BIOL 463 – Final project outline – Anik Muhuri
This is my initial project outline, when I had no idea what I was writing.
Author Archives: anik muhuri
Learning Journal #4 (X chromosome inactivation is really really interesting!)
WEEK 11 LEARNING JOURNAL
- Factual knowledge
Please describe, briefly, two new, distinct pieces of factual knowledge that you acquired or developed since the last learning journal
One piece of factual knowledge I have learned is that the long non-coding RNA called Xist inactivates the X chromosome from which it was transcribed and there are various factors like CTCF, Tsix, and Xite that regulate Xist. Another bit of factual knowledge I have acquired is that there are five potential models to explain how X chromosome inactivation begins: blocking factor, symmetry breaking, alternative states, transvection, and stochastic.
- 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.
CTCF, a binding factor which causes repression of Xist expression, is associated with the transvection model for X chromosome inactivation. The transvection model suggests that physical pairing interactions between homologous regions of X chromosomes allows signal exchange/communication between the two X chromosomes and eventually one X chromosome is shut down. CTCF is thought to aid in these pairing interactions. JPX RNA can target CTCF away from the Xist gene, allowing de-repression of Xist.
- 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.
- Please describe, briefly, the strategy that you employed to complete the task.
I read the paper thoroughly once just to get a jist of the main points. Then I read the paper through a second time, carefully going through all the words or concepts that weren’t clear to me. I also wrote explanations in my own words for what each figure was showing and its importance.
- Thinking about your experience with reading and dissecting this article, what was the hardest part?
I thought that generally the paper was really well laid out. I was very confused by some of the wording and I think that definitely could have been improved upon. I would’ve grasped this article much more quickly if the writing was better.
- Thinking about your experience with reading and dissecting this article, what did you feel most comfortable with/confident about? Why do you think that is?
I was really comfortable and confident with interpreting the first few figures because the techniques used were familiar to me and they explained the reason behind their experiments. Even if they weren’t clear, the way they laid out their figures was very well-thought and I think it helped me grasp the important points of the paper really quickly. I definitely have to grapple with the logic behind why some experiments are done in other papers, but in this paper it wasn’t that big of an issue for me.
Informal post #5 – Are fabrications in science going to become commonplace?
I read the article that was posted on the BIOL 463 facebook page about Biomed Central and their fabricated peer reviews scandal, if it can be called a scandal. It’s really disappointing to think that these kind of things happen in science and there seems to be a lot of these kind of things happening over the last decade. This might be a very naïve viewpoint but I always thought that science should uphold integrity; I didn’t think or I didn’t have reason to think there would be any fabrication, lying, or cheating in science. Starting my third year in UBC, I realized that is not true. People, when they feel desperate enough, will do anything. It’s quite sad actually, especially the situations where people will fabricate their data so that their paper logically flows and so it can be published more quickly. Maybe I’m wrong but it does seem like these things happen because there is so much pressure to get papers out or to publish journals on time (so fabricated reviews are required). People are worried that if they don’t publish more papers, they won’t receive a post-doc position. If they don’t publish more papers after that, they may not get the chance to run their own lab. I think part of the pressure arises from the lack of funding, which I think is unfortunate. I really hope that the funding issues that researchers are having nowadays is stemmed soon or I really do think these mini-scandals will occur at much higher frequencies. I really hope funding improves so that research can continue in all fields uninhibited and people aren’t pressured to fabricate anything.
Informal post #4 – I f***** love science!
I don’t know if this could be considered a valuable scientific resource but the “I f**** love science” website is something that I really enjoy. I am not sure but it seems like the website’s main goal is to make scientific topics more accessible and mainsteam so non-scientists can enjoy and talk about the things that we do. It seems like the website is geared for traditional non-scientists but I really enjoy it. Sometimes there are topics presented on the website in fields that I have never had experience in and the simple explanations the website provides is really helpful. I think they do a great job in making science more communicable, which is something Bill Nye has been working on forever. They also do a great job in sparking discussion or bringing topics to light that might otherwise never get the attention it deserves. I am often impressed by how novel the topic presented is and how I’m learning something new from it all the time. One problem is that they do tend to focus on animal biology too much; I know there are many other topics in science that can be just as interesting. But overall, I think the website does a great job and it’s a great idea to share science through social media platforms because that seems to be where our future is heading,
Informal post #3 – Argument for the use of animals in developmental biology studies
As a human being, I understand that the idea of using animals to run scientific research seems cruel. It’s probably even worse for a humanitarian to see the clinical efficiency with which some scientists sacrifice animals for their research. From that perspective, I can see why people are so against the use of animals in research. I feel like people believe that researchers are cold-hearted and don’t care about the animals that they are cruelly sacrificing. But that’s not the case at all. I think every scientist feels bad about it; if they didn’t then they wouldn’t have the need to establish ethical protocols for sacrificing animals. We take care to make sure that the animal feels as little pain as possible. We don’t want them to suffer. Researchers, more than anyone else, understand the importance of that animal’s life in my opinion. Scientists know that the animal’s sacrifice may mean an advancement in science, or a breakthrough that makes peoples’ lives better. If there was a way to do this without sacrificing animals, then researchers would gladly do it. I think researchers would gladly jump on that kind of chance. But since that is just not possible as of today, then researchers have to do what is necessary and sacrifice the lives of some animals for the improvement in science/academics and other areas as well. I know of a researcher personally who sacrifices a lot of mice for her research and she lights a incense stick in her office after the sacking. For her it’s a way to show respect for the lives lost. So researchers do care and if there was a better way to go about this without sacrificing animals, I think we would have employed it by now.
