Writing in Biology - Section 1

Although plants are sessile organisms with unmoving cells, plant cell organelles are in constant motion. Cytoplasmic streaming is a phenomenon exclusive to plant cells wherein organelles will rapidly migrate around the cell. Streaming is controlled by myosin motors anchored to an actin filament network. This phenomenon necessitates only the actin cytoskeleton as a series of experiments showed that streaming doesn’t require the cooperation of microtubules. Additionally, these experiments demonstrated that actin filaments can maintain cytoplasmic streaming by simply disassembling and reassembling recycled actin monomers. In light of these discoveries, there are three non-mutually exclusive theories regarding the mechanism of cytoplasmic streaming. Active streaming theory asserts that myosin motors riding along actin filaments walk organelles around the plant cell. Passive streaming theory posits that the bulk of organelle movement around the plant cell is driven by a cytosolic stream produced by the active transport of only a few organelles. Endoplasmic reticulum (ER) anchor theory states that the majority of organelles are bound to the ER and that myosin motors move the ER, thus dragging the organelles anchored to it. Research has provided evidence for all three of these theories, and it has yet to be shown if they contribute to streaming in equal part or if one model predominates.

In Fall 2019, I conducted a research project in my Junior Year Writing class to seek evidence of phytophagy, i.e., eating of plants, on the University of Massachusetts Amherst campus. As a word with such a broad definition, it included examples as supporting evidence such as leaf miners, slime molds, part of a leaf eaten by an insect or animal etc. The proof I had picked for this paper was a on a plant that had a single leaf with brown patches. Brown discoloration often indicates fungal or bacterial attack, allowing them to grow on the leaf. This essentially means that they are obtaining their nutrients from the leaf. The plant was also picked due to the easier accessibility. It was situated in the Durfee Conservatory on campus and so it was difficult for any external factors such as strong winds or rain to destroy the evidence. One of the factors to control was the timing of the day. The Conservatory could only be accessed between 9AM and 4PM. The other factors were that the map used for the multi-panel figure had to be captured through Google Maps and the figures were created through Microsoft Word.

Overall, each of the figures followed the same formatting style, with one large photo on the left and two smaller photos on top of each other to the right. However besides that similarity, most of the other characteristics of the complete figures are contrasting. The overall resolution and lighting of each of the photos were significantly different. The resolution of Figure 1 seemed blurrier and the lighting appeared overexposed compared to the sharp resolution of Figure 2. Figure 1 contained even, white spacing between each of the panels while Figure 2 had a more significant gap between panel B and C. This links to the sizing of B and C, where the panels in Figure 1 were horizontal in contrast to Figure 2 where the panels were vertical. The letters that marked each panel in Figure 1 were black letters with no background. In comparison, the letters that marked each panel in Figure 2 were black letters with a white square background and a black border. The overall ordering of the panels were switched, therefore A from Figure 1 matches with B from Figure 2.

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 have been 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. Not knowing they should have their fingers holding the branch, the individual doing the replicate would not have known to have their fingers included in panel C. If specification was not the problem, lack of thorough reading could have also resulted in the differences, especially when considering two different plants were photographed. 

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 is 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. The tube is then 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 a wash buffer to remove any impurities 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 Polymerase are added. This is then heated and cooled at the optimal temperature for the gene, allowing for the duplication of the desired DNA. The resulting solution is then put into a well of the gel, and the gel is then ran using electricity. 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 more crude way of extracting DNA however, it is effective in some tissues, such as mouse ear, and often saves time.