Writing in Biology

During the winter season, I often walk by the campus pond on my way to classes along the path from the ILC to the Fine Arts Center. This path is typically surrounded by numerous flocks of geese feeding on grass, and I make multiple observations and inferences as I pass through. Regardless of my distance from the geese, I observe crescendos of honking as I walk along this path. On days I happen to pass closer to the flocks, I observe approximately one goose per flock stop feeding on the grass and crane its neck upwards. On days I pass further away from the flock, I do not observe this behavior. When this behavior occurs, the rest of the flock continues eating. I have also observed that if I make eye contact with this goose, some additional geese in the flock pause their feeding and start to turn towards me as well. From these objective observations, I infer that the goose craning its neck is in charge of the flock in some way, perhaps the alpha male, and is on guard in case I come too close.

Change in pH can have serious effects on the structure of a protein which ultimately changes the function of the protein. Changing pH can affect the charge of ionizable groups of amino acids. Amino acids make up polypeptide chains via peptide bonds. These peptide bonds are not affect by a change in pH, however the alpha amino group at the N-terminus of a polypeptide chain (the subunits of proteins), the alpha carboxyl group at the C-terminus of a polypeptide chain, and the ionizable R groups of acidic and basic amino acids, as well as the ionizable R groups of tyrosine and cysteine. pH is directly related to pKa, this is the amount of base require to react with half of the acid present. Which in this case means at which point the ionizable group will start to become primarily deprotonated. The alpha carboxyl group at the C-terminus has a pKa of 2.2, so whenever the pH is above around 3 every alpha carboxyl group will be deprotonated. The pH of a cell is 7 so most of the times the group has a negative charge. The alpha amino group at the N-terminus has a pKa of 9.5, so unless the pH goes above 9.5 this group will remain protonated with a positive charge which it almost always is in the cell. A lot of ionizable R groups have a pKa of around 6-10 so if the pH of a cell is significantly raised or lowered the R groups will become deprotonated or protonated. This will in turn affect the charges of these groups and disrupt the electrostatic interactions they are taking part in causing the protein to fold differently which alters the function of the protein.

This study examines the long-term effects of exercise treatment in both type 1 and 2 diabetics. The 78 subjects had no signs or symptoms of diabetic neuropathy and their duration of diabetes averaged at 8.7 years. They were randomized into two groups; one group performed a supervised 4 hour per week treadmill session. The other group did not perform any supervised activity for the entire 4 year period of the study. Neurophysiological measurements were taken throughout the study. The exercise group was enrolled in a treadmill walking program. After 4 years there the investigators found specific changes in some, but not all, parameters in clinical characteristics between the two groups. Although the A1C of the exercise group dropped 0.42 points, meanwhile the control group increased 0.14 points. The nerve conduction velocity of the peroneal motor nerve increased significantly in the exercise group. There was no significant increase in nerve conduction velocity for the sural sensory nerve in the exercise group but there was a significant decrease in the control group. In the exercise group, 0% of the participants developed motor neuropathy at the end of the study while 17% of the control group developed motor neuropathy. Meanwhile 6.45% of the exercise group developed sensory neuropathy compared to 29.8% in the control group.

I would advocate for genetic modifications to prevent disease. Some people might argue that gene-editing technology is unnatural and interferes with natural evolution. To this I would argue that humans have already altered their own evolution in significant ways. For example, antibiotics have saved people throughout history from dying of infections, and yet they are also unnatural according to the article ““Pro and Con: Should Gene Editing Be Performed on Human Embryos.” Like antibiotics, gene-editing is also unnatural, but unnatural can be a good thing if it prevents disease and increases human survival. According to the NYT article “These Patients Had Sickle-Cell Disease. Experimental Therapies Might Have Cured Them” clinical trials for sickle cell anemia are already underway and have shown initial success in a few patients. I think there should be more research in gene therapy for single gene disorders such as Sickle Cell Anemia and Cystic Fibrosis than for diseases that are polygenic or have a strong environmental component. The causes of the latter are more complex and might require more than gene modifications to be cured. 

I don’t think we should genetically modify humans for purposes beyond disease prevention. Using gene-editing to select for traits related to appearance and personality to make the perfect human being can come with dire consequences. For one thing, classifying genes as “good” or “bad” is arbitrary. Genes that control psychoticism for example can confer advantages such as creativity or open mindedness (according to the article “How Gene Editing Could Ruin Human Evolution”). The article also mentions that influential people such as Carrie Fisher, David Foster Wallace and Kurt Cobain can benefit society despite them all having psychiatric risks. On a more personal note, artificially selecting genes to make a designer baby would detract from a person’s individuality. According to the Wired article “You’re only human but Your Kids Could be So Much More”, having a baby would turn into a “model building exercise” or a “project.” People would wonder if their successes are because of their own hard work or because they were genetically programmed to succeed. Everyone would choose the same traits that are considered to be the best, and we would no longer be diverse or unique. 

