Advice in learning

Learning 

"The best way of learning is doing (Murat, May 2012)." Starting with learning vocabulary, I have to spell out the words before I can pronounce them correctly and remember them. this is part of the visual aid but mostly it is actually my senses that have the direct contact to the words; I see it, I write it, I pronounce it, I hear it. Ultimately, I experience it and internalize it that it becomes "mine" or "a part of me".

I admire the idea of Dr. Murat's that we always should have a side-project. I think it is a good intellectual entertainment. Especially, in research, we always focus on a specific topic all day long that it stresses us dramatically. Thinking about research becomes a habit that if we do not actively try to relax, it is difficult to make us share attention to other fun things. A side-project may help us pull our mind off the research for a bit, and it is a healthy habit to establish. Thinking about something else may promote creativity that may be beneficial for our research.  We can see our research from a new perspective or we can generate new research ideas or creative ones. Also, experts know very well about one topic and they appear to be weak in the knowledge of other areas. Therefore, if we know multiple areas besides our research by doing some fun side-project, we actually can "show off" in front of other scientists.  

Never afraid to ask, but I usually think twice before I ask because I want to challenge myself how quick I am and how logical I am. When I have the answer, I should rethink the answer to see if it is actually resolve the question. If the answer is good but not good enough, I will rethink about it and discuss my solution with others to justify my thinking. This is an active learning, but it requires practice, experience, and background in order to be able to judge the answer and establish a better answer. 

Promotion of presynaptic filament assembly by the ensemble of S. cerevisiae Rad51 paraloques with Rad52 - Bernstein - Pitt

Promotion of presynaptic filament assembly by the ensemble of S. cerevisiae Rad51 paraloques with Rad52

Rad55 bridges Csm2-Psy3 in the Shu complex with Rad51 in order to help loading Rad51 onto the ssDNA coated with RPA (presynaptic filament) => if the Rad55-Rad57-Csm2 interaction is disrupted, presynaptic filament cannot occur as well as HR.

Rad51 and Rad52 individually interact strongly with Rad55-Rad57 but weakly with the Shu complex. The role of Rad52 (F. 3e) is to enhance the Rad51 loading onto RPA-coated ssDNA in the presence of Shu complex and Rad55-Rad57. The RPA protein hinders the loading of Rad51 onto ssDNA when there are only Rad55-Rad57 and Rad52; but if the Shu complex is present, it enhances the Rad51 loading even though the Shu complex does not really interact with RPA. However, Csm2-Psy2 heterodimer possesses the DNA binding domain that may help the loading of Rad51 onto ssDNA(?). Then Rad54 promotes homology search and strand invasion and D-loop/DNA joint is resolved by different pathways to generate crossover or non-crossover product.

The Shu1 and Shu2 are not directly involved in presynaptic filament formation even though they are crucial in stalled DNA replication repair; Csm2-Psy2 can help this process as well as the whole Shu complex.

So even though Rad55 in the Rad55-Rad57 heterodimer was found to strongly interact with Csm2-Psy3, does Rad57 directly interact with the Csm2-Psy3 or Shu1 or Shu2  component of the Shu complex? Does Rad57 also interact with either or both Rad51 and Rad52? What happens to the presynaptic filament formation if Rad57 is absent and only Rad55 is present?

The RPA is loaded on ssDNA in order to promote the DNA replication, recombination, and repair in eukaryotes. What happens if  ssDNA is not coated by RPA because of a mutation in RPA, but the Rad51 is still able to be loaded on ssDNA in the presence of other factors except the Shu complex because there is no RPA, so is the Rad51 loading to ssDNA in this case able to rescue with the DNA repair in eukaryotes?

1. Even though Rad55 in the Rad55-Rad57 heterodimer was found to strongly interact with Csm2-Psy3, does Rad57 directly interact with the Csm2-Psy3 or Shu1 or Shu2  component of the Shu complex? Does Rad57 also interact with either or both Rad51 and Rad52? What happens to the presynaptic filament formation if Rad57 is absent and only Rad55 is present?

It is possible that Rad57 also directly interacts with Csm2.  We cannot rule out that possibility although I think it is likely only Rad55.  Shu1, Shu2, and Psy3 are not mediating interactions with Rad51, Rad55-Rad57, or Rad52.  I’m not sure if Rad57 interacts with Rad51 or Rad52 but I would imagine that it does.  Expression of Rad55 is depends on Rad57 and visa versa and so it is impossible in vivo or in vitro to determine what would happen to the presynaptic filament without either of them.

2. The RPA is loaded on ssDNA in order to promote the DNA replication, recombination, and repair in eukaryotes. What happens if  ssDNA is not coated by RPA because of a mutation in RPA, but the Rad51 is still able to be loaded on ssDNA in the presence of other factors except the Shu complex because there is no RPA, so is the Rad51 loading to ssDNA in this case able to rescue with the DNA repair in eukaryotes?

RPA is essential for viability and so it is impossible to eliminate RPA.  There are some temperature sensitive conditional mutants that exist (at least in yeast).  Rad51 readily loads onto ssDNA in the absence of RPA and does not require mediators.

Presenting your work

Presenting your work to others

According to Dr. Murat and my own experience, presenting our work is not an easy job because it requires a lot of practice and a GOOD understanding of topic of our presentation. We often get trapped in the thought of impressing the audience, so we lose the focus on ourselves and our own interest in the topic, which are the factors that actually make impression we want to deliver to others.

When we are presenting, we keep wondering if we are giving an excellent presentation,  if our gestures are appropriate, or if our tone is proper. Therefore, we are too focused on the audience's opinions that we are actually losing the impression of our own presentation. It is true that the impression is automatically delivered and felt by the audience when we talk from our heart and being impressed by the topic ourselves while talking about it. If we are amazed by the topic and have good understanding about the topic, we are giving an authentic, emotional, and professional presentation. 

One more thing is that, it does not hurt to understand the topic we are going to present from different perspectives instead of spending time perfecting the speaking that explains the topic in only one way. Our audience may come from a diverse backgrounds, so being able to explain one concept/topic in different ways demonstrates that we master the topic and we are giving a professional presentation on the topic, and we are able to catch up with our presentation wherever we are left off if there is an interruption during the speak. While we are thinking of different ways to explain the topic, we may explore new things about our topic, because we are looking at it from different levels and perspectives as a diverse group of our audience.