BIOL368/F14:Class Journal Week 5

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Chloe Jones

  1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
    • In performing the research project I learned the necessity to choosing a topic that can be carried out properly. Initially, I chose a topic that could not be proven with the information provided, so that trial and error process taught me to do more research before forming a question to answer. With my head, I learned that research requires times and background information in order to be successful. I think us going into such great detail with the Markham article was key to our research because I became very knowledgeable about the topic. So, from that I learned to get further acquainted with anything I am looking to research. With my hands, I learned how to become an expert at the Biology WorkBench systems because of the countless times I had to run stimulations with different subjects and their clones. With my heart, I learned that although at times it may become frustrating because it can get confusing with the multiple sequences, matrices, and clones it is truly a rewarding feeling when you have the opportunity to complete a research project see it from start to finish.
  2. What is still not clear to you after having concluded this project?
    • The confusion I still have regarding the conclusion of this project pertains to the Markham at el. article. I don’t understand why when they were monitoring the patients why didn’t they keep tract of each clone individually, so they could see how they progressed. The clones in one visit may be called another number in the next visit, and I was not understanding of that because that seems as though that would be some extremely valuable information.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • If more time was provided, I would explore the different clones specifically and how they evolved amongst different rates of progressors. I would get about 30 subjects to participate in my study, because I am studying their clones it would be a lot of work to have a huge number of subjects because they don’t just offer one clone. I would study all forms of clones and see if they are the final factor for the progression of the disease. I would also like study to see what clones are more likely to diverge and create diversity and thus more disease.

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Chloe Jones 03:46, 15 October 2014 (EDT)Chloe Jones


Nicole Anguiano

  1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
    • With my head, I learned the intricacies of reading trees, sequence analyses, and clustal distance matrices. I learned how to draw conclusions from what seemed to be an abstract or random group of numbers and lines. With my hands, I learned how to run multiple clustal distance analyses and sequence analyses quickly. I also learned how to create and utilize external programs to crunch data and make the acquisition of data (especially from clustal distance matrices) much quicker than it would be without it. With my heart, I believe that I learned the most important lesson of all. I learned not to become disappointed if the results were not as expected. Even if it may seem as though a hypothesis has been proven incorrect, at least it's ruled out one way that the HIV virus could operate, indicating that more research needs to be done.
  2. What is still not clear to you after having concluded this project?
    • I still have a lot of confusion on how the HIV virus operates. It seems random which patients are extremely negatively effected, and which are barely effected at all. I think much more study is needed before any conclusions can be truly come to. I feel that I have many unanswered questions about HIV that may, in fact, not yet be answered, which just increases my desire to potentially work in the study of HIV or other currently incurable diseases in the future.
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
    • If I had more time, I would expand upon my project that I worked on this week. I would get many more subjects, as many as I possibly could. I would track them in much the same way as Markham et al, only instead of using 15 subjects, I'd look more at the range of 100+. With the ability to store incredibly large databases of information and sequence genes quickly, I'd follow many more HIV patients for several years, and use the sequences from their HIV viral strains to figure out if there is anything that makes a rapid progressor different from a nonprogressor and a moderate progressor. I'd also look at other factors in each patient that could possibly be a factor, like their family history (see if they had any relatives who have had HIV), overall health prior to infection, etc.

Nicole Anguiano
BIOL 368, Fall 2014

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Isabel Gonzaga

    • Head: I gained a better understanding of the complexity of these types of research questions that deal with a number of variables (over time, multiple sequences, multiple categories of sequences, different genes, etc). It was interesting to analyze this at the molecular level but it would also be interesting to see what the genetic or biochemical pathways and implications are to better this understanding.
    • Hands: I learned to use Biology Workbench to analyze and align sequences. I've also become more familiar with coding for my wikipage, particularly with making tables and thumbnails. I also practiced keeping a good lab notebook as I progress with my work. This is much easier to do on the computer, since taking screenshots is so much faster than hand writing all the data!
    • Heart: I learned that science requires a lot of patience. I also learned that sometimes you need to take a step back away from your work and truly analyze what question you are trying to ask, to make sure that the experiments and tests you are running are designed to answer these.
  1. I'm still unclear on the true functioning of the gene, at the various levels of scientific analysis. I'm also not entirely clear on the value of the theta statistical analyses.
  2. If I had more time, I would like to analyze these at the amino acid levels to see which of the nucleotide changes code for the same codon, and thus may potentially be disregarded as a difference. I would also like to compare a lot more strains and subjects in order to get a more representative sample and make the results more meaningful.

Isabel Gonzaga 02:53, 1 October 2014 (EDT)

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