A recent gene editing method called CRISPR-Cas9 is a technology that allows scientists to alter DNA. Using technology like this makes it possible for genetic data to be edited at specific parts of the genome. This editing entails the removing, adding, and altering of current genetic material. CRISPR is short for clustered regularly interspaced short palindromic repeats. Cas9 refers to the associated protein, CRISPR-associated protein 9. This system of gene editing was derived from a naturally occurring system in bacteria. Bacteria can take the genetic material of viruses and produce RNA segments referred to as CRISPR arrays. If the virus attacks again then the bacteria will use the CRISPR arrays to attack the virus DNA, then send the Cas9 protein to cleave the virus DNA, rendering it ineffective. In vitro, the process works similarly. Scientists will create guide strands of RNA with specific sequences to target specific sequences on strands of DNA. Once the DNA has been targeted, the associated enzyme will cleave this region of DNA. After the DNA has been cleaved, the cell’s own repair machinery is used to replace the missing segment. This cleave, then repair process is a huge breakthrough in the field of gene editing, allowing scientists to alter whichever segments of DNA that they can synthesize an RNA strand for.

A microbiome is a very important community of microbes that live in and on the organs of the human body. Microbes living on your organs sounds like cause for concern but the human microbiome is actually very important in both defending the body against disease maintaining normal bodily functions such as digestion. Microbiomes change often, however, if the balance of populations of microbes in the human body are disrupted, then disease may follow. Microbes start to colonize every inch of the body as soon as you are born; the first batch of microbes comes from your mother. If you are born vaginally, you would be covered in your mother’s vaginal microbes. If you are born via a cesarean section, then you would be covered in skin microbes; a different type of microbe entirely. Some microbes in the birth canal actually help an infant digest its first meal. Functions like digestion are not the only purpose of the microbiome. The microbiome also protects you from harmful bacteria and one example of this is acne. Acne is caused by a bacteria called P. acne, that if more prevalent than good microbes, will cause the widespread blemishes observed in people with acne. These imbalances of microbes can be seen in more communities of organisms besides those residing on the face, which is why it is important to remain mindful. Antibiotics, drugs designed to kill bacteria, can be a problem for the balance of healthy microbes. While antibiotics are effective at ridding the body of harmful bacteria, they also kill beneficial bacteria. This collateral damage can often lead to declines in the immune system, especially in children with developing microbiomes. The nuances of the microbiome are becoming a more prevalent research field as we continue to uncover the importance of the film of protective bacteria covering our bodies.

A microbiome is a very important community of microbes that live in and on the organs of the human body. Microbes living on your organs sounds like cause for concern but the human microbiome is actually very important in both defending the body against disease maintaining normal bodily functions such as digestion. Microbiomes change often, however, if the balance of populations of microbes in the human body are disrupted, then disease may follow. Microbes start to colonize every inch of the body as soon as you are born; the first batch of microbes comes from your mother. If you are born vaginally, you would be covered in your mother’s vaginal microbes. If you are born via a cesarean section, then you would be covered in skin microbes; a different type of microbe entirely. Some microbes in the birth canal actually help an infant digest its first meal. Functions like digestion are not the only purpose of the microbiome. The microbiome also protects you from harmful bacteria and one example of this is acne. Acne is caused by a bacteria called P. acne, that if more prevalent than good microbes, will cause the widespread blemishes observed in people with acne. These imbalances of microbes can be seen in more communities of organisms besides those residing on the face, which is why it is important to remain mindful. Antibiotics, drugs designed to kill bacteria, can be a problem for the balance of healthy microbes. While antibiotics are effective at ridding the body of harmful bacteria, they also kill beneficial bacteria. This collateral damage can often lead to declines in the immune system, especially in children with developing microbiomes. The nuances of the microbiome are becoming a more prevalent research field as we continue to uncover the importance of the film of protective bacteria covering our bodies.

The predicted amino acid sequence from the RZW gene of Brachypodium distachyon, was given by two different programs.  FGENESH provides an ab initio method, while Phytozome compares the RZW gene to known expressed tag sequences (ESTs) in B. distachyon.  The predictions differed in one area.  The FGENESH predicted protein had a string of four amino acids: KSLQ, in the middle, while Phytozome predicted that instead of these four, there was a chain of 109 amino acids.  All amino acids before and after this noted difference were the same. Furthermore, two contiguous sequences were made from the bank of ESTs. These sequences had a gap of a few hundred base pairs in between them; there was a part of the gene that was unaccounted for by ESTs.  This may help to explain the difference in predicted protein sequence. Either way, the Phytozome predicted protein sequence is trusted more, because it analyzes cDNA libraries, as opposed to just known trends in mRNA splicing.

Blood flows through the heart from the atriums to the ventricles. Blood first comes into the heart through the superior and inferior vena cava into the right atrium. The right atrium then pumps the blood through the right AV valve into the right ventricle. From the right ventricle, the blood is pumped into the pulmonary artery to the lungs and back through the pulmonary vein. It enters the left atrium and then is pumped through the left AV valve into the left ventricle. This is the largest chamber of the heart. It pumps the blood to the entire body. 

It is a fact that older adults do not sleep as well as younger adults. The question is, do older adults simply need less sleep or are they unable to generate the sleep that is needed? As we age, sleep duration, sleep stages, and quantity/quality of sleep oscillations change. REM sleep in older adults reportedly reduce however are minimal compared to the big reduction in NREM sleep. Also, the number of daytime naps increase by 10% in adults 55-64 and 25% of adults ages 75-84. It is also important to note that these naps, especially the naps in the 75-84 age group, are unplanned. These are not a universal feature of old age though and older adults don’t all suffer from sleep deprivation at the same degree. This information is vital for me to consider in the lab I am working in this semester, the Somneuro Lab.