mtracy's blog

Enzymes are proteins which work as catalysts to speed up the many chemical processes that occurs in an indaviduals body. Enzymes are never used up or changed during the chemical reaction process. At the most, an enzyme may require a cofactor to bind to it, in order to enter its proper conformation. This allows for a certain level of regulation over the enzyme.

Enzymes speed up chemical reactions by decreasing the activation energy of said reaction. However these never thermodynamically effect the chemical reaction. They do this by orientating molecules in an ideal way, pushing molecules closer together and by stabilizing the transition states of the reaction. Through these methods, enzymes allow our body to perform complex chemical reactions rapidly. For instance, the glycolosis of sugar on its own will take years. However, since we need energy all the time, an enzyme is needed to speed up the process.

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.

African lungfish live in areas where there is a heavy wet season and a very dry season. When it is wet, the lungfish will live in, generally shallow water or very muddy, wet land. It is during this time the lungfish will reproduce. Female lungfish will make a burrow underwater, which it will fill with decaying plant material. The males then guard the egg chamber until the eggs hatch. During this period, the male lungfish will develop pelvic gills. Pelvic gills are very different from respiratory gills. In fact, they act in the opposite direction. Rather than taking in oxygen, they expel it. This is done to oxygenate the water surrounding the eggs, allowing the lungfish embryo’s to survive in stagnant water with their limited gills.

Once mating is over and the waters begin to recede, the lungfish will create a burrow in the ground for itself. While in this chamber the lungfish will excrete a large amount of mucus, filling the chamber and making a mucus cocoon. Lungfish can be sustained in this cocoon for months at a time, until the area in which it lives becomes wet again.

When writing reports it is important to be clear and concise in the methods section in order to facilitate replication. Many of the differences listed above could have been avoided with better descriptions. For instance when it comes to labeling the images, the font size looked to be much larger in the replicate. This may due to improper font size, or it may be because the images themselves are a different size, making the fonts seem different. The angle of the arrow could have been controlled by having an easier to draw arrow. That is to say, one not at an angle, or at an easy to determine angle. Additionally arrow keys could have been used to provide exact inputs to move the arrow from an easy to determine position to its final position. The line thickness differed on the arrow, though this was in the methods and was not followed. Specifying that the arrow head used was the “5^th one down” would have avoided the difference in arrowheads used to point to the web location. Unfortunately there does not seem to be much that can be done about the difference in map image, with the source used. The best that can be done is listing exactly everything visible in the image with the addition of dimensions of the image. Regardless this still leaves room for error.

When taking the photograph, the time of day and weather should have been accounted for in order to replicate the original image well. Since the lightpost and surrounding area was wet in the replicate we can assume it was raining. Also since the light was not turned on, this photograph was likely not taken at the same time. The addition of light shining down on top of the spiderweb would have likely produced a better contrast, allowing the spiderweb to be more visible in the photograph as well, as is true in the original.

Framing and instructions on framing could have been much better. In retrospect the original image of the surrounding area (Fig. 1:B) should have been directly centered around the lightpost, as is true in the replicate. The slight angle at which the original photograph was taken is difficult to describe and provides too much room for error. To go along with this, a specific distance from the lightpost to stand at and take a picture should have been specified.

Object used to provide scale was wrong. This may be due to a ruler just being unavailable at the time. Regardless however, it should have been mentioned that the ruler was to be held with the inches side closest to the lightpost. This point was not specified in the original methods.

Despite these differences, both the original and replicate images are very similar. This project has not only demonstrated the importance of a clearly written methods section but being mindful of how an experiment is performed. Keeping things reasonably simple, at least within the confines of the subject, will likely produce better results and enable easier replicability.

Writing lab reports is an important part of any biologists life and practice in writing all sections of such a report is crucial to being successful. An introduction to the topic, informing the reader of general background information on the experiment and why it was done is necessary. The methods of the experiment provide a blueprint, allowing for replicability, and thus the ability to confirm results or allow others to improve upon them. The results of the experiment must be concise, a statement of just facts. No interpretations, only laying out what resulted from the experiments. Finally, the discussion section reveals how one may interpret the results. Furthermore, this may be used to discuss what may be done to improve the experiment, or what may be done in the future.

To simulate a research report students were tasked with finding a spiderweb and photographing it. A multi-panel figure would then need to be created using the photographs and map images. In order to practice writing clear, accurate methods, the student had to write with the intention of another student following their methods, and then replicating the photographs and figures. This project demonstrated the need to be highly specific and precise with methods writing. Furthermore, comparison of figures only after both were created highlighted mistakes and areas where the methods could have been improved upon.

The ability to identify factors which need to be controlled for is another crucial skill when designing experiments and writing research report. When taking photographs of the spiderweb, there were a number of factors to control for in order to obtain similar pictures. This included things such as the time of day, amount of light, and weather needed to be accounted for. In addition to this, the object used for accurately representing scale had to be noted, as well as where it was held in relation to the spider web. Furthermore, distance from the spiderweb, and the angle at which the photograph was taken had to be taken into account.

Similar factors had to be controlled when describing the editing done to create the figure. The size the photographs were scaled to was noted, as well as their general arrangement. How labeling was implemented on the figure was to be controlled. This included the color, font sizes, and location of the labeling.

