The next project assigned to the class was called the PROPOSAL, a group effort which was essentially a written presentation of our idea for research on a species of flatworm, planarians. This project also helped me to solidify the idea of detail inclusion because a similar event happened where there were many more aspects that needed to be included in the project than I had originally thought going in. Specifically, for this project there were about six sections needed; an abstract, specific aims, background, research design, impact or significance and a references section. It made sense why each section would be required when submitting a proposal, but I had never seen what one was supposed to look like prior to this so I didn’t have high expectations of work when introduced to it. Overall however, I do believe this project was important to assign looking back, because science majors will most likely encounter a research proposal in the future whether they are the ones that must write it or not.
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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.
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.
With regards to the METHODS project, looking back there was a lot of initial confusion as to how to approach it and how it would be performed. I managed to complete the major aspects that were necessary to be completed, however the content was not well organized in the end because I misjudged the amount of work it would take both with the initial methods creation and the final written aspect. The major realization I came upon really occurred first with the following of another’s methods, and someone following my methods. In class, we had discussed the importance for inclusion of many details when writing methodology, and while I had paid attention and thought I understood, this project made me realize that I still did not fully understand starting out. Both when writing my own methods for the figure I created, and when following another’s methods for their figure it became clear to me that a lot more details were necessary in order to create a near-perfect figure replicate.
One major expectation I had for the class was that a lot more writing would take place. Drafts and “perfect paragraphs” were bits of writing to be done each week, but overall I had expected to be writing essays every other week. I believe I had this thinking coming into the class because most other writing courses I’ve experienced generally involved analyzing literature. In this class, we did analyze some writing but the writing was scientific, and the writing we were assigned was also scientific and this proved to be a significant distinction from what I’ve done in the past. This realization came about primarily in the first major project of the class, titled “METHODS”, but was only strengthened in the projects to follow.
Over the course of this semester in Biology 312, I feel that my overall approach to the class and my thinking are what was most changed. I do feel that some of this was obligatory because in general, at least with myself, my “how to approach this class” methodology has always changed with every class I’ve taken. However, each class taken is different from the other and thus, how the approaches and thinking change will be different as well. Additionally, I do believe my writing changed a little, but not to the same extent as what I’ve mentioned. These changes are the opposite of what I expected for this class, especially since it is titled “writing in biology”, but looking back through the semester these results make do sense now, and for the most part I am satisfied with them.
We know from previous studies that salt generally has a degrading effect on most tissues, so we thought to observe the effects of different salt concentrations on the regenerative abilities of planarians. We predicted that increasing salt concentrations would lead to a slower growth/regeneration rate of the planarian head. We observed three sets of three planarians each in a control condition, a low salt condition with 1 gram of salt and high salt condition with 2 grams of salt, over three weeks. We observed the planarians a couple days each week and measured them to see how much they grew or shrunk. In the end, we found that both salt concentrations resulted in the death of the planarians, however the lower salt concentration left the bodies mostly intact, whereas the higher salt concentration left the bodies in a more disintegrated state. So, we concluded that while the salt did significantly impact their growth, further studies at lower more precise concentrations of salt are needed to fully observe the impact.
We know from previous studies that salt generally has a degrading effect on most tissues, so we thought to observe the effects of different salt concentrations on the regenerative abilities of planarians. We predicted that increasing salt concentrations would lead to a slower growth/regeneration rate of the planarian head. We observed three sets of three planarians each in a control condition, a low salt condition with 1 grams of salt and high salt condition with 2 grams of salt, over three weeks. We observed the planarians a couple days each week and measured them to see how much they grew or shrunk. In the end, we found that both salt concentrations resulted in the death of the planarians, however the lower salt concentration left the bodies mostly intact, whereas the higher salt concentration left the bodies more disintegrated. So we concluded that while the salt did significantly impact their growth, further studies at lower more precise concentrations of salt are needed to fully observe the impact.
Programmed Cell Death (PCD) Type 2: Autophagy
- A proteolytic process that can contribute to cell death
- Autophagy genes (ATGs) are conserved across eukaryotes
- Autophagosome: double membrane bound compartment that engulfs the cytosol and degrades the components by fusing to the vacuole.
- The vacuole plays a significant role in PCD - lytic enzymes are stored in the vacuole, and these enzymes either degrade cellular components in the process of autophagy, or the vacuole can rupture and therefore release these enzymes into the cytoplasm.
PCD in plants involves reactive oxygen species (ROS) production and hormone signals
- ROS initiate PCD and necrosis
Autophagy and autophagy genes are induced by starvation
TOR kinase dependant pathway regulating mammalian autophagy:
- TOR kinase: inhibits autophagy when phosphorylated, phosphorylates several autophagy proteins-->making them inactive. Nutrient starvation dephosphorylates TOR which in turn induces autophagy.
While there are still aspects unknown, much has still been discovered about the way in which plants and mammals undergo cell death. First and foremost, one should not confuse plant cell death with senesence, death is a rapid localized process in the plant cells, while senesence is much slower and is systematic. There are three main types of plant cell death, namely apoptosis, autophagy and necrosis. Apoptosis and autophagy are both forms of programmed cell death processes, while necrosis is process controlled by external factors. Apoptosis is the most widely known form of plant and mammalian cell death, and as such is especially well studied. In the process of mammalian apoptosis, the first step is chromatin condensation, followed by DNA fragmentation, then the cell breaks apart and the remains are usually absorbed by other cells. In plants, this process is very much the same except that the cell remains are not taken up by other cells. The mechanism for the early apoptosis signalling pathway is also similar among mammals and plants. Initially, formation of a complex called an apoptosome occurs, and within this complex a specific precursor form of a caspase, procaspase-9, is activated. Now this complex can thus activiate other procaspases in the cytosol, resulting in "caspase cascade" signalling pathway, and apoptosis. The major differences for this pathway between mammals and plants are the specific caspases. In mammals, they are referred to as "initiators" and "executioners", in plants there are "metacaspases" with sequence homology to the mammalian ones, and there are also two types of these, but are just referred to as Type 1 and Type 2. Additionally, plants will also have vacuolar processing enzymes (VPEs) in this pathway. So overall, the process of this type of cell death is conserved between mammals and plants with only slight differences.