Biol 463 Top 4 Assignments (and 1 more ) Throughout the Term

Assignment #1: “Dna Methylation…. Apis Mellifera

The first assignment that I’ll be submitting is the worksheet on the first assigned article read and worked together as a group. It feels like a world away looking back at this first assignment. There were definitely some silly mistakes, but I benefited from the learning growth!

Biology 463 Group 2 _DNA Methylation…Apis mellifera_ Worksheet-3

Assignment #2: Case Study on the Honeybees!

A puzzle piece that required knowledge, logic, and judgement to incorporate what we knew of the different factor and mechanisms of the developmental trajectory of worker and queen honeybees. Attached is a proposed model where we (Tariq, Alice,  and I) pieced together what goes into this trajectory to give rise to observed phenotypes. It was a challenge, but it wouldn’t be a puzzle if it was easy….!

ProposedModel

Assignment #3: The HOTAIR Issue

The third assignment will be when we looked at HOTAIR. Since the first assignment, there has been a notable change (at least for me!) in the way I’ve been answering questions.

Biology463_HOTAIRAssignment

Assignment #4: Chiesa et al. paper reading:

Medical genetics is definitely an interesting area of discourse. A long-standing interesting of mine. If I had to sum up my attraction to it in three words, it would be “logic”, “possibilities”, and “dynamic”.

My response to the question for this paper: What can you deduce about BWS from the pedigree shown in the article?

From reading the pedigree, seems like BWS is an autosomal dominant disease as it

1. Appears in both sexes with equal frequency
2. Affected offsprings have an affected parent
3. When one parent is affected and the other one isn’t, approx 1/2 of the offspring will be affected

Assignment #5: The Final Project

Maybe this is double-dipping, maybe it isn’t… but I would like to say that surprisingly, the student research project for this course ended up being one of my favourites. I’ll admit that I was initially intimated by the task of designing an experiment and I got caught up in reading literature instead of coming up with a question; I took too much time trying to come up with something novel and ground-breaking. But after reaching out for help and guidance, it hit me that it was more about cultivating critical thinking and skills necessary for a successful scientist with this project. How could I not be proud of the efforts that went into this term project? To future students, it may seem daunting but it will actually be a challenge that you will grow to love!

 

 

 

 

 

 

Posted in Assignments | Leave a comment

Biol463 – Final Research Project and Bibliography

Lo, and behold… the final product, I could not be more proud! 🙂

Final Project:

Investigation of microRNA products -mir-675-3p and mir-675-5p – from H19, against the Bone Morphogenetic Family (BMP) proteins BMP 7, BMP 4, and BMP 11 for kidney formation during development

Chen, Buffy_Biol463TermProject_Investigation of microRNA products- mir-675-3p and mir-675-5p, from H19, against the Bone Morphogenetic Family (BMP) proteins BMP 7, BMP 4, and BMP 11 for kidney formation during development

Bibliography

Biol463Annotated Bibliography_Submit

Posted in Project | Leave a comment

R&R #5

Questions:

1. Take a moment to think about your work related to this course (in class and on your own time). What is one thing that that you learned and that stands out to you? Why does it stand out?

Usually when I finish a course, my head is filled to the brim with knowledge on the discourse. It isn’t so much the case with this course… To clarify, I have a understanding of gene regulation during development e.g epigenetics, transplantation experiments, XCI, methylation, etc. but I think I have a finer appreciation for the fact that this course devoted more time to discussing the logic and the thought process for experimental biology. 1) It’s become easier to read journal articles 2) The problem-solving approaches have strengthened my critical-thinking skills 3)  Just even taking the time to focus on figures and whether the results align with what I myself would expect from the experiment and 4) Judging the validity of a conclusion in a paper.

Coming into this course, I expected that it would be similar to BIOL 335: Introduction to Molecular Genetics, where mechanisms, critical genes, and whatnots during development would be memorized. I expected it to be information dense. I didn’t expect so much active engagement with the course material, or to read as many papers as we did!  Since taking this course, I find myself taking a step back and critically evaluating the paper better than I did in the past which I really appreciate as this is a skill that I can keep building on and take with me in my career.

2. Think about a skill or concept that you were not very confident about at the start of term. Has your confidence changed throughout the term? Why do you think is has or it has not changed?

