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Three main steps were involved in the mutagenesis of the yeast cells. A mutation was induced using UV radiation, initiating the experiment. Mutation was induced on wild-type yeast cells, a andα, which under normal conditions are able to synthesize the important molecules required for survival. Secondly, the yeast cells were selected for and screened for mutations. Screening was done by plating the original Yeast cells onto YED media. These plates were then exposed to UV light, damaging the cell’s DNA. Lastly, the mutants were categorized using complementation. 

In order to observe the effects of mutagenesis, dilutions of yeast cells were placed on a YED plates. The control plate contained a 10⁵dilution of cells to allow for comparison. A second plate, to be exposed to UV radiation contained a 10⁴dilution of cells. The plate containing a 10⁴dilution was then exposed in a UV irradiator for exactly twelve seconds. These plates were then incubated for a week at 30°C. Exactly one week later, to observe the effects of the induced mutagenesis, four mutant samples aW, aX, αy, and αZ and four known mutants, ADE1a, ADE2a, ADE1α, and ADE2α were obtained and streaked onto a YED plate. These were then crossed as shown in Figure 3. The plate was then placed in an incubator at 30°C for one day. After two days, the plate was replicated onto two MV media plates (one containing adenine and the other not containing adenine), and incubated for one day at 30°C. 

Saccharomyces cerevisiae, also known as the yeast cell, has been one of the most important organisms for the study of genetics. They are the simplest of eukaryotes and have similar organelles to human cells, conserving important gene functions and containing a nucleus, vacuoles, and a Golgi apparatus. At least fifty percent of yeast genes have at least one equivalent human gene (1). Due to these similarities in gene function and cell structure, yeast cells can be used in the study of Classical Genetics and Biochemistry, as well as in Recombinant Genetics. Yeast is relatively easy to grow, as they can grow either aerobically or anaerobically in simple media. They have an average doubling time of 1.5 hours in ideal conditions. This experiment explores these properties and uses them in the study of Mutagenesis (following the adenine pathway) and in the complementation of genes. 

Yeast cells can exist in either the diploid or haploid state. They can produce sexually or asexually. In this experiment, two haploid cells (MATa or MATα) will be used to explore Yeast genetics. If these two haploid cell types are kept separate from each other, they will maintain their haploid state. In the event that they are brought together, they will fuse to form a diploid cell. The diploid state of the cell can be maintained as long as there is a sufficient amount of nutrition. In extreme cases when the cell’s nutrition is poor, the diploid cell will sporulate and form an ascus with four haploid spores (2). Yeast cells change their morphology as they go through their life cycle, as can be seen in Figure 1. The cell undergoes cell division by mitosis to form a small bud. The bud then enlarges as the cell progresses through G2 and mitosis. The bud then separates from the mother cell. It important to note that the mother cell does not change in size and that the budding process is the same in both haploid and diploid cells. 

In order to fully explore the capabilities of yeast genetics, mutagenesis will be performed on the yeast cells. Mutagenesis is the inducing of a random mutation deliberately. It can be performed in several ways such as using chemicals, x-rays, and UV-radiation. These methods cause random changes in the sequence of DNA molecules and allow for the studying of concepts such as complementation. Specifically, the adenosine pathway will be studied using mutagenesis. Four haploid strands. ADE1a, ADE2a, ADE1α, and ADE2α will undergo mutagenesis and will then be placed on various media to observe growth and characteristics. The “1” mutants have a mutation in ADE1 and the “2” mutants will have a mutation in ADE2 in the adenine pathway. A mutant allele in either of these pathways will cause the buildup of P-ribosylamino imidazole, resulting in a red pigmented cell. The accumulation of P-ribosylamino imidazole also causes a decrease in the growth rate of ADE mutant cells. 

These cells will be grown on one of three types of media, providing with a range of characteristics that can lead to the discovery of the genotype of the cell. The types of media are YED media (which contain all of the required nutrients for the yeast to grow), MV media (a minimal media which contains only the pure chemicals required for the growth of wild-type yeast, it is important to note that this type of media lacks adenine, causing haploid adenine mutants to die off when placed on this media), and YEKAC media, a starvation media with the purpose of inducing sporulation of diploid yeast cells. The growth on each of these types of media will allow us to determine whether two genes are complements of each other or not. Complementation occurs when two strains of an organism with the same mutation on different genes, allow for the growth of the cell and/or the wildtype phenotype to be observed.

