Author Archives: anik muhuri

Learning Journal #1 – There’s so much complexity to gene regulation!

 

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

Rspo2, a protein known to interact with Wnt to activate β-catenin, is required for cranial, facial, and left hind limb development in mice.

 

 

 

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

We were shown a figure from Yamada et al. (2009) paper which highlighted the type of information researchers can obtain from “removing something” experiments. The figure showed the differences in development between a mice strain which has WT Rspo2 and another strain with Rspo2 knocked-out. They determined that mice lacking Rspo2 had abnormal craniofacial development as well as poorly developed left hind limbs. The figure showed that Rspo2 is necessary for cranial, facial, and hind limb development in mice.

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

I learned that there are four models to potentially explain how interactions between transcription factors and enhancers can mediate transcriptional silencing or activation. The four models are looping, tracking, linking, and facilitated tracking.

 

 

 

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

In class, we were talking about distinctions between enhancers, silencers, and boundary elements. When we came to the topic of enhancers, it became obvious that enhancers can significantly distant from the genes they regulate and there must be a mechanism to transmit information from enhancer interactions to regulatory regions of genes. These models were necessary to describe how this information is transmitted.

 

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

I’m beginning to develop a more critical and analytical perspective in terms of what I’m reading. When we go over figures in class, I am starting to analyze figures as in-depth rather than accepting it as what it is. I’m learning to question why the authors chose to do a certain experiment and their logic behind their experimental design.

 

 

 

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

Going over figures in class really helps me to develop a more analytical perspective on things. I have gone over many of the figures in class just like everyone has and sometimes it turns out that I understood some of the figure but maybe I missed on a minor point. Sometimes I may have even missed out on a critical point. Sometimes my fellow classmates will point out things that I didn’t see. I find this to be humbling but also really helpful because it makes me realize the level of attention and focus that is required in order to understand science papers properly. It’s also really good practice for whatever is coming next in my life.

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HW 1: If I was a developmental biologist/geneticist…

This assignment is a very interesting and made me think about what problems I would be interested in solving. It got my mind working…to the point where I was dreaming about the questions whilst sleeping. You know something has really gotten to your core if you are dreaming about it. So here are some of the questions that really pique my interest and maybe your interest as well. Maybe one day we can collaborate and solve these problems once and for all.

  1. The dystrophin (DMD) gene codes for a cytoplasmic protein which forms a complex with other proteins to help attach the muscle fiber cell membrane to the extracellular matrix (ECM). Defects in these interactions to form complexes or deficiencies in expression for these muscle proteins can result in various forms of muscle dystrophy. It would be interesting to determine whether these genes share common cis-regulatory elements. It’s possible that a transcription factor or a group of transcription factors regulate this gene set by interacting with the same regulatory element. It’s also possible that these proteins share the same functional domain that allows them to interact with one another to form a complex. It would be interesting to elucidate further upon this mechanism.

2. Asthma is a chronic inflammatory disease that has increased in incidence significantly in the last few decades. It’s been hypothesized that the increased rate of asthma is due to increased epigenetically-derived changes being passed down to future generations. It would be really interesting to determine what sorts of epigenetic changes could be responsible for higher risk of asthma. Personally, I would find it interesting if some epigenetic markers could be directly attributed to a someone becoming asthmatic.

I really find the muscular dystrophy problem interesting as it is a condition that has huge adverse impacts on a person’s life. I have had the chance to volunteer with events that deal with Duchene’s Muscular Dystrophy and seeing firsthand what muscular dystrophy can do makes me really want to solve the problem.

 

If I was lucky enough to determine that a transcription factor or a group of transcription factors is responsible for directing dystrophin and other proteins to form complexes, it would be huge in the field of developmental genetics just as another example that highlights how much regulation is required in development to get to where we are as adults. The question I posed is one small step, which if solved, can lead to further developments; it may lead to a flurry of research from different labs . Maybe one day it can lead to actually being able to prevent muscular dystrophy (dare to dream), which would be an amazing feat. If this feat is possible, I’m sure it would make a big impact to the community, especially to people who may be affected by muscular dystrophy or knows someone who has been affected by this condition. There is a possibility that we can help people from going through this limiting genetic condition and possibly improve their quality of life, which is a great reward.

 

So this is my first stab at developing some questions that I would like to investigate. I look forward to the day that I can either solve this issue entirely or make some significant contribution to this issue with my research work.

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