Research Reflection

Submitted by jgcahoon on Thu, 12/14/2017 - 21:19

The Research Project was one of my favorite projects throughout my time here at UMass. One reason I enjoyed it so much was how similar this project was to an actual research project, but very simplified in which we still got a lot out of it. I had done cancer research over the summer, and we had displayed our research at the AACR conference in a similar fashion: a poster. I didn’t do too much work formatting and creating the poster itself, so getting this experience was very nice. I also really liked how the overall project was structured: I didn’t feel too stressed, and felt like I could get everything done in the time given. I also learned a lot in this project such as the important elements to include in a poster, and worked on presenting my poster (i.e. elevator speech) to people walking by. Performing the experiment itself was also awesome, and really made for a more engaging project, one in which I actually felt like I was performing an important experiment. Overall, this was a great project. 


Submitted by jgcahoon on Thu, 12/14/2017 - 21:19

Coming into this class, I heard it was a very rigorous course, but you got a lot out of it. Looking back on it, I learned a lot about how to scientifically express various elements needed for a research project. I found it especially interesting to learn about the various ways of attacking a research project because of what I have already accomplished in my career, and what I plan to accomplish later. I thought planarians were a great organism to use for the project because of how interesting they are: they respond to various things you do to them and can view them macroscopically which I think is important! The in-class activities almost always related to different aspects of the project that we were working on which made class time useful. Lastly, there was a lot of freedom in this class, whether it was picking a certain research topic or planning on when you’re going to do what assignments, I really enjoyed doing things, “my way,” in a sense. 

Reflection - proposal

Submitted by vthong on Thu, 12/14/2017 - 16:19

            I thought that writing the proposal was a good learning experience because I didn’t think so much work and thought had to be put into completing the assignment. After our group decided that we wanted to do planarian head regeneration in different environments, I thought that writing the research design for the proposal would be easy because I understood how thorough we had to be in writing out the steps to carry out the project in our proposal. On the other hand, writing the abstract was most unfamiliar to me because initially I was not too sure what a good abstract looked like. The same applied for writing the specific aims. I did not know what would have been considered writing too much. While our group worked through writing the proposal, we were unsure of whether or not we did a good job, and we wished there was a proposal for us to reference off of. Nonetheless, once the proposal was complete, I really felt like we fully understood why and how we wanted to do our project. The proposal made us think about the project in a way that was more than just completing the assignment, which is why I thought it was a good learning experience.

Strengths of the phantom limb study

Submitted by daniellam on Thu, 12/14/2017 - 15:53

Since the study served such a micro-niche of patients (amputated limb, phantom pain, willing participation), it is incredible that they were able to find participants with amputated limbs that were willing to perform in the study. The study was very opportunistic and the experimenters took advantage of the resources they had at the time. Also using humans rather than animals served an advantage in the specificity of the data they obtained. The study was meant to not only led to better knowledge of the thalamus, it also allowed them to pinpoint the source and help the patients that have phantom limb pain. 


Submitted by vthong on Thu, 12/14/2017 - 12:41

Through classification tests and determining its melting point, unknown compound #25 is likely to be phenylethanal. Once the reaction with the DNP reagent tested positive by forming a yellow precipitate, unknown #25 was classified as an aldehyde or ketone instead of an alcohol. The carbonyl group on this aldehyde/ketone is not conjugated. The next step was to do Schiff’s test to see if unknown #25 is an aldehyde or ketone. Because the test was positive, showing a deep magenta color, unknown #25 was classified as an aldehyde instead of a ketone. The iodoform test was carried out, even though unknown #25 is an aldehyde, to classify if unknown #25 was a methyl aldehyde or ketone. Because the iodoform test was negative, unknown #25 is not a methyl aldehyde. After all the classification tests were done, unknown #25 was classified to be an unconjugated (not methyl) aldehyde. The melting point of the derivative was close to the melting point of 2-nonenal (126°C), but 2-nonenal is conjugated and would have formed a red precipitate with the DNP reagent instead of yellow. The H-NMR spectrum shows a one lower and sharper peak at around 10 ppm, five higher peaks over a larger area at around 7 ppm, and two sharper peaks at around 3.5 ppm. There are a total of 8 hydrogens. The one single peak at around 10 ppm represents the hydrogen attached to the carbonyl group on the aldehyde. The peaks at around 7 ppm represent H’s the aromatic hydrogens on a benzene ring. The H-NMR spectrum shows that unknown #25 has a benzene ring, an aldehyde, and an X. Phenylethanal has 8 hydrogens, a benzene ring, and an aldehyde with an unconjugated carbonyl group. These characteristics match the information provided by the H-NMR spectrum and the classification test. The table of derivative melting points provided did not show other compounds containing a benzene ring around the observed derivative melting point of 125-128°C. In the table, phenylethanal has a higher MP of 121°C, which is close to, but still lower than, the observed MP of the derivative acquired in lab of 125-128°C. This may be because the Mel-Temp device was heating too fast since it started at about 20°C and was heating to plateau at 180°C, so the amount of time it took for the compound to absorb the heat was not until the device read at a higher number.

