Drafts

This was also about a talk I went to at Harvard. This talk was very dense on the engineering aspect of microbiology which I found interesting because it was something that I don’t typically think about. The main point of the talk was discovering ways in which we can categorize and catalog bacteria. The proposed method was by looking at bacterial cell envelopes and inducing a dipole on them to determine how they behave. The other half of the talk was about about how we can use electric fields to help introduce new DNA and genes to cells. This is where the talk became incredibly engineering heavy and a prototype machine that could carry out multiple electroporation experiments at once was introduced. The way that bacterial cells were categorized by their cell envelope was with a technique called low frequency dielectrophoresis. With this technique a dipole is induced on the cell by creating a non-uniform gradient. The bacterial cells were then placed in tubes that had a constriction point, it is at this point that the now polarized cells feel the dielectrophoresis force and clump at the constriction point. The bacteria used in this experiment was a mutant strain of Streptococcus mitis. A mutant was used because S. mitis typically has a virulence factor that causes clumping, the mutant had this virulence factor removed so that any clumping near the constriction point would be fully attributed to the dielectrophoresis force and not the virulence factor. Two other bacterial strains were used to observe polarizability. The first, Geobacter sulfurreducens polarizability was studied by observing its extracellular electron transfer mechanics. The second, Shewanella oneidensis polarizability was studied by looking at its Mtr pathway. This gene was later inserted into Escherichia coli to see if it was also impact the polarizability of it. The engineering part was to make a machine that carried out multiple electroporation experiments at once. This was done by condensing the apparatus down to the size of a pipette tip.

There are multiple TAAs common in pancreatic cancer that have been or are being targeted for immunotherapy. Ideally, treatment can incorporate vaccines for a few TAAs to account for patient tumor diversity. Carcinoembryonic antigen (CEA) is a particularly attractive TAA to incorporate into a vaccine as it is overexpressed in over 90% of pancreatic cancer. A clinical trial with 1 mg of the CEA vaccine CAP1-6D elicited robust CD8+ T cell responses in 7 out of 19 tested patients (Geynisman et al. 2013). Other potential targets for vaccines include KIF20-A (part of the kinesin family), KRAS, WT-1, and VEGF (Banerjee et al. 2018). I need to research each of these more to see which ones seem best to incorporate into our treatment plan. Activators of the STING protein, which induces pro-inflammatory responses through the INF-beta and NF-kappaB pathways, seems to contribute to the regression of tumors via T cell recruitment as well as enhance the responses of anti-CTLA4 and anti-PDL1 immunotherapies (Banerjee et al. 2018). More research is needed in this topic as well, but perhaps a cancer vaccine and a STING activator can be used in combination in hopes of creating an overall more effective immunotherapy.

Research was conducted on three invasive herbs- Alliaria petiolata, Cabomba caroliniana, and Glaucium flavium in order to determine which posed the greatest threat to Massachusetts’ economy and ecosystems. The research conducted was used to determine the extent of harm each of the invaders had in the areas they occupied and were compared to against one another. Using a bioeconomic framework that revealed the connection between ecology and economic input on ecological states, the impact of the invaders were assessed. The bioeconomic framework considered the source, transport, establishment, abundance and spread, impact, along with prevention and control of the invasive herbs.

For project 3 so far, I have been working on understanding the basics of the immune system as well as expanding my knowledge of possible immunotherapy routes to take in curing pancreatic cancer. Through many review articles, I have found that there are two approaches to anti-cancer immunotherapy: passive and active. Passive immunotherapy involves treatments with monoclonal antibodies, adoptive T cell transfers, and genetically engineered T cells, whereas active immunotherapy involves vaccine-mediated immunity via the administration of tumor-associated antigens (Banerjee et al. 2018). I would like to focus my research on the active side of immunotherapy. Due to genetic alterations or post-translational modification of proteins, cancer cells can express and display proteins that differ from their normal cell counterparts or are overexpressed in the tumor phenotype (Battaglia et al. 2016). These proteins are known as tumor-associated antigens (TAA) and fail to be recognized by the immune system. As a result, cancer cells that display TAAs are able to evade the normal destructive response of active CD8+ T cells. Cancer vaccines serve as methods of active immunotherapy that can stimulate the CD8+ T cell response to these TAAs and hopefully eradicate all cancerous cells that display them (Banerjee et al. 2018).

