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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.

"Sea star wasting syndrome" (SSWS) is a disease that affects many species of sea stars, causing them to lose turgor pressure until they eventually rip apart and turn into white puddles of goo. The origins of this disease are still uncertain, and while most researchers suspect that it is caused by a virus, other scientists like Melissa Pespeni from the University of Vermont think that SSWS is caused by a combination of environmental and genetic circumstances. Pespeni and her team studied the genome of the microbiota present in healthy and sick sea stars, and exposed a group of 37 healthy sea stars to SSWS in order to record the progression of the disease. Only 8 sea stars remained healthy after the experiment, and the results showed that their microbiomes change as the disease settles in, decreasing the numbers of beneficial bacteria in the Pseudoalteromonas genus and leading the way for opportunistic pathogens to cause more damage in the tissues. Pespeni argues that SSWS is most likely caused by pollution particles that disrupt the microbiome of healthy sea stars, allowing for the virus to attack their weakened immune systems.

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.

The project focused around the photography of a spider web, which is why some of the biggest factors in causing discrepancies were camera settings. Figure 2 included more of the environment than Figure 1, which can be seen by more of French Hall showing. The number of feet was given as to where to take the picture of the environment from, so it is possible that the phone used for Figure 2 had a different focal length. If it was specified to use an iPhone 7 plus, this could have been avoided. In addition, in Figure 1 the bush appears to be darker. This was most likely because the flash was on when the photograph was taken for Figure 2. When the photo for Panel A in Figure 1 was taken the camera was on 1% zoom, in the second figure the web appears closer which suggests that the camera was zoomed in.

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.

To better understand how methods are written in the scientific community, a project was undertaken for my Writing in Biology course at the University of Massachusetts Amherst in the fall of 2018. A figure was built consisting of two photos of a spider-web on the UMass campus, along with a map of the location of the spider web. A methods section was written for this process, and fellow classmate followed this. A replicated image, solely based on the methods section was created, and then compared to the original figure. It was found that unless a methods section is explicit on important factors such as the number of pictures, labeling, and figure size specifications, it is difficult to replicate a figure or process. Regardless of this, small differences will be present, highlighting the importance of being explicit in every way possible when writing a methods section.

Figure 1 is the original figure panel that I created. The creation of this figure panel was described in the methods in order for someone to recreate. Figure 2 was the replicated figure panel that another student created using the methods. Looking at the format of the two figures, the letters labeling each image are different. In figure 1 they are much larger and easier to see than they are in figure 2. The location of the letters also seems to be higher in the original figure panel than they are in figure 2. Starting with image A in both images, the major difference is the map used. Although both are maps of the campus, figure 2 used an older map than figure 1. In figure 2, the design building is not included because the map is outdated. The map in figure 2 also has a black outline around the campus pond where figure 1 does not have this outline. Figure 2 also lacks the red circle and dot that show the location of where the images were taken that is seen in figure 1. Figure 2 also shows a less zoomed in version of the map. There is space shown above the ILC and below the FAC but these buildings are both slightly cut off in figure 1.  

    Looking at image B in both figures, one major difference is the black patch on the cement. In the original figure panel the black patch is only on the right side of the image but in the replicate the black patch touches both edges of the image. In figure 1, windows on the right side of Morrill can be seen but in figure 2, windows on the left side of Morrill can be seen but not on the right side of the building. The image of Morrill in figure 2 also seems to be taken from a head on view but there is a slight angle in image 1.