Discussion

In the Results section, it is mentioned that in the repica figure, there is no figure of the actual building. This error of not including a significant element of the replication figure was a direct result of the methods section not being clear and elaborative enough. The original methods section was mainly an “overview” of the process of obtaining the elements for the figure, and putting them together. This formatting allowed for mistakes in putting together the figure to happen. Similarly, there is a difference in the actual web between the two figures, since they are not the same web. The web in the original figure is much smaller in size, judging from the objects surrounding it, such as the sidewalk in the original figure, and the window in the second figure. Of course, since there is no scale to measure the two objects you can never be sure. Another significant difference is the map. For the original figure, opensource.eu was used to find a map for the Lederle Graduate Building. The second figure seems to be from a different website, judging by the look of it. The map also has different scales and markers. Another difference between the maps was that the original map was much more zoomed in, and did not have as many buildings around it compared to the second map, which had a few more buildings. The marker of where the spider web was on the map was a significant difference. In the original figure, a simple red dot was used to mark the location, but in the replica, a star was used to mark the location (also a major difference). This again, was most likely due to the lack of detail in the methods section. The labeling of the figure was quite different, as in the original figure, there were only upper-case red font letters. In the replica figure, the label was spelled out “Location” and “Web” describing the different elements. The words were also inside gray boxes. The specific font size/type was not specified in the methods, leaving it to the person trying to recreate this image to pick a font. Overall, I think much more specificity could definitely have been helpful in this project. It would have prevented a lot of the mistakes in replication if the instructions were much more clear and less concise.

To better understand how methods are written in the scientific community, a project was undertaken for my Writing in Biology course at the University of Massachusetts Amherst in the fall of 2018. A figure was built consisting of two photos of a spider-web on the UMass campus, along with a map of the location of the spider web. A methods section was written for this process, and fellow classmate followed this. A replicated image, solely based on the methods section was created, and then compared to the original figure. It was found that unless a methods section is explicit on important factors such as the number of pictures, labeling, and figure size specifications, it is difficult to replicate a figure or process. Regardless of this, small differences will be present, highlighting the importance of being explicit in every way possible when writing a methods section.

To better understand how methods are written in the scientific community, this project was undertaken for my Writing in Biology course. A figure was built consisting of two photos of a spider-web on the UMass campus, along with a map of the location of the spider web. It was found that unless a methods section is explicit on important factors such as the number of pictures, labeling, and figure size specifications, it is difficult to replicate a figure or process.

The goal of this project is to describe the procedures used to write a research project paper. The main concept to be gained from this project is the process of producing something and then giving clear and concise instructions on how to reproduce it. The goal should be that someone can pick up your instructions and replicate the experiment you did, if not to the exact detail, then very close. The importance of this concept can be seen in any scientific experiment. Without a replicable “methods” section, a research project is unverifiable. For example, what if Mendel did not give clear instructions on how to reproduce his experiment with peas and traits? There would not have been any validity to his experiment because it is not reproducible (one of the fundamental parts of research).  

A secondary goal for this project is the ability to differentiate between observation and inference. Observing specific details about something, as well as the overall picture is an essential part of science. Distinguishing on whether it is appropriate to make an observation or inference on a situation by situation basis provides a scientist with the tools to figure out what to study/experiment on, and what to just use the simple tool of inference on.