Methods Abstract - perfect paragraph

Submitted by jmazzola on Thu, 12/14/2017 - 11:07

  The METHODS project was an assignment given in order to highlight the some of the key aspects necessary for scientific writing. One was to create a multi-panel scientific figure of their own and then detail instructions on how that figure was made before having these passed to another person for replication of the figure. Both from following another’s figure instructions and from then comparing one’s original figure to the one replicated it was found that a larger amount of specificity and detail in the methodology is required in order for proper replication to occur. Over-generalizing in the methods will lead to miscommunication of the instructions, and thus improper replication. In scientific writing, one needs to be meticulous and explanatory to ensure that the material being discussed is both proven accurate to the reader and is informative enough that others in the field or slightly varying from the field can replicate it.

Methods Intro (P1) - perfect paragraph

Submitted by jmazzola on Wed, 12/13/2017 - 23:11

In Biology 312, the first project of the semester, “METHODS” was assigned in order to strengthen scientific analytical skills through replication and the practice of distinguishing between observations and inferences. In this project, one was to create a multi-panel scientific figure, detail how to produce it, and then pass on these instructions to another in hopes that they will then create the same if not a very similar figure by following the instructions on how to produce it. This process is designed to recreate the certain aspects that come with writing a scientific paper, specifically the need for extensive attention to detail and for good explanation skills. By observing what figure replicate comes about from your own written instructions on how to create the figure, you see how much detail you may have missed, or what features needed more elaboration, thus showing this need for detail and explanation in science.

ALS - Possible treatments

Submitted by msgordon on Wed, 12/13/2017 - 23:02

While there is no cure for the disease, rapid advancements are being made as both our understanding of ALS and our technology improves. As discussed above, Riluzole is the primary medication used to combat the progression of ALS. The drug works by blocking the intake of sodium into neurons, reducing the degree of their activity. Thus, this mechanism reduces the amount of ATP a given neuron demands, partly alleviating the consequences of the inhibited axonal transport of mitochondria caused by mSOD1, thereby prolonging the life of the cell. Despite this, Riluzole only extends the prognosis of patients by 2-3 months, presumably because of the time-dependent atrophy of neurons - the more time that passes, the higher the toxicity of the mSOD1 mutation.  Another physiological barrier to curing ALS is the existence of the ‘bystander effect’ in which astrocytes expressing toxic mSOD1 also affect surrounding astrocytes, even if they do not originally express a damaging genotype, suggesting that the disease must be treated at a systemic level.


SOD1 murine model

Submitted by msgordon on Wed, 12/13/2017 - 21:23

Although the combination of ALS’s brutal effects, rapid progression, and relatively high frequency in the population makes the disease a daunting one, it also ensures that an immense amount of resources is funneled into research for further understanding of the disease as well as possible cures. Perhaps the most common animal model used in ALS research is a line of mice expressing the G93A mutant SOD1 protein engineered by the Jackson Laboratory. It was this line of murine models that was used to observe the possibility that the ALS-causing mutation was indeed a toxic gain of function rather than a loss of function (Brujin et al. 2004). However, some studies came under criticism because the murine line had up to 20 copies of the mutant G93A SOD1 gene. A stable transgenic model was developed shortly after.


Reflection Methods

Submitted by samihaalam on Wed, 12/13/2017 - 20:25

At the start of the Methods Project, I didn't really know what to expect. I was very not used to writing in small chunks. I was used to trying to stay up all night the night before an assignement was due and trying to finish assignment, especially writing ones. So, I expected this class in general to be challenging and new to me. And at first, I did struggle with writing a little bit every day. But, as the weeks went on, I improved. And, it was pretty helpful to write this way, because when the rough draft was due, the night before it was due, I was expecting a long night trying to complete it. But, I had discovered that since I wrote a little chucnk of the Methods project each day, I had already completed most of it, and I only mainly had to edit. This came as a surprise to me, as I had been so used to doing my writing one way, so I was surprised when this method worked out surprisingly well for this project. I think I will therefore try to continue this way, writing in small chucnks, every day for future assignments. 


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