Initially, I wasn’t very confident about speaking up during class e.g paper discussions, asking questions, contributing to the class, defending my answers, etc. as I felt I didn’t come in with as strong of a background as my peers. I was okay with keeping my thoughts in my head mostly because 1) I viewed myself as a viewer in the class instead of a participant and 2) If I was wrong about something, it would stay inside my head. Again, perhaps it was the luck of the draw with who ended up in the class, but the theme of active engagement kept persisting throughout the term. I was highly conscious of the way some of the students in the class interacted with the material, and I admired the way they took charge of their own learning and engaged in a topic that clearly interested them. So while I knew that it’s okay to be vocal about what needs clarification, to encourage your own curiosity, or to contribute to discussions because that’s how you learn and grow as a student and as an individual, I didn’t start to practice it until later in the term. More often than times, I would find myself wishing I had raised my hand and participated which is why I tried to make more of an effort to be actively engaged. Science and research is all about contribution and collaboration. I don’t think we would have made the significant strides in science today if we just bottled up our thoughts. And so while it may be a small victory for me, it’s a victory that I am happy with as I am a person who wants to make contributions in science.

3. Now, think about yourself as a learner and as a researcher (really, when we do research we are constantly learning, so the two overlap in this sense). What is one thing that you have learned about yourself? Do you think this “thing” is important? Why or why not?

I learned that I’m only decent at asking for help. I think this is important to address as asking for help is important for student engagement. When I really don’t understand something, I’ll flag Dr.Kalas down. However, if I feel as if it is a problem I can work out myself (but maybe it is not), I’ll keep it to myself. Sometimes this is good as struggling through a concept is what will retain it in my mind; however, I feel that sometimes… this is incredibly unproductive to me. So much learning and quicker clarity could have been achieved if I just reached out for help. I think this is important because as mentioned before, science is all about collaboration and contribution. This course focused on teamwork a majority of the time. Of course, there are multiple ways to contribute in a team, but I would have hate to be the one to let my team down by not being active with where I am in my learning and what I can contribute. If the roles were reversed, I wouldn’t have thought anything less of it as I would only ever want to see our team succeed.

Posted in R&R | Leave a comment

Unprompted whimsies #6: “Metaphors, Language, and Thought”

Towards the end of class today, the discussion took for an interesting turn as to whether the results of a clinical study could be properly conveyed back to the participants, or other (interested) individuals.

The class seemed to be split on whether the results could be properly conveyed towards a demographic that is perceived to be uneducated in genetics. Personally, I’m part of the half where I believe that information can be conveyed in a meaningful way towards the recipient who is interested in the results. There are plenty of avenues for this communication. One that popped into my head was the use of metaphors.

Earlier this year, I was enrolled in an English Language course where we studied how figurative language, especially metaphors, was used visually or textually in everyday life to convey meaning. For that course, we had a term paper and I had chosen to write it on a New York Times article, “A Family’s Shared Defect Sheds Light on the Human Genome”.  A quick synopsis is researchers were able to trace the  syndactyly limb anomaly to mutations in the topologically associated domains of the genome. When they unearthed this finding, the researchers communicated their findings via metaphors to ensure easy understanding and comprehension by the public.

My paper went on to deconstruct and analyze their metaphor by applying the concepts learned in that English class. I remember when I writing the paper that there is always a way to explain something to somebody.  What’s important isn’t how detailed you are with the explanation, but whether that explanation, without conjecturing, makes logical sense to the recipient.

Link to the NY Times Article:

https://www.nytimes.com/2017/01/09/science/dna-tads.html

English Term Paper:

Analysis of “A Family’s Shared Defect”

Posted in Uncategorized, Unprompted Thoughts | Leave a comment

Finally… the project question I will be exploring!

After talking to Dr.Kalas and reading some of the comPAIR review, I’ve decided to pick one of my two candidate questions for this project. I didn’t expect myself to pick a question so late in the game, but I don’t think I could have produced a project I was proud of if I was exploring a question that I felt lukewarm about.

Selected question:

What is the developmental effect on kidney formation of H19’s microRNA products, mir-675-3p and mir-675-5p, on the following proteins from the BMP family: BMP 7, BMP 11, and BMP 4?

Posted in Project | Leave a comment

Unprompted whimsies #5: Thoughts on ComPAIR

I can’t help but feel excited when I see a notification sitting in my inbox, alerting me to feedback on my project from my peers.

While it took me a while to finally come up with a question and a hypothesis that I was happy about exploring, a part of me was a little nervous about what my peers would have to say about the way I planned to pursue this question: was it too boring, was it too long, was it not well-structured? However, the feedback given has been both helpful and encouraging as I finish this final project. As I am taking a study break, I’m also taking a moment to be appreciative of the fact that I am part of a really strong class this term.

This is because while I like receiving feedback from my peers, I enjoyed ComPAIR because I was able to look and evaluate my peers’ projects. Many of them have really neat ideas and it is incredibly interesting to see them take a question and make it their own. It makes the learning process a lil’ cooler, and is unlike anything I’ve experienced in other classes. I would have liked to see more projects, but I suppose with a student schedule, it would be ambitious to read everybody’s projects while balancing own schoolwork…! Alas!

