Drafts

The electrochemical gradient is one of the most important locomotive forces in animal cells. The first part of the electrochemical gradient is, counter-intuitively, the concentration gradient. This refers to the difference in concentrations of a small molecule across a membrane. For example, in axons, there is a downward potassium gradient out of the axon, that is, there is a higher concentration of potassium in the axon than outside of it. Which means, all other conditions being equal, potassium would flow out of the axon if given the chance. Another example of this phenomenon is osmosis. Plant cells employ a proton pump to push protons into the extracellular matrix against their concentration gradient. They then use the energy generated by the proton flowing down its concentration gradient and back into the cell to import metabolites. This generates a higher solute concentration inside the cell than outside the cell. Water flows from low solute potential to high solute potential, or from high water concentration to low water concentration. The plant cell takes advantage of this phenomenon and increases rate of water diffusion into its cytosol in order to increase turgor pressure. The electrical gradient refers to the difference in charges across a membrane. Charges can interact across membranes as they are, generally, only a few nanometres across. This produces a countering force to the concentration gradient. For example, if the intracellular side of a membrane has a high concentration of both positive and negative ions and is only permeable to the positive ions, then the positive ions should flow down its concentration gradient to the extracellular side of the membrane. However, as it does, it will generate a greater positive charge on the extracellular side of the membrane, which will attract the high concentration of negative ions to the intracellular side of the membrane, generating a negative charge. This charge will pull the positive ions from the extracellular side of the membrane back to the intracellular side despite the concentration gradient. The charge at which the electric force counters the diffusion force is known as the equilibrium potential of the ion. This mechanism is employed across animal cells to passively maintain asymmetrical charge and ion concentrations.

People often equate those who study in the heavily scientific fields to lack highly developed social skills. Many a time I have heard people say, "Oh you're a bio major" as an excuse to misspeak, get mixed up in conversation, or misinterpret social interaction. This stereotype is very incorrect and does not at all apply to biology majors. While in every group of people there will exist differences in social skills, preference for science does not equate to ineptitude in people to people interactions. I have found that in order to succeed in any field, people generally require a high degree of communication and comprehension skills in order to work around others and perform in any work environment with a boss, peers, and employees. The stereotype that this is not the case most likely stems from the thought that science is an independent and often isolating study that people do alone with chemical and compounds in test tubes. This is just never the case in any real life line of work. In order to perform well in any position, people talk to one another about what no to do, what to do, what to improve, what to contiue, etc. Science holds true for this general statement where performing experiments, even if people are not directly involved in that experiment, requires multiple sets of hands and minds working together on a project to find the solution and results. Science also includes an extensive system for sharing knowledge through publications in literature and articles. Without the ability to clearly and precisely detail, explain, and interpret experiments from one person to another, science would never be able to evolve. Working in isolation and solitude is nearly impossible to achieve in this day and age, except maybe computer coders and data analysits who can work completely through a computer and email account. Science and all fields rely on inteactions between people to expand pools of knowledge and jump from one newly found conclusion to the next. 

Comparative psychologista work in a lab setting with controlled experiments. They are interested in the “how’s” of learning, in other words, proximate questions based on the genetics and development which influence behavior in animals. The type of experiment they would conduct involves rats and pigeons in the lab by testing their learning abilities.

Ethologists work in field settings observing nature. They are interested in the evolutionary history and the “why’s” of behavior, in other words, ultimate questions wondering about their evolutionary history and adaptive value. An experiment they might conduct would include observing why spiders live in groups and attempting to understand the value of that behavior.

In this project, I compared the differences between an original multi-panel figure I made depicting phytophagy, the insect consumption of plants, and the replicated version of it made by a classmate. The purpose of this experiment was to test how well the structure of my method’s section was organized by analyzing the differences between our models. I found that the figures were not identical, and contained dissimilarities with sizing, brightness, layout, directions of labels, and morphological differences. The indicated factors that characterized these differences were different leaves being used, weather differences, camera position, font size choice, label placement and size, arrangement of maps, scaling, and choice of software.

There are many factors which could have contributed to the differences between the original and replicate figure. The clear difference in lighting could have multiple factors. The time of day could be different which would lead to differences in light color, intensity, and the direction of the rays on the plant in the pictures. If the replicate was taken later in the day or early in the morning, that could explain the low light intensity. Weather could also be causing these differences, as the original was taken on a day clear enough for the sun to brightly illuminate everything, the replicate could have been taken on an overcast day which limits light intensity. A difference in camera would also lead to the variation in light, color, focus, and quality of the two figures. A combination of these factors could have also been affecting the different outcomes of the photographs. Unspecific directions in the methods section could have led to different subjects being examined as in panels B, C, and D. Since there was no specifications of the angle the pictures should be taken at, or the distance from the subject this could account for the differences in those features.

