Throughout my undergraduate degree, I have not had much lab experience, or experience with research. Many of my courses have been heavily theory-based, and have not had too many practical applications or have not taught me how to apply them in a research setting. However, I have always been interested in genetics, and when I learned about epigenetics, I was even more intrigued.

This year, I’ve had the privilege of working on my directed studies project on epigenetics, and I have been learning several different lab techniques that I have found interesting. I had originally planned on proposing an experiment to investigate whether certain replisome proteins (cmg Helicase, FACT, and Pol α) were necessary for maintaining epigenetic silencing through histone modifications. An article was published in October this year (partway through my project) that found that Pol α was indeed necessary for maintaining genetic silencing, and I had to modify my approach a little. It was still unclear how this process came about, so I decided to investigate further whether this has to do with the proper deposition of histone proteins following replication.

My question now became whether or not DNA POL α was responsible for the deposition of histones onto nascent DNA. I had learned how to perform MNase digestions on DNA to observe chromatin structure in my directed studies, and I figured it would be an appropriate technique to study whether or not POL α had an effect on nucleosome formation.

1. The most challenging aspect of my project was when I found a recently published article that published findings that my original experiment hoped to answer. As such, I integrated this new paper into my background information, and it became the paper which I used as a foundation for my final project. I searched for a knowledge gap left by this paper, and tried to come up with a new experiment or how to come up with these findings. I pored through online stores of information, and looked for different experimental procedures online to come up with something new, and I was pleased with what I found.
2. Although I have learned quite a bit about the topic that I hope to experiment on, I do feel that I have gained a better idea of what it feels like to be a real researcher. I do feel thst I have a better understanding of what it is like to identify gaps in the knowledge, and propose experiments to fill these gaps. I have always wondered how people can idenitfy what is yet unknown, but now I do feel that i better understand how this process works.

1. I stated at the beginning of the term that I would like to learn more about epigenetics, how else hereditary information can be passed on from generation to generation without affecting the gene sequence, the interactions between DNA and proteins, and how these proteins affect regulation of different genes and how one protein can regulate multiple genes. I can say that I have learned much more about these topics than I had originally hoped to. At the beginning of the term, I was not sure about what specifically I would like to learn about since there was so much I did not know, but going through different case studies and different model systems helped me get an idea of what mechanisms and what processes occur in nature. I was able to learn about mechanisms that I had not heard of before, and I feel like I had the chance to come up with models of systems that I would not have been able to imagine without the guidance of this course. Although I may not have learned too many concrete facts in this course, I believe that I developed skills that can be used in the future. Already I am seeing myself apply this logical thinking process in my directed studies project, and when I write papers for other courses. Instead of just learning about what currently exists, I learned to think about what could exist and what the possibilities are, and how we can find out what’s really happening with our genes.
2. I believe that when I was working on my final project, I was very much tested on my ability to respond adaptively and be flexible. A couple of nights before the first draft was due, I came across a paper that was published in October 2018 that published findings to the answer to my original question. As such, I had to dig deeper into this field, and come up with a new research question and experimental design. This was challenging for me, as I had not had to think this creatively or abstractly in many of my other courses, but I enjoyed the assignment, and had genuine excitement while writing many parts of my paper. It was difficult for me to adapt to this new question and angle, but I was able to persist through it and put something on paper that I can be proud of.
3. The most challenging part of the course for me was all the abstract thinking that we had to do with proposing models for mechanisms and designing experiments to test these models, as I do not have much experience with research or research methods. With practice, I was able to develop critical thinking skills that allowed me to develop a more natural tendency to this thought process. I also grew more familiar with research methods after reading more academic papers, and this also gave me an idea of the importance of different controls, and different treatments. I feel that I have a better understanding now of the thought process that goes into different experiments.
4. There was no question 4, but I just wanted to say thank you to you, Pam, as our instructor for this course. This has truly been one of my favourite courses at UBC, and I really enjoyed the material and the style of teaching the course. Even though I could not be as present as I would have liked to be while I was helping my family with some of our personal matters, you were very understanding, caring, and accommodating. I feel that this course challenged me in ways that other classes hadn’t, focusing more on critical thinking and creative processes than with hard fact-memorization. I appreciated the case studies and specific models we learned about, and it was interesting learning about what researchers in different areas of genetics are currently working on. These specific cases helped me feel what it’s like to be at the forefront of academic research, and feels like a taste of what it may be like to be in academia. Additionally, I do also feel that this is one of the classes where I met the most people and made the most connections with people whom I had not previously known, and  a large part of that is because you helped foster this community and safe learning environment. Thank you for a great term, and all the best to you and your future students!

If I were a developmental biologist…

1. I would like to learn more about how chromatin modifications affecting gene expression are passed on through cell lineages, thus maintaining proper gene expression (e.g. through cell lineages in the same tissue). I would like to learn which proteins are used to modify histones, and the process through which that occurs.

2. If we could learn more about these, it could potentially help us learn how to reverse this pattern of gene repression and create cells that could possibly differentiate into more types of cells.

1. Although I have learned more about the caste differentiation process in honeybees and what molecules may be responsible for it and what studies have shown, I feel that the most important thing I’ve learned is how to synthesize important information from different papers and pick out the key details that are needed for further research. I do feel that I was not always comfortable understanding papers, but I now feel much more competent in tackling journal articles and understanding what data I need to learn from each publishing.

2. I do find that I’ve developed better reading and synthesizing skills that will definitely help me outside this class. I do feel more comfortable now reading journal articles, and find myself getting more familiar with different lab techniques that have are being used.