In the Results section, it is mentioned that in the repica figure, there is no figure of the actual building. This error of not including a significant element of the replication figure was a direct result of the methods section not being clear and elaborative enough. The original methods section was mainly an “overview” of the process of obtaining the elements for the figure, and putting them together. This formatting allowed for mistakes in putting together the figure to happen. Similarly, there is a difference in the actual web between the two figures, since they are not the same web. The web in the original figure is much smaller in size, judging from the objects surrounding it, such as the sidewalk in the original figure, and the window in the second figure. Of course, since there is no scale to measure the two objects you can never be sure. Another significant difference is the map. For the original figure, opensource.eu was used to find a map for the Lederle Graduate Building. The second figure seems to be from a different website, judging by the look of it. The map also has different scales and markers. Another difference between the maps was that the original map was much more zoomed in, and did not have as many buildings around it compared to the second map, which had a few more buildings. The marker of where the spider web was on the map was a significant difference. In the original figure, a simple red dot was used to mark the location, but in the replica, a star was used to mark the location (also a major difference). This again, was most likely due to the lack of detail in the methods section. The labeling of the figure was quite different, as in the original figure, there were only upper-case red font letters. In the replica figure, the label was spelled out “Location” and “Web” describing the different elements. The words were also inside gray boxes. The specific font size/type was not specified in the methods, leaving it to the person trying to recreate this image to pick a font. Overall, I think much more specificity could definitely have been helpful in this project. It would have prevented a lot of the mistakes in replication if the instructions were much more clear and less concise.

    The significant difference between Figure 1 and Figure 1 is that the images contain a different amount of elements. Specifically, from Figure 2, a photo of the Lederle Graduate Research building is missing. This element was added specifically to highlight the location of the web in relation to how large the UMass campus is. Another noticeable difference is that the location of the spider-web is different. In the original figure, the spider web is very close to the ground, as can be seen by the sidewalk being a few inches below the spiderweb. The replica figure seems to have been found on a window. The spider web in the replica figure is also much bigger in size compared to its surroundings, while in the original figure, it can be assumed the spider web is much smaller due to how big its surroundings look compared to the web. The map in the original figure is noticeably much more zoomed in on the graduate building, as it contains much less of the buildings next to it. This is not true for the replica image, where multiple buildings can be seen, in addition to the Graduate building itself. The labeling is also different, wherein the original image, it is uppercase, standalone letters in a red font. In the replica image, the labels are inside gray boxes and use a different font/sizing.

To find a spiderweb on the UMass campus, I had to go through many trials and errors. The first spiderweb I found was too small for my phone to recognize. I had to go search for a bigger (more-defined) spider web. After a few days of searching, I found a spider web on the side of the Lederle Graduate Research center. On the section facing the main road (N Pleasant St), there was a spider web at about hip height. Photographing this web was quite difficult. I had to try to photograph it at several angles, with and without flash. I found that flash worked the best in making the web visible on in my photo. I had to angle the phone so that the camera was parallel to the main part of the spider web. (Addendum --- In addition to the spider web picture, I found a picture of the Lederle Graduate Research Center building (from the UMass Amherst website -- https://www.umass.edu/llc/lcc/lcc) on which the spider-web was on. This was to better show the location of the spider web in addition to providing a guide as to which side of the building the web was on.

    To create the figure, I gathered the location of the spider web on openmaps.eu, my photos of the spider web, and the picture of the Lederle Graduate building and put them in the inkscape app. I put the map on the top, the photo of the web on the bottom rights side, and the Graduate Building on the left bottom side. Then, I created labels to point out where the location of the spider web was, on both the map, and the pictures of where the web was. I labeled the map A in red font, the picture on the bottom right B in red font, and the picture on the bottom left C in red font. The organization of this was mainly to highlight the locations, starting from the furthest, the map to the closes, an actual picture of the spider web.

To find a spiderweb on the UMass campus, I had to go through many trials and errors. The first spiderweb I found was too small for my phone to recognize. I had to go search for a bigger (more-defined) spider web. After a few days of searching, I found a spider web on the side of the Lederle Graduate Research center. On the section facing the main road (N Pleasant St), there was a spider web at about hip height. Photographing this web was quite difficult. I had to try to photograph it at several angles, with and without flash. I found that flash worked the best in making the web visible on in my photo. I had to angle the phone so that the camera was parallel to the main part of the spider web.

    To create the figure, I gathered the location of the spider web on open maps.EU and my photo of the spider web, and put them in the Inkscape app. I put the map on the left side and the photo of the web on the right side. Then, I created labels to point out where the location of the spider web was, along with a label that highlighted the spider web on the photo.