Drafts

I wanted to write about the most significant word in my life right now. This word is “counteract”. It means “to act against (something) in order to reduce its force or neutralize it.” Now you may ask why it is so significant to me, and why I think it should be significant to anyone going through a hard time right now. In my personal experience, this word has helped me push through my darkest moments, and I hope it can do the same to you. Depression makes us feel worthless and makes us feel like we are in an extremely dark place. However, what I learned recently is that to overcome it, we must do the opposite of what our mind is convincing us. We are being “hijacked” by our brain, convincing us that we cannot do things, and we cannot feel happy at that exact moment. This is where I learned the word “counteract”. When we think negative thoughts, our mind cycles into telling us to keep thinking it. I call it automatic negative thinking, or ANT. 

Phytophagy means “the eating of plants”. This can be done by animals, insects, or even humans. There is plenty of phytophagy around us, in our dining hall, on the ground or you can even spot phytophagy just by staring closely at a plant. In this project, every student will have to find proof of phytophagy, make a multipanel, create their own methods, and have someone else follow their methods. I chose a leaf that was right in front of Tobin Hall, the reason behind why I chose this leaf is because it stood out to me as it was very nicely shaped compared to the other leaves on campus. Also it was not too far from Boyden Gym, where I am most of the day. 

I have always wondered about the psychology behind dreaming. I always wake up the next morning delusional because I wish my dream had been a reality (sometimes). They can be scary, and sometimes people think that dreams can be preminitions to the future. I believe they help with emotional reguation, depending on my mood, I can have a really scary dream or a really happy dream. The ancient Egyptians believed that dreams were communication between Gods. Then Freud made a theory, but many scientists disagree with this theory. I will continue to do research about this topic as I am very curious. 

Chikungunya is an infection caused by the chikungunya virus (CHIKV). This is spread by a mosquito, like Zika and dengue.  The most common symptoms of this virus are joint pain along with a fever. It can become very severe leading to severe headaches, swelling of limbs and even death. There are recent outbreaks in the United States, but this virus is primarily spread in parts of Africa, the Caribbean’s and India. Researchers from the University of Bristol and the French National Centre for Scientific Research (CNRS) in Grenoble, France, have come together and created a vaccine that can withstand very warm temperatures.  They worked with a synthetic protein scaffold with no genetic material inside that is still extremely stable, even without refrigeration. Additionally, it can be easily engineered which is a great step in the medical industry. The greatest part about their discovery is that they can insert harmless bits of the Chikungunya to generate a mimic to further use as a vaccine. Although they are still figuring out the logistics of it, computers and technology have helped them create a digital model of the vaccine. Intriguingly, because of this great beginning to fight again CHIKV, they can now rapidly engineer similar vaccines that can combat many other infectious diseases.

The goal of the research is to use the bioinformatics and homology model to obtain three dimensional native and mutated PMP22 models, and show how it is anchored to the cell membrane to determine how L16P and T118M mutation affect the conformational behavior of PMP22.

The conclusion obtained in the experiment tells that there is less stability with mutated protein compared to the normal proteins, resulting specifically from residue 16 and in alpha-helix h1-h2. The data obtained in the experiment also concluded that there was less hydrogen bonding at the side near the mutated site and as a result of this deviation from the normal protein, the mutated protein has a harder time getting out of the ER.   

The impact on the disease is that when the structure and how the protein complex interacts, it would make the mechanism of the disease easier to understand, and by understanding the mechanism of the disease at a molecular level, a relatively noninvasive treatment can be created to combat the effect of mutated proteins. 

The data from anchoring the protein complexes into the membrane tells that there is no spacial difference between the converged area per lipid values (table1).  In addition, there is a higher delta g binding in the mutated protein compared to the normal protein(table 2,3). Another difference includes the delta g total was higher in the mutated protein compared to the normal proteins (table 2,3). The results of the experiment also showed that residue 16 was crucial for changes that are induced by the mutation, and both of the mutations alter the structure and the interaction of the proteins by changing the binding properties. In the PCA, it’s revealed that PMP L16P hsd more negative eigenvalues on the first PC and PMP22 T118M had a more positive eigenvalue (figure 2). Revealing that the mutants are more flexible compared to that of the mon mutated protein, which suggests a higher number of conformational states.  The data that the mutated system is more flexible is supported by the data that the mutated systems have are less stable than the normal protein. The PCA also showed that the highest fluctuation was concentrated along the alpha helix 3 loop and the alpha-helix 4 loop in normal protein and in the mutated protein, the fluctuation was highest at lppo alpha-helix 1-2. In both of the mutations, there was a reduced number of hydrophobic contact and less hydrogen bond around the mutated parts of the protein (figure 2,4,5). The mutated complexes also have a higher delta g binding, leading to the inability of the protein to leave the ER(table3).