Posted in Unprompted Thoughts | Leave a comment

ComPAIR: Draft of Project Handed In & the Accompanied Peer Review Feedback

1. PDF File of the Final Project (Draft) turned in to ComPAIR

Biol463_FinalProject_DraftforComPAIR_YJChen

2. Feedback from my Peers

Student #1:
You did a great job explaining the background information about lncRNA, H19, and kidney development. It would be good to have a justification for your hypothesis. And, of course, more specificity in the experimental methods.

Student #2:
I would maybe include a little bit more detail to your introduction. There were a few terms, I would have defined if I were you. It would be easier for the reader in case they aren’t familiar with your choice of topic. Also, it would be nice if you could include an abstract.

Student #3:
I really like this final project draft, especially the introduction part. I feel like it gets my full attention from the first line. Overall, it’s very well-written and I really like your hypothesis. I’m sure that this will make a great final project once completed. I wish you the best of luck and I’ll see you in class!

Student #4:
Your experiment is testing multiple things. I recommend simplifying it, or fusing the question into a single one, even if it leaves out some details. I appreciate the ambition, but focussing on one good experiment is prefered.
I also recommend a diagram showing the interactions of the different elements mentioned.

Your writing is very clear. Good job making the flow of the text.

Student #5:
Good points:
1. Very straight to the point
2. Awesome introductory paragraph

To improve:
1. A few typos/formatting (ex: spacing between words)
2. Unclear if having 2 hypotheses means you will require 2 experimental procedures?
3. Describe how you came to your predictions

Student #6:
Good introduction to why the topic is relevant. The background information was a little long and this sentence is odd “It is important to note the interaction of the microRNA’s interaction with members of the BMP family as the BMP family are a group of signaling molecules that is ubiquitous in all organ systems for its role in embryogenesis and development”.

Overall a nice draft and it will be nice when text is added to the tabels in the last sections to see your own interpretations.

Student #7: Very good introduction. Don’t forget to write your potential impact part and explain why you expect those phenotypes.

Posted in Project | Leave a comment

Final Project: Change in Questions

I had switched questions earlier in the term because I had wanted to look at at the long non-coding RNA H19. I was attracted to H19 for the wealth of information waiting to be discovered from the ample research that is currently in the literature. Little to my surprise (and chagrin), H19 proved to a really interesting topic that I’ve been finding it hard to narrow my question to something specific until now…

The questions that I have are in two parts: (May have to pick just one as I do think I am being too ambitious…)

  1. What is the developmental effect on kidney, of H19 microRNA products, mir-675-3p and mir-675-5p on the following transcription factors from the BMP family: BMP7, BMP11, and BMP4?
  2. Will the mir-675-3p and mir-675-5p produce the same results observed in skeletal muscles for Smad1 and Smad5 as they would in kidney cells in a transplantation experiment? In other words, are the microRNA products pre-programmed or can they adjust to their surroundings via environmental cues.
Posted in Project | Leave a comment

R&R #4

1. I don’t think there is too big of a difference between an inconsequential situation and for an exam situation. The strategies build on each other. For an inconsequential situation, I try to cover all my bases in answering the question, but I am much more bold in my thought process. When I know there is nothing on the line, I feel comfortable in challenging my understanding of a subject material by wondering different questions, possibilities, and tinkering with ideas so I can truly understand. When answering a question on a midterm, I answer the question based off the knowledge and concepts acquired prior to the midterm. Usually, there is something about the question that is obvious, to me, that a certain concept should be mentioned. Therefore, my answer for a midterm question is usually much more structured and is less likely to be bold in its thought process.

2. An example of an inconsequential situation would be questions that arise during readings or during class. I am comfortable with bouncing ideas (as long as the idea is within reason) and thoughts with myself, and with other people. By doing this, I acquire a good understanding/idea of the importance of what is discussed and of the potential different school of thoughts! Understanding whether my ideas/thoughts had potential/merit allows me to transfer over the knowledge with confidence during an exam situation.

3. I think two of the biggest challenges for me with the upcoming midterm is 1) being comfortable with answering questions that asks me my opinion on how a mechanism (that remains to be elucidated) operates and 2) pushing past the “panic” mode that kicks in at the half-way point, and remind myself that I know and understand the material so there is nothing to panic about!

Posted in R&R | Leave a comment

Unprompted whimsies 4: Learning in Development Part 2

While I have participated in group work/projects over the course of my undergraduate journey… I don’t think I have been in a course that encouraged active group work consistently and with different people!

It was a little weird for me at first as I’m used to working with the same people in a course, but I’ve come to enjoy the process. I like meeting different people in the class and see how I can contribute to the group through meaningful discussion or responsibilities in the group. At a fourth year level, you get to engage with people who intentionally choose to be in the class because they want to learn about that topic. As cheesy as it sounds, working with a group of people who take responsibility for their own learning encourages me to do the same with mine.

Posted in Uncategorized, Unprompted Thoughts | Leave a comment