Learning Journal #3 – All of the things that go into embryonic development is just way too difficult to wrap my head around!
A. 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).
One thing that I learned recently is that non-coding RNAs such as AIR and Kc1qnot1 can prevent transcription of certain genes in cis. Air prevents the expression of paternal Slc22a3 while Kc1qnot1 prevents the expression of paternal Kcnq1. These are examples of genetic imprinting that can have some adverse effects in development. Another thing that I have learned is principle 6B: the three determinants of value are location, location, and location. It’s just so interesting to see through research that regulatory proteins such as Bicoid, Hunchback, Kruppel, and Giant are expressed at specfic timepoints in very specific locations; changing these locations or even preventing expression of these regulatory proteins can significantly divert development away from its normal path. In addition, I have also learned how important asymmetric distribution of maternal transcription factors/proteins is to the development of an embryo. If you don’t have asymmetric distribution of certain factors, there may not be any development to speak of. I thought that was really cool.
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).
The non-coding RNAs AIR and Kcnq1ot1 preventing transcription is factual knowledge because there is research/evidence supporting this statement. Regulatory proteins such as Bicoid and Hunchback regulating development is also factual if you consider research that shows that these proteins are expressed in very specific locations within an embryo and knocking out these genes can alter development significantly. The asymmetric distribution of maternal factors being necessary for development is more conceptual because a lot of different examples can be encompassed by this statement. Since nothing specific is mentioned for this topic, it’s more of a concept than a fact.
C. What makes “things” stand out for you
For each of your three “things”, please indicate what made it stand out for you.
All of the three topics mentioned here just makes me realize that development is so complex; so much has to go right for me to be able to be where I am right now. It makes my brain hurt just to try and think of all the mechanisms that must be involved. It would be interesting to see if someone could compile every single genetic mechanism that is necessary for one aspect of human development as we know it today. I would imagine this compilation would be larger than a collection of encyclopedias, maybe bigger than Wikipedia. What’s even more interesting is that there is more information coming in everyday and we might have to scrap some of our knowledge base because it’s just not accurate. This is why it stands out for me.
D. 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?
|
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 | Air and Kcnq1ot1 prevent transcription of genes in cis. | Factual | This is a mechanism of genetic imprinting and genetic imprinting has so much impact on development. | Describe to students the exact research associated with Air and Kcnq1ot1 and ask them what would happen if these non-coding RNA genes were knocked-out. |
| 2 | Bicoid, Hunchback, Kruppel, and other regulatory proteins are involved in specific processes in development | Factual | Normally, we are told in science that a certain phenotype we see is a result of many factors and is quite complex. This is for me a rare example of how knocking out one regulatory protein can give such huge differences in phenotype. That’s why it sticks out in my mind much more than other examples. | To determine if students really understand the concept, ask them what would happen if any of the regulatory genes are overexpressed or the genes are artificially expressed in different combinations in different times. If students can reasonably guess at the outcomes of such experiments, they have grasped the concept. |
| 3 | Asymmetric distribution of maternal factors is important for development | Conceptual | It’s just to difficult to wrap my mind around the fact that asymmetric distribution of certain proteins had a big role to play in me being where I am right now. | Provide students a hypothetical example in which asymmetrical distribution is prevented, by giving a drug that will stop transport around cells or ablate a transport protein. Ask students to predict what will happen if this situation occurs. |
Informal post #2 – Place, time, and identity!
We were asked to look at a timeline that laid out the history of the land that UBC sits on and relate it to the history of biology. I looked at the timeline and some of the years really jumped out at me. 1914, for example. 1914 was the year UBC construction began. In high school, we are taught that 1914 is when WWI starts, an events that displays human nature at its worst. It’s actually amazing to think that 3 years prior in 1911, Thomas Hunt Morgan described that genes are arranged on a chromosome. We never look back at history but it’s really cool to think that more than a 100 years ago this idea came to light. And so much has been discovered since then. Thomas Hunt Morgan can be considered a pioneer and to think his discoveries came around the same time as WWI. I think it’s a perfect example of how much positivity and negativity exists within the human potential.
In 1937, Hans Krebs discovered the citric acid cycle, something that is an inherent part of our cellular physiology. Two years later, WWII broke out, the worst display of human nature known in history. It’s just really amazing to think that around the time that human history is going through the worst wars ever known, there is advancement being made in other areas. Some advancements were bad but most of them has made a positive impact on our lives somehow or another. It’s just really interesting to look at it from that perspective.
