Drafts

To obtain the images of the spider web and its relative location, I left the BCRC and proceeded down North Pleasant street toward the Northeast residence halls. Once I arrived at the crosswalk before the Integrated Learning Center, I crossed the street and headed down the walkway towards central campus and the library. Soon, the Student Union building was on my right and I proceeded along the side of the building until I was at with the corner of the building. I turned to the right and traced along the front of building, past the set of windows, until I came across an air filtration system. To the right of the air filtration system was the spider web that the figure was based on.

The two photographs were taken at approximately 3 PM. A bike rack with an overhang was in the close proximity. On the right side of the aforementioned air filtration system was a small metal box with the words “Elect IN rm. 208” written on it in marker. The web was located under that box, and it extended to the right.

Because the web was large and relatively flat, I decided to only focus on the right most portion. To take the photo, the camera was held about one foot above it and pointed directly downwards. A quarter, held between the pointer finger and middle finger of my left hand, was held at the level of the web and positioned so that it would show up at the bottom left corner of the image. Flash was turned on. Once a satisfactory photo was taken, I moved back towards the bike rack. I then positioned myself between the windows of the Student Union and the second pillar of the bike rack structure. The camera was pointed directly at the location of the web and the shot was framed so that the air filtration unit was at the center. The second photograph was captured.

Lamid sharks, such as the great white and mako, actively regulate their internal temperature and can even reach 20 degrees higher than their surrounding enviornment. They do this through a special arrangemnt of blood vessels. Cold oxygenated blood enters through the gills and passes by warm deoxygenated blood vessels. The warmth of the deoxygenated blood is transfered to the cold blood in this way. This mechanism is called counter currency. Heat is generated in large red muscle masses found at the midline of the shark. Red muscle is used for relatively slow, long duration periods of activity and will generate a lot of heat through its aeorbic metabolism. This differs from white mucsle, which is used for quick bursts of activity. Unfortunately white muscle tires very quickly. Thermoregulation is important for a shark due to its predatory nature. When an organism is cold, chemical reactions slow down. By maintaining a warm body, the shark is able to also maintain a rate of chemical reactions. This also improves the sharks awareness and its overall agility.

Cells can be generally categorized as being either haploid cells or diploid cells. Haploid cells are cells that have only one copy of the genome in the nucleus. Diploid cells, on the other hand, have two copies of the genome in their nucleus. This is an important distinction of any class involving biology. 

The results of both reactions were not expected. Originally, there were supposed to be three jumps in pH change in both reactions with different acids. Yet, in the citric acid reaction, only the third jump in pH was visible on the graph because the first two jumps were so miniscule. On the graph of the phosphoric acid reaction, only the first two jumps in pH change were visible because the last jump in pH change was too diminutive to observe. The hydronium concentration that was calculated for the citric acid reaction was 4.027 x 10^-9 M. This concentration was similar to the hydronium concentration given in the procedure: 4.0 x 10^-7 M. The hydronium concentration was found by using the pH halfway through the jump in pH change and using logarithms to isolate the concentration. The calculated hydronium concentration in the first jump in pH change of the phosphoric acid reaction was 2.137x 10^-5 M. This calculation was not as accurate as the citric acid calculations. The given hydronium concentration of the first jump in pH change was 7.5 x 10^-3 M. This variation may be because of human error when adding the NaOH to the acid or the time gaps when recording the changes in pH. The second calculated hydronium concentration for the second jump in pH change was 1.135 x 10^-9 M. This calculation was also not accurate. The given hydronium concentration for the second jump in pH change was 6.2 x 10^-8 M. This variation could possibly be from the same errors made on the first calculation of hydronium concentration in the first jump in pH change of the phosphoric acid reaction.

For easy replicability, it was important that the camera position was something that anyone could achieve. The picture was taken from between the break in the bushes. This area was used because it was the closest you can get to the web without disturbing it. To include the whole web and the gift card that was used for scale the phone was held about 1.5 feet above the web. At 1.5 feet above, the gift card that was placed on the bottom right side of the photograph was easily seen. The phone was placed completely horizontal as the web was also flat against the bush. 

To get the pictures if the spiderweb, first exit the Biology Computer Lab and take a left. Continue to that end of the Morrill building until there is a staircase on both the left and right sides of the hall. Take the staircase on the right all the down to the first floor. Stand at the foot of the stairs and turn left. Facing the wall so that the wooden doors are on the right, look for the red air duct on the wall. There is a missing panel on the bottom left corner. Approach the duct and place a blue Bic ballpoint pen on the ground, with the cap facing away from the wooden doors and toward the exit to the street. The pen should be placed along the edge of the duct where the hole is. This will be used for scale and kept in every picture. Take the first picture with a phone on normal picture mode. Take the picture close to the hole to view the web. The square hole in the duct should match along the edge of the photo to get the correct size. Take a step back to get a wider shot of the area. About half the grate should be seen, with five of the grate sections to the right of the hole. Take another step back to be closest to the wall and take another photo of the whole duct. There should be four tiles in the picture to show the floor before the grate. These three photos will compose part of the figure and should be sent to an email so that they can be downloaded and imported to the inkscape program. To get the map image, use google to search for “Free Map Tools Radius Google My Maps”. Using the google my maps link, search for Morrill Science Center at Umass Amherst. Take a picture so that the campus pond is on the left, the Franklin permaculture garden is on the right and Morrill complex is centered. Use the street view, not the satellite feature. This image should also be saved so that it can be downloaded into inkscape.