The first step of the experiment that they did is to obtain a 3D model of PMP22 and RER1. The three-dimensional structure was determined by homology modeling using mouse PMP22 protein which shares 29% of its PMP22 genes with humans. The 3D model was then mutated at L16P and T118M to generate the mutant protein. RER1 was then docked to the constructed protein to simulate its behavior in the ER. The PMP22 system was then anchored to POPC bilayer membrane and submitted for .5ul MD simulations, which mimics what happens in real cell membranes.  

    The second step was the analysis that was done with the data that was obtained in the MD simulations (figure 1). The researchers did Principal component analysis, which reduces the complexity of the data and extracts the relevant motions of the atoms examined (figure 2, 6). In this analysis, eigenvectors, which describes the motion of the protein and eigenvalues, which in this case describes the total mobility associated with each eigenvector, were identified. The protein-protein docking calculations were also performed (figure 3,4,5). This calculation generates a detailed model that indicates where each atom is at any time. The effective binding energy was also obtained through the MMGBSA approach.  This allows for the estimation of effective binding free energy, which is the energy needed to disassemble a protein or a molecule. The researchers then calculated the effective binding free energy for each of the PMP22- RER1, which is a measure of total free energy differences in the molecules that are involved (table 2,3). Clustering calculation was also performed to identify the most popular conformations. 

During fractional distillation, a steady, slow rate of one drop every twenty to thirty seconds is necessary for the proper separation and purification of the compounds.  The thermometer of the apparatus will keep track of the temperature of the vapors as they reach the top and condense into the vial at this consistent drop rate.  While the drops are being collected, there will be one plateau of drops at one consistent temperature.  Then, a slight dip in temperature will be observed.  During this part of the distillation, the first component of the mixture has been used up and the higher boiling point substance is being vaporized.  Because of the higher boiling point, more energy is needed to achieve this explaining the dip in temperature.  This was seen in both the known mixture and the unknown mixture.  In the transition phase between the first plateau and the second plateau, the drops, if any are produced, are not pure and should be separated from the first plateau's drops and the second plateau drops to ensure two pure compounds are formed.  To continue distillation, additional heat needed to be added to both distillations. 

Blood doping has been an issue in the athletic community for quite some time now. Oxygen is a key component when it comes to taking part in any athletic competition. It allows the muscles to create energy and assist the athletes in taking part in their sport. In most cases, blood doping allows the person to increase the amount of hemoglobin in their blood. This helps because hemoglobin is responsible for transporting oxygen in the red blood cells. It can be done through blood transfusions, injections of erythropoietin (EPO) or injections of synthetic oxygen. Our kidneys normally produce EPO to activate the production of red blood cells and so when additional amounts are injected, they allow more oxygen to be transported to our muscles. However, what the athletes sometimes do not realize that they are at a risk for heart attacks, strokes or blood clots through these methods of blood doping. Other alternative methods for increasing oxygen levels in the blood should be taken into consider. For example, training in higher altitudes slowly but surely start increasing the amount of red blood cells we have to compensate for the lack of oxygen there and so it can really help when taking part in a sport later. 

The Field research was conducted on September 16th, 2015. The sites used to conduct the research were Mt. Norwottuck, Amherst, Massachusetts (42o 18'N, elevation 400 m),  Plum Creek, Amherst, Massachusetts (42o 19'N, elevation 60 m) and at Deer Brook, Swanton, Vermont (44o 06'N, elevation 50 m). The density of Vaccinium vacillans was measured on 11 4x4m plots within each site. The 4 x 4 m plots were randomly chosen on each site. The number of individual Vaccinium vacillans per site, were counted, recorded and compared.