Drafts

The anatomy of the hypothalamic pituitary axis is essential to its function. The neurons from the hypothalamus which synthesize hormones to be released by the posterior pituitary gland synapse directly onto the veins in the posterior pituitary, so they can release the hormones there to be sent out to the rest of the body. The hypothalamic-anterior pituitary section has a more unique structure. There is a portal system, 2 capillary beds connected by a veinous system, that joins them. One capillary bed is in the hypothalamus and the other is in the anterior pituitary. This contrasts normal veinous systems, where an artery goes in and leaves as a vein. Instead, the two capillary systems are joined. A set of neurons in the hypothalamus produces releasing factors and synapses in the capillary bed that is also in the hypothalamus, which is connected to the capillary bed in the anterior pituitary where hormones such as ACTH, FSH, and prolactin are synthesized. This connection allows it to trigger their release. The hormones in the portal system would degrade and be at concentrations too low/dilute in the general circulation, but when contained in the smaller portal system where they can flow, they are at a sufficient concentration.

When comparing the labeling present in either figure a total of 7 differences are noticable. The labeling has differences when it comes to font size. In Figure 2, font size when labeling the images “A – B – C” looks to be larger than in Figure 1, which has a font size of 72. The font size of the “Web location” label in Figure 1:C is 28. However in Figure 2:C this font size is notably larger; with the addition of an absence of capitals at the beginning of each word. Rather than facing upward and pointing towards Morrill 1, as is the case in Figure 1, the arrow which sits above this “Web Location” label is facing the downward direction in Figure 2:C. The line width of the arrow is not set to a width of 3.0mm as indicated in the methods either. The arrow head of this arrow is significantly wider than in Figure 1, which had used a more narrow arrow head. The arrow itself is also pointing to a different location in the two figures, with Figure 2:C having its arrow more to the left

The amount of sun exposure is a factor that was not accounted for when taking the replicate photos; this is seen the amount of sun beans present throughout the panel B and panel C pictures of Figure 2. The yellow beams over the tree and in the background of the spider web shows the presence of sun that was not there in the original multi-panel figure.

    The weather is another factor that was not controlled in the replicate figure due to the difference in lighting in the photos. The original photos were taken on a day of overcast weather, meaning there is a layer of clouds blocking the sun. Panel B and C in Figure 1 have a dull lighting, whereas the replicate photos have harsh beams of light.

As for the formatting of the figures, discrepancies in the methods may have caused the differences between the two multi-panel figures. For example, the font size and type were different in the replicated figure due to a lack of explanation in the methods. Additionally, the lack of gaps in between the photos in the replicated figure is a difference due to the disregard of the written methods.

    Despite there being many differences between Figure 1 and Figure 2, the overall project was a success in practicing scientific writing and replication.

One of the most important aspects in the science community is the ability to replicate processes and get the same results. In order to be able to achieve this goal, clear and concise writing is required. In Fall 2018 the Writing in Biology Class at the University of Massachusetts Amherst conducted a project to observe differences between the two figures. Figure 1 was created by me and Figure 2 was created by another student who followed my methods section to try to create a perfect replicate of the Figure I already created. The following section focuses on the subject of the figure including why it was selected, and the factors that were attempted to be controlled in the writing of the methods section. 

Professor Brewer gave the class the subject of spider webs to focus the figures on. The photographing of a spider web is not the easiest. Webs are fairly thin, and hard to see. Spider webs come in many different shapes and sizes and by using a spider web the class was forced to follow methods very carefully to try to get two figures that looked similar.

When taking the pictures for the figure panels there were a few elements that I considered to make controls. I used the back of a ucard as a way to create a scale so that the size of the spider web could be compared to demonstrate size because  all UMass students have a ucard, so whoever was recreating the image could use the same object to scale. The orientation of the ucard was also a control. The location of the images was a control and the time of day in which the picture was taken. The format of the figure panel was a control although the platform used to create the figure panel may not have been because not everyone has access to inkscape, although in this case it seems the person did use the same platform to create the image.

Methods

At 9:50 in the morning I entered Morrill 2 from the front of the building (the side facing the rest of campus). I went up one flight of stairs and walked to the back stairwell and left through that door. I was now facing the area of campus where Frank dining hall is. At 9:55 in the morning, I took a picture of the spider web in the bottom left corner of the glass door. I was standing outside and saw a web in the corner of the glass frame. I squatted like a duck and held the back of my ucard up to the web, at this time there was a little spider.