    To make the figure for the spider web series, insert all four images from above into inkscape. Arrange them in a two by two fashion so that the closest image to the spider web is one the top left, the second closest is at the top right, the farthest from the web is in the bottom left and the map is in the bottom right. Adjust these images so they are about equivalent sizes, the final size will be adjusted later. Create a square box using the “create a square or rectangle” setting and set its color to red. Using the text feature, type a lowercase “a”. Bring this to the front of the image. Make sure the letter can be read on the box, then center the letter. Use the group button to group the letter and the box. Duplicate the box three times, so there are a total of four boxes. Change the letters in the three new boxes so that they are b-d. Center and group these as done previously. Place the box and letter in the upper left hand corner of each picture, so that the picture closest to the spider web is labeled “a”, the next closest is labeled “b”, the farthest from the web is labeled “c” and the map is labeled “d”. Finally group all the images together and adjust to fit the page. Make the height 3388.23 and the width 2560.94. Export the image and then save it into a google document.

I think I understand why they would need to be variable in their interaction speed and time. If all transient protein interactions took equal amounts of time to perform their function or all travelled at the same speed, then I don't believe the body could properly function. For example, the various ligands involved in a number of homeostatic systems, such as the HPA axis, need to be different from one another in terms of speed and efficacy because that is what allows them to perform their specific functions. But there are still questions I have about how it all comes together.

Does "far-western blot analysis" mean that there is multiple proteins involved/ it is a quaternary structure that is being examined? I know the a western blot analysis means that proteins are being analyzed, so is far-western just a more specific term?

I wonder how they are able to tell which domains/regions of the two proteins in question are responsible for the binding. It later states that they use DSS for intracellular proteins and BS3 for cell-surface proteins, but I feel like there is not as much specificity. So aside from the new molecular weight of the quaternary structure, what can they infer based on the induced artificial bonds?

To make the multi-panel figure using the three photos/figures described above, I used the application Inkscape. The picture of the spider web is labeled Figure A, the environment is Figure B, and the map is Figure C. Import the upclose photo taken of the spider web and put it in the top left corner of the page. The exact dimensions of Figure A are x: 0.000 and y: 166.031. The width of the photo is 94.728. I then imported the environment/setting photo for Figure B. I placed the Figure B right next to Figure A. The exact coordinates of Figure B are x: 93.968 and y: 166.032. The width of the figure is 95.885. I then imported the screenshot of the map I took. I placed the map underneath the two other photos. The coordinates of the map are x: 0.00 and y: 39.031. The width of the map is 190.613 and the height is 128.058. You can see/enter coordinates underneath the Extensions and Zoom commands. To complete the multi-panel figure, I made boxes to label each figure. To make a box, I clicked the “create rectangles and squares” button located on the left side underneath the ruler icon. I adjusted the height and width of the box to 18.517 x 18.517. I clicked on the Fill and Stroke icon located to the left of the Text icon. I selected the white fill and the solid, black line for the dashees and the width for the line is 2.642 mm. I then created two copies of it by selecting copy once and selecting paste twice. I put one of the boxes at coordinates x: 76.37 and y: 278.50 and put a bold, size 36 Times New Roman “A.” in that box. I put the second box at x: 171.08 and y: 278.55 and put a “B.” in the box the same style as the “A.” described above. I repeated that with a “C.” and I put the box at x: 172.141 and y: 149.074. I saved the multi-panel figure and exported it as a png image.

The R-K Selection theory postulates that organisms reproduce using either R or K selected mechanisms and behaviors. When an organism is R selected, it will generally produce a lot of offspring and invest very little energy, if any at all, into rearing them. Due to the large amount of young, offspring are smaller at birth and thus less viable. Many will die before maturity, though since there are so many, the idea is that at least some will survive. When an organism is K selected, it produces fewer offspring throughout its lifetime and invests large amounts of energy into rearing them. These offspring will be larger and have a higher chance of living until maturity.

An example of a K selected organism is the spiney dogfish, a species of shark. Female dogfish are pregnant for 2 years and thus will reproduce quite slowly. Recently there has been concerns about the population of sharks. While dogfish are technically a threatened species, they are still susceptible to bycatching while fishing for other fish. This is especially bad considering that dogfish sexually segregate when not mating. That is to say, males and females will form separate schools. This means that when caught, either a large haul of females or males are being caught, which will further reduce the chance of successfully mating and producing offspring as the populations of either sex decreases.

I entered Morrill 4 south and went up the flights of stairs to the second level. I walked out into the hallway and turned to the right, where I saw doors that led to the bridge that connects Morrill 4 to Morrill 2. If you look out at the bridge, on the left there should be a blue sign that has “Morrill 4 South” written on it. Underneath this sign is a blue radiator, where I found the spider graph shown in Figure A. If you stand facing the Morrill 4 sign and the blue radiator, the spider  web is located on the bottom left side of the radiator attached to the pipe and black part of the wall. To take the photo used in Figure A, I placed a ticonderoga pencil on the ground, angled at roughly 15 degrees from the wall. I then held my iPhone, with the bottom of it resting on the ground, about 6 inches from the wall and faced it towards the spider web. I then took a photo of the spider web and the pencil with my flash on. To get a photo of the environment (Figure B), I stood about 5 feet away from the blue radiator, closer to the stairwell than the doors to the Morrill bridge. I then angled my phone so I captured the blue radiator, most of the rug on the floor, the blue Morrill sign, and the left door that goes out to the Morrill bridge.

    Once I had the photos of the spider web I found and its environment, I used the UMass campus map, which can easily be found online, to make the map. I opened the campus map pdf and took a screenshot of the a smaller portion of the map to show the location of the web. For the width of the screenshot, I included the Student Union to the edge of Brett. For the height of the screenshot, I included Fernald up to the Integrative Learning Center.