Genotyping is a common technique learned in the genetic lab used to figure out the genotype of animals form their DNA. a proper genotyping done in three distinct steps. The first is DNA extraction, the second is PCR, and the third is gel electrophoresis. The first step is DNA extraction this is typically done using silicon columns. In this method, the lysis buffer and proteinase k is added to the tissue and incubated. After this is done the tube is spun so that the supernatant can be removed without contamination. When this is done the supernatant is then put into a spin column. It is then spun. This allows for the DNA to bind to the silicon and the rest of the supernatant to be separated from the DNA. the column is then washed using wash buffer and the column is then put into a new collection tube and eluted. The eluted solution contains DNA. the DNA is then put into another tube, and buffer, forward primer, reverse primer, MgCl2, and taq PCR are added. This is then heated and cooled at the optimal temperature for the gene. The resulting solution is then put into a well of the gel, and the gel is ran. The resulting gel is able to show whether the gene is present or not. However, every gene is different in how it shows in the gel. One of the things that can be done if there is a relatively large amount of soft tissue is to skip on DNA extraction and just boil the tissue at 95 degrees in NaOH, adding tris HCl after. this is a rougher way of extracting DNA however, it is effective in some tissues, such as mouse ear. 

3d Fluorescence imaging is accomplished similar to how flow cytometry works. Both of them rely on tags that have fluorescence attached to them, are used most often in molecular biology in order to determine what enzyme is interacting with which ligand. The two things that are being looked at are both tagged in different colors. The tags are then scanned for with a laser to produce the raw data. The data is then processed so that the information can be processed. This is accomplished by establishing how close the two tags are. It is assumed that if the tag that has the molecules attached are close to each other, then it would make sense that the two are interacting in a chemical way. However, this would depend heavily on the quality of the imaging because the precision of the data is wholly reliant on the quality of the image. In addition, this also has a problem of never actually proving that they are interacting. They can appear to interact but never actually interact. In addition, the coefficient that is obtained from the result is heavily dependent on which one it is based on. For example, if there were a large amount of the ligand, and small of the receptor, the coefficient of ligand to receptor would be much smaller compared to receptor to ligand.  The positive of the technique is that it is relatively cost-efficient, and provide quantitative data from the image. However, this technique is als extremely labor-intensive and can only work well in a few experiments. 

In Junior Year Writing Class at the University of Massachusetts, Amerhst, Professor Brewer assigned a project to capture and replicate signs of phytophagy on the UMass campus. This project allowed students to study what controllable factors and unavoidable discrepancies appear when replicating an individual’s methods. Furthermore, capturing evidence of phytophagy on the UMass campus offered a process to learn about how to create a perfect figure and follow others’ methods. The focus of my figure was a leaf found on a large bush in the rooftop garden of the John W. Olver Design Building. I chose this specimen due to its convenient location and obvious signs of phytophagy. In addition factors were more easily controlled since this is a privately maintained garden therefore the bush would not be destroyed. The time of day, zoom, perspective, and quality of the photos were also considered when this example of phytophagy was captured so that it can be replicated accurately.

I've had the opportunity to work with mice over the summer. It was really interesting to me because I've only ever worked with cell culture before. one of the things that I noticed while working with mice over working with cells is how variable the data was. There were some major differences between the highest number and the lowest number. I asked the postdoc about it and he told me that this is actually quite common. It interested me that there was so much to work with mice, especially working with mice that often didn't live until the reproductive age and as a result, the mut mice could only be produced by two het parents and praying for lots of pups. I've learned what to do and what not to do when making mice lines, and what is possible but still not a good idea.  I've also been quite good at handling the mice and doing oral gavages while the mice are still awake, although I was not quite as good as to do collect the blood without anesthesia. On the other hand, I did manage to collect blood without killing the mice I'm proud. 

I've also learned the reason why mice work was not for everyone. I ended up having my fingers bitten, and because a permanent mice line could not be produced, many of the mice had to be euthanized. This was quite a bit painful to watch and the way of being euthanized was not always framed in a way that looked painful but was not as direct as dislocating the spine. I think I will work with mice again, and it was a really good learning experience, but I think I will be less judgy when people are unwilling to work with mice. 

(Work in progress paragraph from METHODS project)

Between the two pictures, the most evident difference is that these figures are describing two separate trees, located in completely separate areas. The order of the photos is different: all three photos (close, medium, far) are located in different quadrants in both figures. The map, however, is located in the correct quadrant in the replication. Secondly, the aspect ratio of the two figures is quite different. While the second figure was consistent in making a starting template of 1600x1200 pixels in the photo editor, they captured their images-presumably from a cellphone-in a portrait orientation. The result is unused space to both sides of the central figure. Also, a much thinner, longer arrow was used when pointing out information in the replicated figure. In terms of other graphical additions to the figure, the text in the top left of each image is of a different color, order, size, and font than the ones originally used.