This experiment used spectrophotometry to measure E. coli growth at four different temperatures (27°C, 37°C, 45°C, and 55°C) over the course 75 minutes. The aim was to measure cell numbers by measuring the turbidity of samples inoculated with E. coli. Growth rates and generation times were then obtained using the data collected. It was expected that the E. coli would have the highest growth rate and shortest generation time at 37°C. This temperature is most similar to E. coli’s natural environment, the human intestinal tract. At 37°C, E. coli should spend a substantial amount of time in the exponential phase of bacterial growth, and have a prolonged stationary phase before entering a period of cell death. The E. coli grown at 55°C were expected to show a decreased growth rate and a longer generation time. At this temperature, proteins and other cellular components become denatured and cell lysis occurs. It was expected that E. coli grown at 45°C would have a growth rate and generation time in between that of the 37°C and 55°C samples. At 45°C proteins should not become denatured and most cells will not lyse. The increased heat was predicted to slow cell metabolism and mitosis enough to distinguish a difference in growth rate and generation time compared to the 37°C sample. The last sample, grown at 27°C, was expected to show a lower growth rate and higher generation time compared to the three other samples. At this lower temperature, the metabolic processes of E. coli were predicted to slow significantly, which would reduce the number of new cells forming and increase the generation time by slowing mitosis.

Enzymes are an important class of proteins that help in cellular processes. Enzymes are particular in their binding and can be allosterically regulated. In enzyme-catalyzed reactions, the enzymes lower the activation energy needed for a certain chemical reaction. The free energy of the reactants and products do not change, just the threshold energy level needed for the reaction to commence. Enzymes can lower the activation energy of a chemical reaction in three ways. One of the ways the activation energy is lowered is having the enzyme bind two of the substrate molecules and orient them in a precise manner to encourage a reaction. This can be thought of as lining the binding pockets up for the substrates so that it is not left to random chance that they will collide and be oriented in this way. Another way enzymes can lower the activation energy by rearranging the electrons in the substrate so that there are areas that carry partial positive and partial negative charges which favor a reaction to occur. Lastly, the enzyme can strain the bound substrate which forces it to a transition state that favors a reaction. By manipulating the substrates of the reaction, the enzyme can lower the necessary energy needed to make the reaction occur. The enzyme itself is not a component of the chemical reaction and is the same molecule at the beginning of the reaction as it is at the end.

A figure panel featuring a spider web, the location of the web, and a map of campus that shows the location of both of where both of these images was created and a methods section was written that described how these images were taken and placed together to create a figure panel. This methods section was then given to a different student and class to be followed and a second figure was created based on the methods describing the first figure panel. Once the second figure was constructed and posted, I used it to finish this assignment and analyze and discuss the differences found between the two figures and why they occurred. This assignment was not fully successful because although the figure panels are similar, there were many differences that occurred in each image within the figure panel. This assignment shows the importance of a clear and precise methods section because there can be a lot of room for error when creating something based solely on an only word description. Following someone else’s methods can be difficult because you might not have access to the same materials and other factors such as camera angles and placement can result in different images.

Discussion

In the Results section, it is mentioned that in the repica figure, there is no figure of the actual building. This error of not including a significant element of the replication figure was a direct result of the methods section not being clear and elaborative enough. The original methods section was mainly an “overview” of the process of obtaining the elements for the figure, and putting them together. This formatting allowed for mistakes in putting together the figure to happen. Similarly, there is a difference in the actual web between the two figures, since they are not the same web. The web in the original figure is much smaller in size, judging from the objects surrounding it, such as the sidewalk in the original figure, and the window in the second figure. Of course, since there is no scale to measure the two objects you can never be sure. Another significant difference is the map. For the original figure, opensource.eu was used to find a map for the Lederle Graduate Building. The second figure seems to be from a different website, judging by the look of it. The map also has different scales and markers. Another difference between the maps was that the original map was much more zoomed in, and did not have as many buildings around it compared to the second map, which had a few more buildings. The marker of where the spider web was on the map was a significant difference. In the original figure, a simple red dot was used to mark the location, but in the replica, a star was used to mark the location (also a major difference). This again, was most likely due to the lack of detail in the methods section. The labeling of the figure was quite different, as in the original figure, there were only upper-case red font letters. In the replica figure, the label was spelled out “Location” and “Web” describing the different elements. The words were also inside gray boxes. The specific font size/type was not specified in the methods, leaving it to the person trying to recreate this image to pick a font. Overall, I think much more specificity could definitely have been helpful in this project. It would have prevented a lot of the mistakes in replication if the instructions were much more clear and less concise.