You are here

cdkelly's blog

Metformin mechanisms

Submitted by cdkelly on Wed, 10/03/2018 - 18:59

In terms of antidiabetic properties, metformin is typically used to combat type 2 diabetes mellitus. It is thought to decrease the hepatic (relating to the liver) production of glucose and increase the sensitivity to insulin as well as use of glucose by peripheral tissue. In addition metformin has been shown to successfully combat polycystic ovarian syndrome, which results in metabolic disorders due to the development of insulin resistance(Ikhlas, et al.). The anticancer properties of metformin were first discovered when researchers realized that cancer patients who were on metformin showed less mortality than other diabetic cancer patients on different drugs to deal with their diabetes (Ikhlas et al.). Mechanistically, metformin targets a number of important players in cancer pathway, but specifically the inhibition of mTORC1 via AMPK independent and AMPK dependant pathways.

    Activated AMPK causes the p53 to become active. This then induces cell cycle arrest at G1/S phase, simultaneously upregulating pro-apoptotic genes including p21 and Bax. In addition Foxo3a, a tumor suppressor that affects genes including Bim, bNIP3, and Bcl-xLon are activated by AMPK as well. Furthermore, lipogenesis (acetyl CoA is converted to fatty acids) is inhibited (Ikhlas, et al.). AMPK finally leads to the inhibition of mTORC1, which is a huge player in proliferation and cell growth via its control of autophagy, translation of mRNA and metabolic effects (Ikhlas, et al.).


Comments for assignment 2

Submitted by cdkelly on Tue, 10/02/2018 - 23:54

When a signal binds to a receptor, it undergoes a conformational change that leads to the desired effect on the cell it is attached to. Based on what we have learned about protein folding and the chemical interactions at the different levels of structure, I believe that these conformational changes that happen to receptors are similar. For instance, if the ligand that binds to a receptor contains a lot of negatively charged amino acid residues, it could repel certain parts of the polypeptide comprising the receptor. This would cause it to physically shift and take on a new conformation.

I wonder if the number of signals that meet at an integrator can vary? If there was say ten signals bound to an integrator versus 20, would there be a more rapid response? Or maybe there is a threshold that needs to be reached in order for the integrators to perform its function?

An example of this is how epinephrine travels through the blood and binds to a number of different cells in the body. For instance, the resulting signal cascade and effect epinephrine has on cardiac tissue is much different than epithelial tissue. Because of this, epinephrine (adrenaline) has a huge variety of different functions within the body.

Something that is interesting about receptor binding sites and their corresponding ligand binding partners is that shape plays a massive role. Similar to how a block fits into hole on a child's toy, each receptor has a specific binding site shape that corresponds with the signal that is meant to bind it. This ensures that molecules that fit into the binding site are the only thing that can bind. This goes hand-in-hand with ways that drugs interact within the body. Biochemists and pharmacologists design drugs to mock that shape of the binding partner of a given receptor to elicit a specific response within the cell and consequently the body.

I'm also a little confused by this concept, but I do know that tyrosine kinases are fundamental molecules that perform signaling transduction in a massive number of cellular pathways. It has the ability to transfer phosphate molecules, which are crucial units of energy within the cell. But I think that SH2 and SH3 are able to modify the activity of a receptor and consequently result in a more specific signaling cascade after something like a growth factor binds.


Figure comparison

Submitted by cdkelly on Fri, 09/28/2018 - 14:05

I immediately observed that the figures had a lot of dimorphisms. The three images were all quite different across the original figure and the replicate. The original images were more zoomed in and centered, and they did not include any arrows for indication. On the other hand, the replicate had pink arrows designating the area of the subject, and the images were further zoomed out. On the original figure, the label boxes were placed in the bottom left corner of each of the parts of the figure. The replica had them in the top left corner and they were much larger. The first and second image of the original figure show the same area, but the grass looks darker and the shadows projecting from the flagpoles moved. The most similar parts of the two figures were the placement of the images and their sizes they were both very similar in that regard. Each image was placed under the one before it, and they were all uniform in size for both of the figures. In the first part of the figure, the sidewalk leading into Whitmore is not present, but in the second, it is. Most notably, the bush at the bottom of the figure is not present in the first image on both of the figures.

    With all of these observations in mind, I would infer that the methods for how the original figure was created were vague. They probably did not specify how zoomed in the locations were, or how they chose to frame them. Also, I think that it’s safe to assume that they did not give specifics to the placement or construction of the labels. But since all of the images in the figure were organized in same way across both of the figures and the sizes were so similar, I believe that that part was clear.

    Because there was a very similar movement of shadows from the first part of the figure to the second part, I assume the map images were taken at different times in the day. This would explain the difference in shadow placement. Due to the fact that the bush at the bottom of the image or the sidewalk leading into Whitmore is not present in the first part of both figures but is there in the second means that these images were taken at separate times.  Nonetheless, these inferences pertaining to the way that the methods were constructed could all be wrong because the methods may have detailed all of these things but the person tasked with copying them just didn’t put in enough effort.

PP 9/28

Submitted by cdkelly on Fri, 09/28/2018 - 10:44

Since the web I chose was large and relatively flat, I decided to only focus on the right most portion of it. To take the photo, the camera was held about one foot above it and pointed directly downwards; this way the camera was horizontally parallel with the web, with the screen facing upwards. 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 photo, with little finger showing. 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 coming from the web location. 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 then captured.


