Category Archives: Learning Journals

1.    Finding classmates that agree to let you see their wordpress blog/portfolio…

Name of the classmate whose portfolio you will be viewing: Alanna!

2.    ‘Evaluating’ the portfolio …

If I didn’t know Alanna at all and had to use only the content of her portfolio to evaluate her skills, knowledge and learning.. I would say her greatest strength is demonstrating her learning by making her Learning Journals very reflective in nature. She pulls a lot of examples from the lectures and from our in-class discussion and then further expands on them and reconsiders the major points covered. It is also evident that she regularly refers back to her notes to remind herself of the ideas that came up in class since the phrase “looking back at my notes…” commonly appears in her posts. This demonstrates that with every learning journal written, she has considered all perspectives of the topic including her own notes and discussions in class. She does a very good job at further analyzing the things that she may have found confusing at first and things that may have sparked her interest and curiosity. I think this is a good way of keeping track of complex thought processes, which is also one of the purposes of the learning journals.

Overall all the reflective journals and extra assignments were very well written and explained what we covered in class fully! Perhaps one way to change up how you present your learning is by relating the class material to other outside sources or things you’ve learned outside the class. This would just integrate in-class and out of class learning together. But otherwise, I was very impressed at how reflective and detailed your learning journals were!

3.    Comparing the portfolio …

The biggest difference is that Alanna refers back to what we learned in class (specifically in class discussions) a lot more in her learning journals. I think this great to review the main points and questions that may have come up in discussion and can be a way to reflect on the key points. Alanna has also added a few extra comments to some of her blogs to further explain her learning and understanding of the topics which would also be useful when referring back to them later. A similarity in our blogs is that we’ve both tried to include specific examples to further support our ideas and explanations.

1.    Two “things” that stood out

The first thing that really stood out to me is how different concentrations and combinations of regulatory proteins can control the expression of genes in different areas of a developing embryo. For instance, morphogen gradients are used to determine “stripes” and the expression of various other gap, pair-rule and segment polarity genes. This is done when different regulatory proteins bind to various enhancer regions responsible for stripe expression. They can act both as enhancer or repressor proteins and may have various affinities for different bindings sites. I find this very interesting since segment/ stripe determination is more complicated than it seems due to the large network of various genes/ regulatory proteins and their expression patterns and binding affinities at different regions in the embryo.

Another thing that stood out to me were the various types of enhancers. These include fail-safe enhancers, shadow enhancers, super- enhancers, tissue-specific enhancers and HOTS (Highly Occupied Transcription Sites). All these enhancers work in various ways such as in the case of fail-safe enhancers, both pieces of enhancing regions must be present and activated in order to ensure the gene isn’t activated by accident. Even though they all work to regulate transcription, I didn’t expect there to be so many subtypes of enhancers that perform in various ways.

1.    One new (or ‘improved’) concept

Chromosome remodelling is the dynamic modification of chromosome architecture which alters the way regulatory elements and transcription machinery control gene expression. Changes to chromosome structure includes methylation can have an impact on gene expression and interactions between enhancers, insulators/ boundary elements and other regulatory elements. The role of histone modification had also been brought up in the guest lecture and also acts as a mechanism involved in chromosome modification.

2. Thinking about your new or ‘improved’ concept

The concept that chromosome architecture and remodelling control gene expression is not a fact, skill or technique as the concept incorporates and integrates many other processes and concepts, such as how loops in the DNA created by a complex of regulatory proteins can promote binding of cis-enhaners to promoters to up regulate transcription. The formation of the loops allowed me to visualize how the presence of inhibitors/ boundary elements functions to prevent enhancers from interacting with promoters  by “blocking” them. Similarly, in class we talked about how removal of CTCF could destabilize the loop and cause the enhancer and promoter to not interact as well.  When we examined how ES cells can become neural cells in class, I feel like I gained a better understanding of how different combinations of methylation and demethylation of enhancers and promoters can cause certain genes to turn on/off. For example, H3K4me3 (histone methylation) is usually associated with transcriptionally active genes so it’s presence at promoters allows transcription to occur. Dr. Phoebe Lu also described how post-translational control of histone modification and ATP- dependent chromosome remodelling activities work in concert to control transcription. They control histone acetylation and deacetylation which interact with specific DNA-binding transcription factors that recruit histone acetylases/ deacetylases to promoters to activate or repress transcription. This integrated model of DNA regulation and chromatin architecture allowed me to gain a broader perspective of how different mechanisms (e.g. histone modifications, methylation, DNA loops, regulatory elements/ proteins) could all interact together in combination to regulate expression of different genes, ultimately controlling different cell fates and identities. This also helped me realize how gene regulation is controlled at multiple levels spanning from the overall chromosome structure to specific DNA sequences controlling transcription. Having a good understanding of this chromosome remodelling is important in that it helps us understand the role it plays in epigenetic regulation in various biological processes such as DNA repair, apoptosis, development and pluripotency. Many therapeutic strategies in the treatment of disease and cancer have begun targeting chromosome remodelling pathways as well, demonstrating its crucial role in the future of clinical therapies. From a development standpoint, findings have shown that ATP-dependent chromosome remodellers are essential for establishing and maintaining pluripotency and multipotency. Our understanding of regulation of chromosome remodelling at various developmental stages could allow us to gain insight on the induction of various cell fates which could also serve as a model for studying developmental disorders and even iPSC technology (in regards to reprogramming differentiated cells).

1. Factual Knowledge: In BIOL 331 and 335, I had learned about some of the experimental approaches used to study development including the “Look”, the “Remove something” and the “Add something” approach. Additionally, in this class we learned about some of the advantages and disadvantages of each approach and the types of information we can obtain. For instance, the “Add something” approach can investigate what factors are sufficient to induce the formation of iPS cells and in which combinations. Induced pluripotent stem cells (iPSCs) can be reprogrammed by specific transcription factors and have the ability can differentiate into various cell types in the body. If the specific transcription factors are indeed sufficient, they could transform something like skin cells to pluripotent IPSCs, similar to embryonic stem cells.

2. Making Connections: From previous courses, I knew what the different techniques (e.g. amino fluorescence, In situ hybridization..etc) were but the past few classes have made their application more easily understandable and have clarified their advantages/disadvantages. The “Add something” approach can be used on IPSCs to screen for different therapeutic compounds and test for disease-specific drugs. This is important in that using human cells would eliminate the need to test on mice or other organisms that may express different developmental factors and genes. Since iPSCs are also generated directly from adult somatic cells, they bypass the need for embryonic stem cells and can have many beneficial applications to regenerative medicine.