Writing in Biology

The American Dream is something that a lot of people hold sacred. Many American’s and people who come to America cling onto the dream so as to have some hope for success. The definition of the American Dream according to the book “Chasing the American Dream” by Mark Rank has three parts. First, you have the opportunity to follow your passions. Second, if you work hard you will be successful economically. Lastly, being able to successfully tackle your problems, and have hope and optimism. These definitions were formed according to people’s answers on what the American dream is. Do these definitions really hold true to this day? People who have money would likely tell you yes. You would find a different answer from poverty level Americans.

The methods project requires students to construct a multi-panel scientific figure of an interspecific interaction on the UMass Amherst campus and write a detailed methods section describing how it will be made. Another student will then follow those methods and try to recreate the original figure. Because a primary goal of science is replication, the goal of this project is to write a method section with enough detail to allow another student to reproduce the same results as the orignial. This project also promotes critical thinking skills as it requires students to distinguish differences in observations and inferences by comparing and contrasting the original figure to the replicate and by helping students to think about what potential factors need to be controlled in the expirement. 

The interspecific interaction in this project is a tree and moss. Because another student has to recreate it, the two organisms should be immobile in order to allow relocation of the same organisms. The location of the organisms are limited to the UMass Amherst campus, however it is also important to make the location of the interaction of the organisms accessible. Therefore, the interaction between the tree and the moss will be near the ground making it accessible to all heights. Specific distances, camera angles, and body positions will also be factors that need to remain constant to recreate the image. Controlling these variables will help allow for similar amounts and areas of background. It will also keep the proportions of the images similar. 

Lassa virus is a very severe virus that kills nearly 20% of those infected with it. The most interesting thing about this virus is that it is rarely spread from human to human. It is mostly spread through a vector, which in the case of Lassa virus are rodents. This virus is also primarily spread in places where people are in close contact with rodents. In a area in which rats or mice travel from home to home. The virus doesn’t affect the rodents it just lives in them, so they are essentially a reservoir of the virus, they just keep giving and giving. This is very scary in countries where sanitation is poor and rodent control is minimal. Another problem is the virus can live in the rodents experiments and saliva. So when a rodent sneaks into a house and maybe takes a bite out a loaf of bread and people don’t notice or choose to eat it anyways because that is their only food source they can become infected with the Lassa virus. The problem why Lassa is so bad is because it just seems like a common cold or flu for a while so it goes undiagnosed relatively often. But after a certain period of time those infect start to develop a hemorrhagic fever. This means that blood vessels begin to break and host starts internally bleeding. This can cause a lot of internal problems and also causes the body to become rapidly dehydrated. Blood also comes out of the body's orifices. Something that can further transmit the disease.  

The lab, "Restriction Enzyme Digestion of DNA" was done to observe how restriction enzymes function in DNA.
Different restriction enzymes were used to compare the difference in the DNA. The
method of gel electrophoresis was used; however, the data did not appear properly
because the bans on the gel did not appear. There was no observable evidence that could support
that different restriction enzymes create different typr of DNA fragments.

The journal I viewed for homework was for aquatic mammals. The intructions for submitting writings was on their websites homepage. Submittions they accept include full articles, reports, notes, and letters to the editor. It says that the journal accepts review papers but authors have to directly contact the editors. The editors of the journal offer "early stage of manuscript preparation" consultations if the subject material make it difficult to follow formatting instructions and the paper is 25 or more printed pages. The journal requires manuscripts to be in a Word document and not a PDF, to have a cover letter attached, and any figures and tables included as a separate file when submitted.

Just like babies enjoy being rocked to sleep, apparently adults do too. There is a new study that suggests that rocking puts adults to sleep faster and makes their slumber deeper. These adults were also found to have much sharper memories the next morning. This tips at first seem to solely just sleep aids, however, they also may be telling of how the brain refreshes itself every night. To test this, researchers built a custom made rocking bed and analyzed the quality of participants naps. The researchers measure the people’s brain activity by EEG which can spot electrical signs of certain sleep stages. They believe rocking while asleep might be helpful to people with insomnia compared to sleeping pills.

Exergonic reactions are spontaneous, while endergonic reactions are not. However, it is not the free energy change that determines the rate of a reaction. The rate of a reaction is determined by the activation energy instead. An exergonic reaction can be slow, while an endergonic reaction is fast. The activation energy is the energy needed to reach the transition state between reactants and products, and all reactions require activation energy, even exergonic reactions. Reactions with smaller activation energies have faster rates than those with larger activation energies. With a high activation energy, fewer moleules have enough energy to reach the transition state, causing the reaction to proceed slower. When the activation energy is lower, more molecules can easily reach the transition state, accelerating the reaction. This is precisely how enzymes work to speed up a reaction: They lower the activation energy of the reaction. They do so by stabilizing the structure of the transition state, which then requires less energy to be reached. Enzymes do not affect the free energies of the substrates or products, and they do not alter the equilibrium of a reaction. They simply allow equilibrium to be reached quicker. Enzymes can enhance the rate of a reaction in many ways. They can form favorable interactions with the transition state in its active site. It can also orient two subtrates to react easier. An enzyme can also directly participate in the reaction, or it can strain the bonds in the reactant(s). Enzymes usually use more than one of these strategies to stabilize the transition state, lower the activation energy, and speed up a mechanism. 

The paper investigates the divergence of cephalopods. The limited fossil record makes it difficult to find divergence times and patterns. The researchers used molecular clocking, a technique to track the timing of when groups in the cephalopod phylogeny split off from one another. Molecular clocking measures genetic mutations over time in different groups to show measure how they evolve differently, and this data is subsequently compared to their fossil records. The paper showed that cephalopods diverged during the Mesozoic Revolution, 160-100 millions of years ago. During this time there were not only dinosaurs above land, but there were also dramatic changes below the sea caused by competition. Many adaptations arose around this time in response to the competition. For example, cephalopods lost their shells, which made them more lightweight and improved their agility. Predator-prey arms races influenced many of the adaptations that arose among cephalopods. The researchers tracked when these adaptations came into existence in different groups in addition to the rate of diversification.   

The paper talks about the divergence of cephalopods. The limited fossil record makes it difficult to find divergence times and patterns. The researchers used molecular clocking to figure out where groups split off from one another. Molecular clocking measures genetic mutations over time in different groups to show measure how they evolve differently, and this data is subsequently compared to their fossil records. Cephalopods diverged during the Mesozoic Revolution, 160-100 millions of years ago. During this time there were not only dinosaurs above land, but there were also dramatic changes below the sea caused by competition. Many adaptations arose around this time in response to the competition. For example, cephalopods lost their shells. The researchers tracked when these adaptations came into existence in in addition to the rate of diversification.   

You could use antibodies specific to cdc20 protein to see if it is expressed in the Naegleria. The primary antibodies would bind to cdc20 (if it is present) and the secondary antibodies would bind to the constant region of the primary antibodies. Using polyclonal antibodies as the primary antibody would be a good idea because they can detect low expressing proteins. If we detect cdc20 protein in our experimental group, then the gene silencing and RNAi didn't work. If we do not detect cdc20, then it was silenced, which is what we expect. In our negative control, since cdc20 is not silenced, we expect detection of it. Antibodies can therefore help us make sure that any changes in phenotype between the negative control and the experimental group are because we silenced cdc20.