Informal Post #1 – Group portion of the 1st midterm exam
The group of the exam was interesting because on the one hand, I learned something new both in terms of factual knowledge and working in tandem with others. On the other hand, I also learned that I was wrong on a lot of questions and I lost marks. I think there is a lot to learn from the group portion. It really is a great learning moment, particularly if you are at odds with the other members of the group. As you defend the position of why you think your answer is more applicable than another suggested answer to a question, the concepts and ideas that you are trying to communicate become more engrained into your mind. I think that is really great. My answers also greatly improved in the group portion because I saw how other people perceive the same question that I had; you learn to think about questions from different angles. Overall, I think group activities/exams are a good idea. I know it’s been in development for several years. I remember going through BIOL 112 with group activities. I think it’s something that UBC needs to look at and focus more attention on. I really think it can improve the amount of information students absorb during their time at UBC.
Learning Journal #2 – Conceptual vs. Factual Knowledge
- Factual knowledge
- Please describe, briefly, one new piece of factual knowledge that you acquired or developed so far in the BIOL463.
I have learned how maternal genes regulate gap genes, how gap genes regulate pair-rule genes, and how pair-rule genes regulate segment polarity genes. It was also very interesting to learn that gap genes can regulate other gap genes and pair-rule genes can regulate other pair-rule genes. It is amazing to see the intricate levels of regulation that goes into development. In particular, we learned that Bicoid and Giant interact with the eve2 enhancer and this interaction directs eve expression in stripe 2 of the Drosophila embryo.
- Please describe how you know that you have acquired or developed this piece of factual knowledge, and provide some evidence for it.
Before the Feb 4th class started, Dr. Kalas drew a diagram of segment polarity regulation in Drosophila, which displayed everything I mentioned in the above question. In addition, we analyzed figures from the Arnosti et al. (1996) paper to draw conclusions about what the data represents. In this way, we were able to convert conceptual knowledge about gene regulation in Drosophila into factual knowledge (Bicoid and Giant regulate eve expression in stripe 2 of the Drosophila embryo.
- Conceptual knowledge
- Please describe, briefly, one new piece of conceptual knowledge that you acquired or developed so far in BIOL463.
I have learned that the collective techniques 3C, 4C, and 5C are great for determining which segments of a genome are closely interacting with each other. All three techniques use the same procedures initially but differ in the end; 3C requires qPCR, 4C requires inverse PCR, and 5C requires LMA.
- Please describe how you know that you have acquired or developed this piece of conceptual knowledge, and provide some evidence for it.
During the techniques “speed-dating” session, I saw a presentation about the 3C, 4C, 5C techniques. This is still conceptual knowledge for me as I have never personally conducted these techniques nor can I verify whether these techniques are capable of providing of providing the results they are known for. Although many scientists have likely conducted and verified these techniques, I have yet to see the evidence; hence I consider it conceptual knowledge.
- Skills
- Please describe, briefly, one skill that you acquired or developed/are developing so far in BIOL463.
BIOL 463 is challenging me to develop my ability to critically analyze and question data that is put in front of me. This is a very valuable skill to have. I am excited to see how I can develop this skill further for the rest of this course.
- Please describe how you know that you have acquired or developed this skill, and provide some evidence for it.
We are asked to analyze figures and draw conclusions rather than read explanations for what the figures indicate directly from the paper. We just did this with the Arnosti et al. (1996) paper where we analyzed the figures to determine which transcription factors regulate eve expression in stripe 2. If I was only asked to read the paper, I don’t think I would have gotten as much out of it. I think this is the best way to develop analytical skills in a research-based capacity and I look forward to doing more of this.
- What is factual knowledge useful for?
Think about a piece of factual knowledge that you developed/acquired. Briefly describe what you think it is useful for.
From the Arnosti et al. paper, I have learned that Bicoid and Giant interacts with the eve2 enhancer and helps regulate eve expression in stripe 2 of the Drosophila embryo. This knowledge is useful for many reasons. It reiterates that Bicoid/Giant are important transcription factors for development. This information is also useful because it shows that gene regulation doesn’t occur with only one transcription factor or one level of regulation. Multiple modes of regulation (transcription factors) are required in specific combinations at specific locations within an embryo to direct the expression of a gene. Without this complexity, we wouldn’t exist. Finally, this knowledge is important because it can help elucidate other regulation mechanisms that dictate developmental patterns.
Final Project question for feedback
When we were asked to do the first homework assignment for BIOL 463, I talked about focusing on dystrophin as a project topic. My second question was about Asthma. After thinking about it more, Asthma and all the research associated with it has really captured my attention. Asthma is gradually becoming a major issue in North America, and despite all the work done on it, we can’t really say that there has been much of an advancement in terms of solving this chronic disease.
As there is so many different variables to asthma, it’s better to focus on a certain aspect of it. So my research question would be this:
Q. The increased incidence of asthma in North America over the last decade has been hypothesized to be a result of increased epigenetically-derived changes being passed down. What epigenetic changes are responsible for higher incidence of asthma? Can certain epigenetic markers be associated with someone being at higher risk for asthma incidence?
Please let me know if the question is too broad or if you find any other issues with it. I’m always looking for feedback.
Cheers!