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One of the new techniques that has revolutionized the genetics field is CRISPR-Cas by cutting DNA. This important discovery provides a way of editing the genome that was applied to DNA in many organisms such as bacteria, fruit flies and yeast. There is an immunity that CRISPR-Cas has by being in bacteria and archaea and are used to defend these organisms against invaders. Scientists have invented a system known as CRISPR-Cas 9 that requires two RNA molecules, crRNA and tracrRNA. At the end it will facilitate the use of gene editing and by recognizing the specific sequence of DNA that works better than restriction enzymes. 

CRISPR-Cas is a new procedure that has transform the field of science, especially genetics that is used for cutting DNA. They occur naturally in bacteria and archaea and protects these organisms against anything that would harm them. A common system used in genetics is CRISPR-Cas9 that facilitates the use of gene editing. This system makes advances in recognizing a sequence of DNA than restriction enzymes.

Introduction

    The goal of this project is to create a multi panel scientific figure that is about a spider web, then write the methods of the procedure followed to create it.  Someone else will then follow the original methods and attempt to replicate the original image.

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.

Psephurus, or chinese paddlefish, is a large cartilaginous fish of the order acipenserifomres. These live in freshwater rivers, such as the Yangtze and its associated lakes. Historically, Psephurus could reach 7 meters in length. Unfortunately over time, these large fish were fished nearly out of existence. Additionally it was a major victim of the construction of the three gorges dam, as the migration that takens place between mating seasons could no longer take place. The last known specimen was killed illegally in 2007 and was only 3.6m long. No other Psephurus have been identified since.

The North American cousin to Psephurus is known as Polydon. Polydon lives in large freshwater rives as well, such as the Misissippi and Ohio rivers. Its long snout is covered with sensitive electrosensors, which can be used to detect swarms of plankton. The fish will swim forcefully through the water, injesting the plankton which are filtered through the gill rakes. Plankton are diverted to the fish's stomach, while water exits through the gill slits. Unlike Psesphurus, Polydon does not get as large; only about 2 meters in length. Unfortunately, much like Psesphurus, Polydon is a victim of overfishing, and due to dams can only be sustained by captive breeding.

In the original picture the spiderweb is in the middle, the environment is in the middle and the map is on the right. On the replicate the spider web is on the left, the environment is on the middle and the map is on the right place. The arrow is pointing at the spiderweb on the original and in the replicate is pointing at the environment. The labeling letters in the original are in the picture and in the replicate are underneath of the pictures.  The original pictures are more zoom in and the replicate is taken from a far-away angle. Although it was taken in the same location it doesn’t show the spiderweb picture as the original. The maps are different in the original the ISB is emphasized and zoom in and in the replicate the map doesn’t specify the location.

The pictures themselves also differ from original to replicate.  Due to the quality of the pictures and lack of arrows on the environment picture of the replica, it is difficult to tell if the two spider webs are the same. The appearance of the stones relative to the spider web is different between the original and replicate in the close up picture.  In the environmental picture of the original figure, the curb and a blue building are visible in the background, but in the replica picture an orange building is visible and the curb is not. There is also a different number of posts on the fence visible in the replica vs. the original.

The pictures in the replica figure of the environment and close up have water on the stones and a relatively dark complexion, while the pictures of the environment and the spider web have a bright complexion and no water on the stones.  

Observations of the replicated figure panel indicate many differences in the photographs between the two figure panels. The fact that the replicated picture shows a different amount of the tree next to the stair case suggests that the picture was taken a different angle than the original image. It was also observed that the picture showed more of the background of the spiderweb. From this difference, it is inferred that the photograph was taken from farther away in the replicate photo, thus, showing part of the student’s hands and more of the background behind the spiderweb.

The quality of the photographs taken are different between the original and replicated figure panels. The factor that’s most likely creating these differences in the lighting of the photographs would be the time of day that these pictures were taken.The weather also could be a factor affecting the picture quality, as the original pictures were taken on an overcast, cloudy day. This is most likely points to the camera exposure and focus.

The observed differences between the original and replicated figure panels are likely due to the in discrepancies in the methods. For example, the font size and type were different because the methods failed to completely describe the formatting. It is also inferred that a different version of Microsoft Word was used to create the replicate figure, as this would explain why the formatting differed.

The layout of the pictures and the labels is one of the most obvious differences presented in the figures. This is from a lack of exact actions and clarity in the methods section. The methods said that the images should be “adjusted to about equivalent sizes”, when in actuality, they should have been the exact same sizes. Furthermore, the exact width and height of each picture is provided by the inkscape program and should have been provided to remedy this inconsistency. As far as the labelling, the methods section provides that a red box should be made for each of the labels and a lowercase letter used. It is true that a color was not specifically given for the text. Additionally, the methods section provided where the location of the box and letter labels should go. However, given that the pictures of figure 2 were not the same size, the final adjustment given in the methods section may have distorted the picture further from the original Figure 1. This could also be fixed if the exact sizes of the images were provided.