The study of proteins is important in fields like genetics, biochemical research and medicine because the role they play in most if not all biological functions can be used to understand how diseases work and more importantly how to treat them. The function of the protein comes from its structure, so an understand of how the protein is built could shed some light on how it works. The goals of this lab were to successfully purify and crystallize the protein using methods such as chromatography, which is used to separate molecules by size; a Bradford Assay which determines the concentration of protein in collected solutions and subsequently the volume for the gel electrophoresis; an SDS-PAGE which confirms the presence of GFP protein in the solution; and finally handing drop vapor diffusion which ultimately crystallizes the protein. Throughout this lab, we feel that we obtained an ample amount of 6xHis-GFP protein due to the bright green color of our eluate samples. Though we did not make a large GFP crystal, we successfully made scattered GFP crystals under 25% PEG 8000 precipitant concentration.

For our project we wanted to determine the places students travel to most frequently  while taking the PVTA. Participants of our survey were asked to select the place they transport to the most from a list that included both on and off campus destinations. These main six destinations are class, Hampshire Mall, downtown Amherst, off campus housing, traveling to campus and Northampton. We hypothesize that each of the six destinations that we chose, each will be visited by an equal number of students. The null hypothesis that there is a significant difference between the locations that students decide to travel. From the data collected we were able to analyze and conclude which are the most popular places students travel to.

The height is the most uncertain thing we measured because we mostly had to rely on estimation and obscure math. The height of the library could not simply be measure like that width or length due to it’s vertical nature. The height could also be an issue as we measure the height of a single stair, counted the amount of stairs per floor, and then multiplied those number be the number of floors in the library. However with so many different factors the room for error increases exponentially. Additionally we might have been unable to take into account differences related to step height. Also, our lack of access to the upper levels of the library prevented us from being able to take into account the different dimensions of these floors that could have affected their height. The length and width were also uncertain in terms of the variations in brick length, but the height was the most difficult attribute to access. Based on the several issues noted above we estimated that we would arrive at a standard deviation of 1200m^3.

The methods we used for measuring the library was to find the height of each stair in centimeters (cm) in the indoor staircase and multiply that number by the amount of stairs on each floor. Then multiplying that number by the number of floors to get the height. To get the length and width we measured the outside of the building by finding the length of a single brick (cm), at the base of the library, and multiplied that by the number of bricks on that side of the building. Finally, we multiplied the three dimensions together, after converting to meters, to get our calculated value for the volume of the library (m^3).

After collecting data of the observed behaviors and placing them into behavioral categories, we concluded the categories to be normal, innate behaviors of young foals. Each behavioral category is seen multiple times in the total 48 minutes and 55 seconds of footage and a total number of 65 individuals behaviors were documented. The playful behavioral category had 11 specific behaviors performed by the foals that were described and documented (Table 1). The aggression category shows 9 different behaviors of the foals (Table 2). The feeding behavioral category had a total of 10 unique foal behaviors (Table 3). Locomotion behavioral category of the foals had a total of 7 behaviors (Table 4). The grooming behavioral category had the most classified behaviors with a total of 15 (Table 5). The affection behavioral category had the least amount with 3 behaviors (Table 6). The behavioral category of observation had a total of 8 behaviors listed (Table 7). By weeding through the repetitions and similarities of the collected behaviors, we were able to formulate a well organized set of tables and learn about the constant signals that Morgan horses use to communicate.

These seven categories were broken down into playing, aggression, feeding, locomotion, grooming, affection, and observation. The playful category includes behaviors such as chasing bucking, nipping, or behaviors that displayed foal excitement. Aggressive behavior was categorized by actions such as ears back, pursing lips, pushing and any behavior in which the foal appeared agitated. The foals spent a large amount of time feeding, either grazing in the grass or nursing from the mares, which prompted a feeding category. Running, trotting, cantering, rearing, and other types of movement that changed of location of the foals were classified under locomotion. Grooming movements such as tail swatting, mane shaking, itching, etc.are innate behaviors of the foals, occuring often and seemingly unknowingly to the foal. The foals showed affection to the mare through behaviors such as necking and nuzzling. Observation included behavior such as surveying, sniffing, sticking their head through the fence and any behavior that involved the foals assessment of their surroundings. There is one table for each category that we organized, and at least three behaviors in those categories. Every table lists the behavior and is accompanied by its description, and a still image of the horses performing the behavior.