught in class. I also read the supplementary readings associated with each topic to get a better understanding of certain concepts such as chromatin remodeling. Going through past midterm and practice questions, it was evident that all the questions were conceptual rather than having regurgitate a bunch of memorized facts and that is science. I have to say that I thorough enjoy and appreciate the conceptual stimulation involved in processing, figuring out and designing experiments to tackle questions and problems and that is exactly how the midterm was designed and carried out.

 

 Learning Journal 4

1.        A technique

What is a technique that you learned about (or, that you learned more about) in BIOL463? Name it and briefly describe it.

CRISPR/Cas9 System. A method that allows the user to edit genes/genomes with guide constructs.

2.        Anything difficult?

If someone were to learn how this technique works, what do you think would be the most difficult or confusing part, and why? (If you think nothing would be confusing, why is that?)

One of the points that intrigues me is how the Cas9 protein with the guide RNA can localize to the exact intended location of a particular gene or regulatory region considering the vastness of a genome.

3.        A question to test one’s understanding

If you were to test whether someone truly understands how the technique above works, what question would you ask them, and how would you interpret their answer (i.e., what answer would you consider evidence that they understand?)

I would ask to design a particular CRISPR/Cas9 construct that would cause a break in a certain gene and edit the gene to a specific sequence. I would look at their guide RNA construct, repair template and homology arms used to assess the efficacy of their design and hence their understanding of the technique.

Learning Journal 5

This Learning Journal is a bit different from the previous ones…

1.        Finding a classmate that agree to let you see their wordpress blog/portfolio…

Find a classmate who is comfortable sharing their portfolio with you, and whom you are you are comfortable sharing yours with.

Notice that you can choose to have an ‘open’ wordpress site and still make some of your posts private (inaccessible to those who do not have the password).

Name of the classmate whose portfolio you will be viewing:

Elena Guichici

 

2.        Commenting on the portfolio …

Browse through all the viewable parts of your classmate’s portfolio.

• Imagine that you did not know this person at all, and you had to evaluate their skills, knowledge and learning using only the content of their portfolio. What would you say the biggest strengths of this person are, and why (what evidence did you use to come up with the answer)?

I found that the summarization of the assignments and prompts in her portfolio were very thorough and clear.

• After answering these questions as part of your own LJ5, post them as a comment on the classmate’s portfolio.

 

3.        Your final project and your classmate’s final project

 

• What is the most valuable thing that you learned from doing your Final Project (mini-research proposal)?

Even though it was not apparent at first, looking back at it now, I can confidently say that the research project integrated a lot of the things I had learned since first year. The skills that I acquired throughout my degree, were put to use, from the basic fundamental biology ideas to browsing through the literature to postulate a question, and all that is a measurement of how much I’ve come to learn during these years.

 

• Look at what your classmate has posted under their Final Project section. What do you think your classmate may have learned, that you have not (and/or what do you think you have learned, and they may not have)? After the end of term, feel free to check your classmate’s portfolio again to see if your answers match.

Only the final project was posted, and reading through her research proposal, I’d say it was quite well organized. She also gave a well structured summary of her final project.

Also, her prompts were very interesting to read and they were on topics that I hadn’t thought about writing about.

Other comments (optional)

Yes, I would like to mention that I was uploading the LJs to the wrong section the entire time, and looking at the time this is being posted, you guessed it, I just figured this whole blogging thing out (well, at least partially).