Writing in Biology

Regarding the Emlen funnel tests, 40.9% were discarded for being either inactive (7.4%) or disoriented (33.5%). There is no further information about which birds had their tests discarded, which could be an interesting fact to consider because it could change sample sizes and induce bias. In order to support the discarding of such tests, the researchers could refer to the variables that may have influenced the results, such as the weather or the age of the bird. It is possible that some of the discarded results belonged to juvenile birds on their first migration, which would use vector navigation since they still lack part of the map component of navigation that is gained through experience. Since birds may rely on multiple cues for navigation, this study does not provide the whole picture of bird migration because it was performed at fixed locations. An interesting follow-up study could track the same birds with satellite tagging to determine if they reached their breeding grounds despite having a sectioned V-1.

One cue for determining position is using magnetic parameters. Birds may process such information using the ophthalmic branch of the trigeminal nerve (V1). The goal of this study was to test if V1 plays a role in the navigation of migratory Eurasian reed warblers after being displaced 1,000 km toward the east from their breeding ranges during spring migration. The hypothesis was that V1-sectioned birds would use vector navigation and behave like intact birds in Rybachy, while sham-sectioned birds would readjust their orientation because an intact V1 plays a role in true navigation.

In the Fall of 2018 at the University of Massachusetts Amherst during Biology 284- General Genetics Lab, my partner and I designed an experiment to mutate Saccharomyces cerevisiae, or baker’s yeast, and categorize the resulting mutations.  

Baker’s yeast has two almost identical mating types, MATa and MATɑ, which can sexually reproduce with each other and asexually reproduce themselves.  If the environment they are in is nutrient poor, the yeast cells can exist in a haploid form of MATa or MATɑ. A colony of haploid cells can be maintained by asexual budding.  If the environment they are in is nutrient-rich, the different mating types will become shmoos, a nodule of the original cell that the cells use to join together. Once they become an a/ɑ diploid, they can bud to asexually reproduce two yeast cells, the new cell being exactly identical to the first. If a diploid cell is starved of nitrogen and also on a carbon-poor source, it will sporulate to form four ascospores within an ascus.  Those spores can be released from the ascus membrane and become 4 haploid yeast cells, two a and two ɑ cells.

Mutations come about by mutagenesis, which is a relatively rare event in nature.   DNA replication is a highly regulated event that rarely lets imperfections slip by. Even when a mutation occurs in DNA, it does not always lead to a change in phenotype. Mutagens such as UV light, as used in this experiment, X-Rays, and chemicals are often used to increase the frequency of mutations for scientific study. In order to successfully study mutations, the cells must live and be able to reproduce through the mutagen exposure and contain a non-lethal mutation.  

The cross bridge cycle is responsible for the contraction of muscles. A muslce is made up of myosin and actin. Actin is the thin filament and myosin is the thick filament. The muscle recieves a stimulus from a nerve cell that results in the release of calcium from an internal storage within the muscle. The increase of calcium concentration within the microfibules is what allows the cross bridge cycle to take place. The cross bridges cannot form without calcium because calcium is what allows the active sites to become exposed and without exposed acctive sites, the bridges cannot form. Calcium binds to troponin and as a result troponin changes it's shape. This shape change alters the positioning of the tropomyosin which exposes the active sites. The cross birdges then form. In the presence of calcium, the myosin binds to the actin. The next step is the powerstroke which is when the myosin head pivots, pulling the actin to the center of the sarcomere. ADP is released in this step. In the next step, ATP binds which triggers detachment. The cross bridge detaches as a result of atp hydrolysis. During the last step, ATP hydrolysis the myosin head is coked. The use of energy from ATP to ADP is used to rebind. This is one full cylce of the cross bridge cycle. 

There are two factors that are necessary in cross bridge formation; elevated calcium concentrations and ATP. Elevated concentration of calcium concentration is a requirement because cross bridges cannot form without calcium changing the shape of troponin. An adequate supply of ATP is also necessary because this process requires energy. 

Cesium -gluconate Preparation

Add 35 mL of stock CsOH to a clean beaker, while the solution is stirring add gluconic acid until the pH is 7.2, this will be around 65-95 mL and will take a while to stabilize ( this step is an exothermic reaction and you will be able to feel the beaker warm up) the solution will be light brown

Evaporate to approx. half of the total basic volume

Add methanol p.A.(~50-60 mL)slowly while stirring until you can see crystallization(they look like stringy clumps falling to the bottom)

Let it sit overnight at around 4 degrees C / put it in the fridge

Crystals should be white and about ¼ inch thick on the bottom and side of beaker. Use the ground frit to separate as much of the saline as possible from the crystals

Transfer crystals to a 600 mL beaker and clean the frit filter out, dissolve the crystals with as little H2O as possible ~ 30 mL ( solution should turn light brown)

Add 2 spatulas of activated carbon, stir and heat to 80 degrees C

Filter immediately with the filter for activated carbon, the filtered solution should be light brown again

Pour the filtered solution into a clean beaker and add methanol p.A. (~35 mL) slowly while stirring until you can see crystallization( this time it will take less methanol to crystalize)

