Unprompted whimsies #3: CRISPR-CAS9

CRISPR-Cas9 is a hot topic!

During Alice’s presentation, Shannon raised a question on the ethics of of genome editing with this technique. I didn’t expect the presentation to end without this question appearing from somebody in the audience as it is an important and interesting question.

The risks of this topic has been explored and published by many lab groups: off-target mutations, unintended cleavage of identical/homologous DNA sequences, efficient delivery of the system, etc.

Perhaps a question that is still too early to address at such a nascent time would be societal implication and access to CRISPR-Cas9. How would the FDA handle and integrate the possibility of this new technology? What about patent rights? To my knowledge, private biotechnology companies have already attempted to patent the technology. How would it be integrated into healthcare systems in Canada and the US? Who would have access to it? Would it be fair if those who need access for therapeutic treatments are unable to gain access because of financial reasons? What would have to be met for an individual to be in need for therapeutic treatment of CRISPR-Cas9?

CRISPR-Cas9 is a hot topic. And I’m sure I will be keeping a close eye on the integration of this technology with the rising emergence of medical genetics in our healthcare system.

 

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Seeking to Understand DNase-Seq? ;)?

Continue reading

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R&R #3: Assessing Progress on Understanding the Material

1. How would you describe your progress so far?

I’m not too sure how to describe it; while I would say that there has been improvement since the beginning of the term, there is still room for improvement. The material that we learn in class is incredibly interesting, but there are still moments where I feel a mental roadblock or confusion in understanding concepts. (I do think this is fair though as I think everybody goes through this at some point during a course!) It’s moments like this where asking questions, reaching out to classmates, has definitely help shed clarity on the subject matter.

2. Are you satisfied with your progress so far?

I remember feeling quite lost and intimidated beginning of term! I don’t feel that way so much now and actually feel more comfortable with the subject material!

Although while I do feel satisfied with my progress so far, I don’t feel 100% satisfied. I’m not quite as engaged in class discussions as I would hope to be. I definitely hope to use the remainder of the term in a resourceful way to further my education of gene-regulation.

3. What evidence/pieces of evidence did you use to determine whether you have made progress?

I’m finding that as I read assigned papers for this course, or genetics papers for other courses, I’m linking themes that we have learned in class and applying it critically to the readings.

I also found it helpful to keep a little section for myself in my notes to jot down questions or interesting tidbits as they come up during assignments/lectures. Following on these thoughts of mine often lead me to a paper, article, etc. that contributes to a bigger picture understanding, which is really helpful for me!

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Final Project Outline [With and Without Feedback]

Final Project Outline (Submitted)

Chen, Buffy_Biology463TemplateforProjectOutline

Final Project Outline (Received back with comments from Dr.Kalas)

Chen,Buffy_Biology463TemplateforProjectOutline_PamelaKalasEdits

 

 

 

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Unprompted whimsies #2: piwi interacting RNAs and development

For one of my other courses, we were asked to select a paper centered on transposons to present in small groups.

I stumbled upon piwi interacting RNAs and its function in relation to transposons, and thought it was a pretty neat molecule. This prompted me to research if there was any associated roles during development.

This led me to Ishizu and Siomi’s review “Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines”. Overall, I thought this paper was well-written and set the reader up well for understanding PIWI-interacting RNA molecules and illuminate insights of this molecule during embryogenesis.

Fun fact: Animals lacking piRNA (impairment in the protein or its expression) can exhibit sterility! Whether this is also found in humans is still to be discovered.

 

Link to the paper:

https://www.ncbi.nlm.nih.gov/pubmed/23124062

 

 

 

 

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Response to The HOTAIR Readings:

One thing that came to my mind after reading the three articles was that the first article raised a good point about how it is important the way researchers address a controversy as opposed to the importance of the controversy itself. With the emerging importance of lncRNA in gene regulation in development, as well as the increasing importance of HOTAIR for regulating Hox Genes.. it is clear that there will be conflicting results as research in this topic progresses e.g Chang and Dubole lab group. With conflicting results, would the lab group that isn’t as open to sharing their data/resources/methods have less credibility than the researchers who do?

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Schorderet and Duboule, 2011 reading Response

One main question that I have after still reading “Structural and Functional Differences in the Long-noncoding RNA Hotair in Mouse and Human” by Schoderet and Duboule:

It is interesting to read that a depletion of Hotair cognate lincRNA in mouse has had no severe effect upon Hoxd gene activation, trump development, or limb morphogenesis. Especially since it is an area where Hotair is expressed. I’d be curious to know the answer to the question of whether these processes are being regulated directly, or indirectly, by another lincRNA instead of Hotair. And if that is the case, what the selective advantage was against Hotair in mouse.

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Jumping Ship! From Smaug to H19

This post is exactly as it sounds…  After doing some research on the Smaug protein, and stumbling across H19, I’m switching the focus of my project from the Smaug protein to the long non-coding RNA (lncRNA) H19.

This is because 1) I am attracted to the idea of furthering my knowledge of how lncRNAs function in development 2) H19 is a player in development that is starting to receive some traction again from the scientific community and 3) I feel as if with H19, in comparison to the Smaug protein, I would be able to integrate more of the concepts and techniques learned in class.

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R&R #2

1. Two things that I learned in drafting my research question for the final project is that

A. It is easier to come up with a question in an area that you are interested in studying. I thought I had been interested in looking at the distribution of maternal gene products in developing embryos, but I was actually more interested in genomic imprinting and epigenetics! At first, I was initially focused on looking at the RNA-binding protein, Smaug as it plays an important role for pattern-differentiation. However, because I was more interested in genomic imprinting and epigenetics, I switched my interest and have decided to look at H19.

B. I learned that reading lots and lots of primary articles on the interested gene/protein/RNA gives a good understanding of what has been understood, what hasn’t been understood, and how other researchers have approached their hypothesis. 

I expected to learn these lessons for sure. I didn’t expect myself to stick with the first question that came to me. I actually expected myself to explore what was out there in the literature before I found something that I was happy with studying.

2. I had expected myself to read conflicting results from researchers as I would be looking at an area of active research. I was also expecting myself to have difficulties in reading the paper and critically evaluating the experiment. 

For the most part, I have not come across any controversy on H19, nor any conflicting results. This could be because I haven’t read enough papers yet though! 

As for difficulties reading papers, I’ve yet to encounter any difficulties in understanding papers.

3. In developing a sound, well-research hypothesis, my strategy is to 1) do my research 2) know exactly what I want to test 3) make sure my hypothesis is testable and 4) Decide if it will be a 1-sided or 2-sided hypothesis. As the hypothesis will influence the research design, I’m sure I’ll be spending time fleshing out my question!

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Assigned readings to prepare for Oct 2

The first three words that come into my head after reading the article, “Royalactin is not a royal making of a queen” and Kamakura’s reply are: Dynamic. On-going. Evidence.

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