FDA approved cancer treatments

Submitted by cdkelly on Fri, 09/28/2018 - 10:29

There are currently four FDA approved treatments for glioblastoma multiforme. They are all drugs that cover a pretty broad aspect of cancer mechanisms: Temozolomide is one of them and it is an alkylating agent, meaning it attaches an alkyl group to the guanine of DNA and effectively disrupts its ability to copy itself. The problem with this approach is that it will affect more than just cancer cells and this lack of specificity makes it detrimental to the rest of the body as well.  Bevacizumab is another FDA approved treatment for GBM. It inhibits angiogenesis, which means that it is good for stopping the metastasis of cancer. It is actually considered a relatively safe drug in general, but there are definitely still side effects including blood-clotting, allergic reactions, retinal detachment, etc. It slows tumor growth in GBM patients, but it doesn’t increase the survival rate. Lomustine and Carmustine are the other two FDA approved GBM treatments and they are both alkylating agents as well. With all of these treatments in mind, brute-force approaches seem to be the only thing they will approve, and specificity is not really brought into the picture. Without that I believe that these treatments will only briefly prolong the inevitable.


Homework draft

Submitted by cdkelly on Fri, 09/28/2018 - 02:11

Inference allows you to put pieces of evidence together to come to a logical conclusion. Recently I noticed that there were relatively frequent puddles of water that would appear in the basement of the house that I rent. It only happened when it would rain outside, and the size of the puddle would vary based on the amount of water we would get on a given day. This let me rule out that it wasn’t some sort of internal leak and that the water had to have come from the outside. As it continued to occur, I saw that there was always a large wet spot on the wall adjacent to the puddle on the floor. The wet spot lead directly up to a window at the top of the wall. With this information in mind, I figured that the water had to be coming in from that specific window some how. Following this thought, I checked the outside of the house where the small window was located. Covering it was a plastic rain guard riddled with cracks and holes. When I looked into the area where the rain guard was supposed to cover, I saw there was a build up of water. With all of this information in mind, I was able to confidently say that this was the source of the water in my basement.

Methods redo draft 3

Submitted by cdkelly on Tue, 09/25/2018 - 16:37

The red circle was placed directly over the location of the web. Following the placement of the circle over the web location on the image of the relative location, I began working on detailing the scale. The line tool was utilized to draw a straight red line across the middle of the quarter from the web image. The line was 0.900 in width and placed directly above the quarter with a small gap between itself and the quarter. Above the line, I used the text tool to write out the width of the quarter in millimeters (24.25 mm). The font was chosen to be red like the line it sat above, and the font size was 18. These steps led to the completion of the first two components of the figure.

Finally, I started to add the details to the map location. The words “Student Union” were written in red with the text tool and superimposed onto the corresponding building at the center of the map. I designated the font size to be 30. I then created a small red dot (W=2.268 x H =2.268) on the map at the location where the web was found. The dot was filled with the same color red. A black line was then created that extended from the newly placed dot at an approximately 45 degree angle. The line was black and had a width of 0.265. It stretched beyond the student map depiction of the student union and continued a little farther. At its terminal end, opposite the dot, it connected to another box created using the rectangle tool (W=39.997 x H=13.539). The box had a black outline with a width of 0.819 and a white fill. Inside the box the word “Location” was written in black with size 24 font. With this step done, the figure was complete and it was exported at a PNG image file.


methods redo draft 2

Submitted by cdkelly on Mon, 09/24/2018 - 20:13

To prepare the third component of the figure, a completely zoomed in screenshot of the University of Massachusetts campus on the website was taken. The Student Union building was at the center of the screenshot. It was then imported into the program Microsoft paint and cropped so that the map was all that remained in the screenshot.

Next, each image was imported to image editing software InkScape. The overall orientation of the figure was constructed so that the two images, one showing the web and the other the location, were equivalent in size (W=106.032 X H=106.032).They were placed directly next to one another on the top of the figure. The image of the web was put on the left of the figure and the image of the relative location was placed on the right. I connected the screenshot of the map (W=210.480 x H=109.370) directly below the two photographic images. Three black boxes of equivalent sizes (W=18.074 x H=18.074) were then made with the rectangle tool by holding down ctrl while dragging the cursor. By opening the fill and stroke tool under the object bar, I set the stroke style width to 1.065 and set the color to black. Then the color of the fill was set to white. Next, by using the text tool, a lowercase “a” at font size 28 was placed into the center of the newly created box. The other boxes were prepared via the same method, but they differed in the letter contained within them. The box corresponding with the image of the web, located at the top left of the figure, had the box that contained the “a” superimposed onto it while the image of the location next to it had the “b”. Finally, the box with the “c” was placed on the image showing the screenshot of the map. Each label box was placed at the top left corner of their respective components of the figure and the text size was universally 28.

A perfect red circle (W= 9.308 x H= 9.308) was drawn on the location image by holding ctrl while dragging. Again, I opened the fill and stroke tool while the circle was selected and opted for no fill. Then, I set the outline of the circle width to 1.414 under the stroke style tab. The red circle was placed directly over the location of the web.

Methods redo draft 1

Submitted by cdkelly on Mon, 09/24/2018 - 20:12

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.

Comments for assignment

Submitted by cdkelly on Sun, 09/23/2018 - 23:02

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?



Subscribe to RSS - cdkelly's blog