Adult african lungfish are obligate airbreathers. While they spend most of their time in shallow water, they must come up at least once an hour for air. When needed, the lungfish will pop its head above water and open its mouth.  The hyoid arch of the fishs jaw will retract, opening the oropharyngeal cavity in the mouth. This creates a negative pressure, unlike what occurs with our own lungs, and allows fresh air to fill the cavity. Once full, the glottis opens, allowing passage to the lung. Air already in the lung will be expelled, passing over the fresh new air in the oropharygeal cavity. Unfortunately some old and new air mixes, so this process is not entirely efficient. Elastic recoil occurs as the lung deflates, causing the shape of the lungfish itself to deflate with it. The mouth of the lungfish will then close and its hyoid arch will return to its position, closing the oropharyngeal cavity. The fresh new air in this cavity will instead be directed to the lung, filling it. After this process, the lungfish is free to sit at the bottom of its shallow pool of water, gobbling up shrimp or other small organisms until it needs to breath again.

Students were tasked with finding a spider web somewhere on the University of Massachusetts campus and photograph it. In addition to this, students were tasked with creating a figure using these photographs, which included a map for reference. A detailed methods section describing where the spiderweb was photographed and the specific approach used to photographing and editing figures needed to be written. These methods were to be followed by another student, with the attempt to recreate the original figure. Once a replicant was created, students had to observe differences between the figures.

The goal of these tasks was to simulate a research report, giveing students practice at writing them, as well as creating figures for the report. Following another students methods demonstrated the need to be highly specific and precise when describing what is done. Overall, this project was designed to help students understand how to more accurately present and describe their methods in a well written research report.

When taking photographs of the spiderweb, there were a number of factors to control for in order to obtain similar pictures. Things such as the time of day, amount of light, and weather needed to be accounted for. In addition to this, the object used for accurately representing scale had to be noted, as well as where it was held in relation to the spider web. Furthermore, distance from the spiderweb, and the angle at which the photograph was taken had to be taken into account.

Similar factors had to be controlled when describing the editing done to create the figure. The size the photographs were scaled to was noted, as well as their general arrangment. How labeling was implimented on the figure was to be controlled. This included the color, font sizes, and location of the labeling.

Nomally fish have an opening on thir snout called a naris. A naris is essentially the fish's nose and is packed with olfactory receptors. Water enters the naris, and leaves through a posterior naris. Some fish have this posterior naris in their mouth, where it is refered to as a choanae. The water will then enter the gills and exit the fish body that way. The lungifsh has a special case of Naris however, where both the posterior and rostral ends are within the mouth. It has been highly debated whether or not this may be refered to as a choanae.

African lungfish live in very wet areas which are prone to completely drying up. During this dry period, the lungfish will burrow into the ground and make a chamber for itself. It will then fill this chamber with large amounts of mucus, forming a coccoon like structure. The lungfish can live in thi cacoon fo months at a time, until another wet period begins. During these wet periods is when the lungfish nest and lay their eggs. The female will create a burrow and lay its eggs in a chamber, which will be filled with decaying plant material. The male lungfish guard the egg chamber. Due to the need for african lungfish to breath actual air, and not soley oxygen from water, while guarding these eggs the males will develop pelvic gills. Pelvic gills work in the opposite ways of respiritory gills. These gills will expell oxygen from the males body and oxygenate the surrounding water. In thi way the embryo's within the eggs will be able to breath more easily. The male lungfish will only have to surface for a gulp of air about once per hour.

When light enters the human eye it is refracted by the cornea, lens and both the aqueous and vitrious humor and is focused onto the eye's retina. This refraction is not entirely perfect however, and so the eye can use cillary muscles to contract the lense for further adjustments. When the image from reflected light is not focused properly, this can lead to either hyperopic or myopic conditions. These are what is more commonly known as far sightedness and near sightedness respecively. When an indavidual is far sighted the image is focused behind the eye. When they are near sighted the image is focused in front of the eye.

The retina of the eye is covered in photoreceptors. These come in two forms, rods and cones. Rods are very plentiful, outnumbering cones nearly 20:1. These are used mainly during situations of dim light. Cones will however detect color and are used in bright light. When light enters the photoreceptor cells a protein called rhodopsin is bleached, causing a conformational change. Rhodopsin will then activate a G-Protein called tansducin, and the signal continues to propogate until sodium channels in the photoreceptors are closed, which in turn halts the release of glutamate. Post synaptic biopolar cells will respond to this lack of glutamate by either turning on or off, depending on the type. These bipolar cells then signal (or don't) ganglion cells, which continues to propogate th single to the brain where it is processed.

The Ampullae of Lorenzini are electrorecepting organs found on the snout of shark. These tiny pores enter into a mucus filled canal, fillled with glucopolysaccharides, which aids in directing the electrical signal down to the base of the canal where the sensory cells are found. The receptor cells innervate at cranial nerve 7, along with the lateral line systems fish use to detect current flow of water. Rather than sensing its environment, a shark uses it electroreception to pinpoint prey it cannot see. This is especially important due to the positioning of the eyes on the shark. They are on the side of the sharks head. Therefore, when a fish is directly in front of the shark, it cannot see it. Thus, the shark relies its ability to detect electric fields to sense what is directly in front of it.

The Ampullae of Lorenzini are extremely sensitive organs and can detect charges down to a billionth of a volt. This means that the shark can detect cell depolarizations, such as those that occur during the contraction of a muscle. However the voltage of cell depolarizations is actually a much higher voltage than what the ampullae can detect. Rather, these electroreceptors are fine tuned to be able to detect the ions flowing through the gills of other fish. So as long as a fish is alive, moving and breathing, a shark can sense it.