jonathanrubi's blog

In this experiment, we sought to understand the effects of tree management techniques by the University of Massachusetts - Amherst compared with the surrounding town of Amherst on tree health, ecological diversity, and safety hazards. UMASS-Amherst characterizes the tree management needs as a strategy for the removal of hazardous conditions and improving the overall wellbeing of the trees including, ruining, irrigation, fertilization, cabling and other programs on an “as need” basis. In abandoned, unmanaged areas, research has shown that species diversity is increased particularly those that are dependent on tree coverage. Tree management also been shown to have a positive effect on invasive species and a negative effect on native species. By observing trees in the jurisdiction of the university and those in the surrounding area, we were able to identify differences in factors related to overall tree health, safety hazards and ecological diversity.

Effects of tree management techniques were gathered by randomly selecting trees on the University of Massachusetts - Amherst campus and the surrounding area. Factors identified were

- Number of tree cavities: characterized as a semi-enfolded hallow that naturally has occurred within the trunk or branch of a tree.

- number of branches: counted from the main trunk of the observed tree

- understory diversity: characterized as the underlying layer of vegetation and measured at a maximum of 4 feet from the root of the trunk. Understory diversity also includes nests and species inhibited on the trunk or branches of the tree.

- human infrastructure: characterized as the distance from an area of the tree to the closest man-made structure. These structures included roads, pavement, cable wires, storm drains and buildings.

    Overall I felt this class taught me a variety of useful skills that I can apply in a number of different ways in the future. For instance proper time management and planning when it comes to writing drafts, editing as well as constructing projects. Also the use of various software programs such as R, Scribus, Inkscape, and text formatting. I also learned various writing skills and how to critically analyze my own as well as other peoples writing. In addition, I learned how to write and pay attention to detail, especially when it comes to formatting and use of language. One thing I wish I knew earlier in the class was how valuable it was to ask for help from the professor in terms of receiving feedback. I think I could have done much better on my Methods project if I had done so.

Overall I felt this class taught me a variety of useful skills that I can apply in a variety of different ways in the future. For instance proper time management and planning when it comes to writing drafts, editing as well as constructing projects. Also the use of various software programs such as R, Scribus, Inkscape, and text formatting. I also learned various writing skills and how to critically analyze my own as well as other peoples writing. One thing I wish I knew earlier in the class was how valuable it was to ask for help from the professor in terms of receiving feedback. I think I could have done much better on my Methods project if I had done so.

    The final project, creating the poster yet again provided its own challenges in regards to data collection, data representation, and effectively using various softwares. I quickly learned that data collection often does not go as according to plan and methods often have to be tweaked and improved. In addition, creating useful and valuable graphs and charts proved challenging. Learning how to input data into R however was one of the skills I am glad I learned and I know I will use in the future. I also found it more difficult than expected to effectively create the poster. Using Scribus taught me a lot about how proper planning can save time in the long run. This includes helpful formatting tips like creating different standard header types for fonts. Also organizing and accumulating all the elements prior to inputting them into the poster helped tremendously. It also taught me how to use concise language and including only vital information in the form of text.

The Proposal Project presented unique challenges as well. I felt the main challenge in constructing the proposal was effective planning. Coming up with a research proposal with a credible research design as well as feasibility was difficult. Also finding background research on related topics presented challenges. In regards to the research design, coming up with specific criteria in regards to my specific project, tree management, was difficult because it is not an area of expertise for me. Because of this, it proved challenging and required more background research then initially thought to come up with the right design. As a whole, I think the project taught me important lessons about creating a proper research proposal with specific aims and repeatability.

Beginning with the Methods Project, I felt as though I learned a lot about structure and scientific writing. One of the biggest challenges I faced was structuring each section of the project correctly and including the correct elements in the abstract and introduction. What I learned, that I feel is just as important is what not to include in each section, and to keep each section separate in their purpose and what they provided to the project as a whole. For instance, actually including specific results and main points of discussion in the abstract. Also not including portions of the methods in the introduction. I would say that another challenge was using the correct type of writing. Although I felt that I was using descriptive language, I learned that a lot of what I wrote was vague and contained judgements as opposed to facts and observations. Also not writing in conversational speech or as a narrative was a big challenge. Overall, I felt the learning curve for this project was steep given my lack of exposure and experience but I thought it helped greatly with future projects.

    Before enrolling in the Biology 312, pretty much my entire career as a Biology major here at UMass - Amherst has consisted of sitting in lecture, taking notes, and taking exams. This class was much different in its format and the information and skills that were taught. Learning to write in a different way than I have been taught my entire life was a challenge, but one that I believe will prove useful in the future.

Flavivirus is a genus of viruses that includes west Nile virus and cause severe disease such as yellow fever. Flavivirus genomic RNA replication occurs on the rough endoplasmic reticulum, in membranous compartments, and the focus of Dr. Chao and his advisor Dr. Stephen Harrison’s research at Harvard was the fusion of the viral and cellular membranes. Cellular entry by the virus requires this membrane fusion and in order to do so, viral fusion proteins undergo dramatic conformational rearrangements. These proteins must undergo conformational changes to create a thermodynamically favorable chemical reaction and overcome the energetic barriers to merge the two membranes and create hemisfusion.  They discovered that the envelope protein comprised of three main domains, with one being largely hydrophobic and involved in the fusion loop. In its pre-fusion state, the hydrophobic domain is tucked in the protein, however the hydrophobic domain extends into cell membrane then collapses to bring membrane together and create hemifusion and full pore opening.

    Some of the factors we did not consider however, were tree species, tree size, and time. Tree species and size can have a big effect on the species diversity and ecological value of a tree. Also, when observing trees for our experiment, we only observed for a few minutes. In future experiments, observation for hours or days may be needed to get a more accurate understanding for the true ecological value of a tree.