Overnight at 4 degrees C

Use frit filter to separate crystals from saline

Transfer crystals to a 600 mL beaker and clean the frit filter out, dissolve the crystals with as little H2O as possible ~ 20 mL ( solution should turn light yellow/clear)

Again add methanol p.A. (~30 mL) slowly while stirring until crystallization

Overnight at 4 degrees C

Use frit filter to separate crystals from the saline

One may repeat this procedure once, but by now Cs-gluconate crystals of sufficient quality and bright white color should be obtained

If the solution before you add methanol is yellowish then do another round of precipitation. If the solution is more clear and barely yellow then go ahead to the drying process

To dry the precipitate put the Cs-Gluconate in a 10 cm petri dish, (weight the dish before) and put the dish in an exsiccator with the dish top slightly ajar

When the precipitate is fully dried take a mortar and pestle and crush the precipitate until it looks like flour

Now weigh the precipitate and record it on the petri dish

I took ResEcon 220 my second semester freshman year to fulfill the statistics requirement for biology majors.  I remember the first thing we learned was how to use excel in the most basic way. The next class was simple review from high school math class about ratios and other basics for statistics.  We then learned basic statistic material such as variables and what it means to have a hypothesis and a null hypothesis. I then remember we started to learn about standard deviation and learned how to calculate it, how it is used, and why it is used.  After we learned all about standard deviation we learned how to use it in excel and how to write formulas to do out the work for us. Pretty early on into the semester we were assigned a group project looking at football statistics. This was my first group project in college so not only did I learn about statistics but also how to work in a group setting and facilitate a 7-8 member team to develop a research paper about football statistics.  This project also taught me about how to write a lab report for a subject other than biology, physics, or chemistry, as those were the only classes I had to write reports for yet. At the time It was my least favorite class but I can honestly say I learned alot from Professor Wayne and his ResEcon 220 class.

Part of the reason that wildtype Abl and the Bcr-Abl fusion act so differently is the change in form that occurs. The structure of a protein relates to the function of the protein, so any minor changes could end up changing the function completely. The change expressed in the fusion is what disrupts the regulation that wildtype Abl usually provides and increases the level of signaling beyond wildtype Abl. Wildtype interacts with multiple signal adaptors, phosphatases, transcription factors and cell cycle regulators.  It is tightly regulated and has nuclear import and export signals so it is capable of interacting in the nucleus and cytoplasm. It is regulated by intramolecular interactions and phosphorylation. When Abl kinase becomes Bcr-Abl, the new N-terminus creates a binding site for other proteins, causes the loss of the CAP domain (which is important for cell regulation) and causes the localization to be purely cytoplasmic. Overall, Bcr-Abl has binding sites for cell proliferation signaling pathways that Abl doesn’t have and has a greater kinase activity.

This video contained two mare and two foals of about 6 months. Throughout the half hour of video, you could watch them interact with each other as well as the environment in a number of ways. We grouped the behaviors into a different groups that included: feeding, playing, communicating, and other. The other contained behaviors that did not match another group well. Behaviors found under play included the foals running, jumping, prancing, and nudging one another. The foals would nuddge one another with their heads and this would entice a reaction out of the other foal, so this one could also be placed under communication. Many of the acts fall somewhere in between categories and they are not completely concrete. Feeding was put as its own category because the horses were often observed to be grazing. Even at points where they may not have been eating, they often had their heads toward the ground nudging around the grass. They looked to be continuously grazing almost. Communication was another big category of traits observed. Horses can be seen nudging other horses and neighing. Communication is observed when a stimulus from another horse that entices a reaction from another horse. When a reaction is observed of the second horses behavior is alterede as a result of the stimulus. Some behaviors under the other category include the horses scratching along the fence and other random movements. 

In the crossing of the mutant strands, there were fewer colonies observed than was expected on the control plate (one-hundred and fifty). This might have been due to a dilution error. For the MV plates, there were approximately ninety colonies observed. The reason for this proportion colonies may be due to not plating the same number of cells on the control plate as there should have been. Theoretically, there should have had a 20% survival rate if the optimal exposure was achieved. For the MV plate, the survival rate was 3.3%. This is significantly lower than expected and might be due to errors as mentioned above. There were no mutant phenotypically red colonies observed. This was expected, as you need about 10,000 surviving yeast cells for each mating type (3) to observe surviving mutant colonies that express a red color. The survival rate for our control plate was 6%. This was also much lower than the 20% expected survival rate, for reasons similar to the first plate. 

Some key principles that I remember from statistics include probability, regression, standard deviation, and the empirical rule. Probability is the chance that something will happen given certain conditions. Regression an estimation of the relationship between variables (for example X and Y). Standard deviation is a measure that is used to quantify how far a value is from the mean of the population and/or sample. The empirical rule states that 68 percent of data on a standard distribution will fall within one standard deviation from the mean, 95 percent of the data will fall within two standard deviations of the mean, and finally 99.7 percent of the values fall within three standard deviations of the mean.