Drafts

A methods section of a scientific paper has the potential to have the greatest impact on the lasting legacy of a scientific paper. The methods section is what is used to replicate a paper’s experiment and serves to try and replicate the results. In the fall 2018 Writing in Biology class offered at the University of Massachusetts, Amherst, a project was assigned to demonstrate this point.  I conducted this project by first writing a methods section that included how to find a previously discovered spiderweb, photograph it and then turn the images into a multi-paneled figure.This was followed by another student in the class being given the methods section with the task of following as best as possible so as to try and produce an identical replicate of the final multipanel figure. Once a duplicate figure was made, I set out to identify observable differences between the two figures and from that, infer what could have caused the differences. I noticed that the figures had differences in the layout and size, the panels had differences in the location of the labels as well as the label’s color, capitalization and border, and there was a difference in the map type that was used. There were differences in the objects in the photos, such as a leg in the replicate, the pen that was used for scale, the amount of visible floor and wall tile, a wooden door in the corner of the photo and how much of the heating duct could be seen. From the observable differences, factors could be identified that may have led to the differences seen. The factors identified were the familiarity with the Inkscape program for composing the figures, the angle of the camera, the distance of the photo taken from the object, and the availability and access to resources. Being able to identify differences in an end product and what may have caused them will be an important part in understanding not only the data that this experiment generated, but data that any experiment may produce. Even if the methods section is written as precisely as possible, small variables may still cause an end product to be different and the ability to recognize what is different and why is how best to understand what the experiment’s results mean.

 

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. 

There are six main factors and reasons for why the original and the replicated figures came out differently. The angle of the camera, the positioning of the photographer, the lighting, the type of pencil used, the interpretation of the methods, and nonspecific instructions are the factors that led to the differences observed in the two multi-panel figures.

The angle of the camera as well as the position of the person holding the camera led to differences in the photographs used for Panel A and Panel B. Since the replicated Panel B has the ceiling of the building, it seems like my partner’s camera was pointed upward while mine was straight on. Additionally, my partner did not include as much of the rug, wall, or doorway as I did. This is most likely due to them standing closer to the Morrill 4 sign than I did. In the duplicated Panel A, the photograph is focused on the radiator pipe rather than the spider web. While I did state to take the photo 6 inches away from the wall while facing the doorway, they may not have completely understood what I meant.

The Emlen funnel tests at Rybachy of previous studies indicate that the mean orientation of intact Eurasian reed warblers is 42° towards the Northeast (43° when combined with actual data of this study), while the same intact birds after being displaced to Zvenigorod had a mean orientation of 334° towards the Northwest. Regarding the displaced birds of this study, the sham-sectioned group in Zvenigorod had a mean orientation of 354° towards the Northwest, while the V1-sectioned had a mean orientation of 40° towards the Northeast.

All the mean values of the orientation tests were highly significant (P<0.001), except the V1-sectioned data which had P=0.04, good enough to be considered significant but close to the cut value for significance (0.05).

Look at Results section in the text and add supporting comments like: sham-sectioned corrected their displacement... look at significance values to support those claims.

Figures 1 and Figure 2 featured 23 differences between them that occurred due to certain factors that were not controlled carefully or explained precisely. The following section will discuss what factors caused the differences that were described in the results section.

One of the most important aspects in the science community is the ability to replicate processes and get the same results. In order to be able to achieve this goal, clear and concise writing is required. In Fall 2018 the Writing in Biology Class at the University of Massachusetts Amherst, conducted a project to observe differences between two figures. Figure 1 was to be created by me and Figure 2 was to be created by another student following my methods section to try to create a perfect replicate of the Figure I already created. The following section focuses on the subject of the figure, including why it was selected, and the factors that were attempted to be controlled in the writing of the methods section and.

The Methods project showed the importance of controlling factors, replicability in scientific works, and the importance of clear and accurate documentation of procedures. The methods project was about creating a figure and describing how it was created through writing. The original figure was then replicated by another student based on the exposition text of the methods. Through the project, the following findings resulted: differences in materials used, differences in location of objects, differences in colors, differences in camera position, differences in camera settings, differences in the range of the map and photographs, differences in weather and differences in the superimposed elements. The results showed that in order to allow for your work to be replicated accurately your methods have to be very specific and the factors to be controlled need to be followed strictly.

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.

During Fall 2018, as part of the Writing in Biology course at the University of Massachusetts Amherst, I conducted a project which simulated a research report. This project was designed to demonstrate the importance of a clear, concise methods section, the importance of variable control, and the difference between an observation and an inference. A spiderweb was located under a short lighpost between the Morrill buildings. A close up photograph was taken of the spiderweb, a photograph of the general area surrounding the spiderweb and a map of the area in which the web was found were compiled into a multi-panel figure using inkscape image editing software. Once figures were completed, a detailed methods section was written for another student to follow in an attempt to replicate the original figure. The original and replicate figures were compared. Differences were observed in the presence or absence of background or foreground structures and objects, font sizes used, general labeling differences, the presence or lack of light and the presence of water on the ground. Weather and time of day, angling and distance at which photographs are taken, labeling consistency, image resolution, device used to take the image, and the object used to provide scale are factors which were identified as being responsible for these differences.

Part A:

p^2 +2pq + q^2= 1 hardy weinberg equilibrium equation

p=S q=N S= dominant allele spots N=recessive allele no spots  107 spotted/752 total fish

103 heterozygous SN 4 homozygous dominant SS 752-107=645 homozygous recessive NN

To get number of alleles: N=2*645+103=1,393 N allele

                 S=2*4+103=111 S allele

    Total alleles=2*752=1,504

Hardy weinberg done with percentages so: S=111/1504=0.0738=p

                               N=1,393/1504=0.9262=q

p=0.0738 q=0.9262 Lets see if it equals 1

0.0738^2 + 2(0.0738*0.9262) + 0.9262^2=

0.00545 + 0.1367 + 0.85785 = 1

Yes this population is in hardy weinberg equilibrium

Part B:

Imagine you and a competitor are given the basic blueprints to a condominium complex and asked to put small tweaks (furniture, wall type, counter placement, etc.) on each individual condominium and the best blueprint design for each condo will be chosen and used.  So basically the allele is represented by the different blueprints for each condo because it shows the small differences in the same blueprint. The dominant and recessive aspect is represented by the two competitors both submitting a minorly tweaked blueprint ( allele) and having the best one (dominant) chosen.  The instructions for individual rooms and things like furniture are the genes that are coded for in a chromosome. The locus is represented by the individual rooms in the house aka fixed positions of genes in the blueprint(chromosome) The upstairs bathroom would be a locus for the gene for the upstairs bathroom.

Part C:

Suppose there was a small island in which a large group of turtles lived.  Some of these turtles had pointed mouths while others did not depending on the food they ate.  One year there were many rough storms killing off an unusual amount of pointed nose turtles and when the scientist went back to the island they observed a drastic decline in the pointed nose turtle.  This is known as the bottleneck effect and represents genetic drift. Another example would be if the rough storms made the island split into a large one and a small one and the small one only contained pointed turtles. If you came back 15 years later there would be a much higher number of pointed alleles on the small island than flat mouthed turtles.  This is called the founders effect. The genetic drift is caused by random not by natural selection.