3. I do feel that I still struggled with understanding some studies and journal articles, but I definitely do feel like I am getting much more used to reading and understanding them.

i) I analyzed the Spannhoff et al paper with my partner, Melissa Liu. The paper investigated the ability of 10HDA, a lipid found in Royal Jelly, to epigenetically modify genes. They found that it had histone deacetylase inhibitor activity, and may be responsible for some of the epigenetic effects of Royal Jelly. A copy of our analysis of the article can be found here.

Spannhoff, A., Kim, Y.K., Raynal, N.J., Gharibyan, V., Su, M.B., Zhou, Y.Y., Li, J., Castellano, S., Sbardella, G., Issa, J.P., Bedford, M.T. (2011). Histone deacetylase inhibitor activity in royal jelly might facilitate caste switching in bees. EMBO Reports, 12(3), 238-43. doi:10.1038/embor2011.9

ii) Here is a copy of our group’s model:

Group members: Evan Gibbard, Hayden Wood, Melissa Liu, Miguel Oreta, Oline Pade Jensen

iii) A document with the class’ models for Queen bee development can be found here.

iv) Summary of the model: The class generally agreed that components of Royal Jelly (e.g. royalactin) upregulated the EGFR pathway, while components of Bee bread (e.g. vein, km) downregulated the EGFR pathway. The EGFR pathway induced Queen bee phenotype through downstream pathways (e.g. mapk, S6K) that induced Queen bee phenotype.

Contradicting evidence was found in the paper “Royalactin is not a royal making of a queen” which found that royalactin alone was not enough to induce Queen bee phenotype, and had no measurable effect on influencing phenotype.

Spannhoff et al. also found that the large fraction of Royal Jelly (components larger than 3kDa) could not induce epigenetic modifications in their system, and did not think that proteins could be responsible for the epigenetic effects of Royal Jelly.

One way of testing this would be through the creation of a synthetic royal jelly with all necessary components for Queen bee phenotype development. Once the synthetic RJ is shown to be sufficient to induce QB phenotype, we could selectively remove components of RJ or a combination of different components to see which are necessary for the development of QB phenotype.

Another way of testing this would be by identifying which factors influence the larvae towards the QB or worker bee phenotype. For example, 10HDA and royalactin would be group together as QB factors, and the plant miRNAs and vein + km would be grouped together as worker bee factors. This would work well with the synthetic Royal Jelly experiment to determine which factors induce caste differentiation.

v) Reference list:

Buttstedt, A., Ihling, C. H., Pietzsch, M., & Moritz, R. F. (2016). Royalactin is not a royal making of a queen. Nature,537(7621). doi:10.1038/nature19349

Ashby, R., Forêt, S., Searle, I., & Maleszka, R. (2016). MicroRNAs in Honey Bee Caste Determination. Scientific Reports, 6, 18794. http://doi.org/10.1038/srep18794

Kamakura, M. (2011). Royalactin induces queen differentiation in honeybees. Nature, 473(7348), 478-483. doi:10.1038/nature10093

Spannhoff, A., Kim, Y.K., Raynal, N.J., Gharibyan, V., Su, M.B., Zhou, Y.Y., Li, J., Castellano, S., Sbardella, G., Issa, J.P., Bedford, M.T. (2011). Histone deacetylase inhibitor activity in royal jelly might facilitate caste switching in bees. EMBO Reports, 12(3), 238-43. doi:10.1038/embor2011.9

Zhu, K., Liu, M., Fu, Z., Zhou, Z.,. Kong. Y., H., Lin, Z., Luo, J., Zheng, H., Want, P., Zhang, J., Zen, K., Chen, J., Fuliang, H., Zhang, C., Ren, J., Chen, X. (2017.) Plant microRNAs in larval food regulate honeybee caste development. PLOS Genetics 13(8), e1006946.

1. Although I have learned more about the caste differentiation process in honeybees and what molecules may be responsible for it and what studies have shown, I feel that the most important thing I’ve learned is how to synthesize important information from different papers and pick out the key details that are needed for further research. I do feel that I was not always comfortable understanding papers, but I now feel much more competent in tackling journal articles and understanding what data I need to learn from each publishing.

2. I do find that I’ve developed better reading and synthesizing skills that will definitely help me outside this class. I do feel more comfortable now reading journal articles, and find myself getting more familiar with different lab techniques that have are being used.

3. I do feel that I still struggled with understanding some studies and journal articles, but I definitely do feel like I am getting much more used to reading and understanding them.

During the DNA replication process, the DNA and proteins that form nucleosomes are disassembled and then reassembled exactly on the newly-replicated DNA. Histone chaperones are a broad class of proteins that deposit histones on the DNA, but which of these assist in the reassembly of chromatin in the newly-replicated DNA is unknown. Some proteins involved in DNA replication also have similar functions to these histone chaperones, which means that the replisome itself may mediate the replacement of histones after replication. My research question hopes to cover:

1. Which proteins are responsible for the deposition of histones and reassembly of nucleosomes immediately following DNA replication?

1. I learned more about chromatin architecture, and how cis-factors do not necessarily have to be close to each other in sequence, as long as they are in the same topologically-associated domain (TAD). Moreover, I also learned about different techniques that are used to study chromatin architecture and TADs (such as 3C and its derivatives), and I find all the progress being made in this field to be quite interesting.
2. These fit nicely into my learning objective of how proteins can regulate genes, and moreover how one protein can regulate different genes. If genes are in the same TAD, they can be regulated by the same trans-acting factors as well, and boundary elements that barrier this TAD from others can prevent those trans-acting factors from acting on other genes instead.
3. I think the most challenging part of the course so far has been learning what to directly conclude from experimental data, and how to analyze data. I am surprised by this as well as not too many of my other courses rely heavily on reading real papers, and instead focus on hypothetical data sets for experimental data.

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