Writing in Biology

All tetrapods have the same body layout, or plan. This is further striking evidence for common descent. Even fish have remnants of limbs from their ancestors. Additionally, animals share similarities in embryonic development. This abundant evidence supports another main theme in Your Inner Fish, that similarities between animals can be explained with common descent. Shubin makes this work of scientific literature more readable for the average person by using reasonable prose and frequent humor. Because of this, I believe this was an extremely effective book. One of the most difficult challenges a scientific author can face is having their book not be read because it is too dense and dull. Shubin wrote a novel about the evolution of the human body and made it enjoyable for the average person, a remarkable feat.

These researchers studied wolf spiders and the relation between mating success and predation. Male wolf spiders are known to court females by drumming dry leaves with their abdomen. However, this action is energetically demanding and poses mortality costs. To study wolf spiders, they constructed a plastic arena and filled it with dry birch leaves. Three males and one female were placed inside, their behaviors were measured and analyzed until the female responded to one of the males. Then a lizard was introduced into the arena and the rank in which the males were predated was determined. The researchers concluded that higher drumming rates benefited males by increasing their mating success. However, mate searching and drumming also directly increased predation risk. This experiment is similar to Endler’s because it deals with the same sexual selection and predation balance. It shows that Endler’s experiments and conclusions regarding guppies can be applied to more species.

For centuries, we have studied cancer and the affects it bestows upon the human body. Today, we try a variety of methods to tackle cancer and beat it. For our project, we decided to focus our attention on lung cancer. In specifically, non-small cell lung cancer. According to the American Cancer Society about 80%-85% suffer from non-small cell lung cancer. Squamous cell carcinoma, adenocarcinoma, and large cell carcinoma are subtypes of non-small cell lung cancer (NSCLC). We will be focusing on KRAS and its association with lung adenocarcinoma. In addition, we will also be discussing Keap1 and AATF. One challenge will be facing during our research, is in delivering a treatment that would only target the cancer cells. One idea we are looking into at this moment is to create a drug that will be delivered intravenous. We will be targeting the lungs via the pulmonary vein. Non-small cell lung cancer is a type of cancer which we will be able to build off since it is also known to be metastatic. 

Human activities have been responsible for many of the major changes in the global climate. The major human activity responsible for these drastic changes is the burning of fossil fuels, which contributes to massive amounts of carbon dioxide in our atmosphere. As a result to the high levels of carbon dioxide in the air, the ocean acts like a carbon dioxide sink, meaning it absorbs a large amount of carbon dioxide. The reason why the ocean is able to absorb so much carbon dioxide is because carbon dioxide readily dissolves in water and there is a continual cycling of equilibration between the levels of carbon dioxide in the atmosphere and in the ocean. Increased levels of carbon dioxide in the ocean has many negative effects, but the two most significant impacts include increased acidity and decreased formation of aragonite.

The Neuron Doctrine resulting from Cajal's discovery took over 40 years to be confirmed. Cajal and Golgi were both awarded the 1906 Nobel Prize for Physiology or Medicine. Cajal believed that neurons communicated by contact while Golgi thought the nervous system was one contiuous network. These two ideas went against each other until the electron microscope was invented. The electron microscope allowed scientists to have a closer look at how neurons actually communicated. It was confirmed then that Cajal was right about neurons communicating by contact. The Neuron Doctrine stating that neurons are the basic unit in the network of discrete individual cells in the nervous system was validated in the 1950s. 

Over the past few semesters, excelling in courses such as Biology of Cancer and AIDS, Genetics, and Cell and Molecular Biology has expanded my skills and knowledge and excited me about the possibility of doing research related to oncology. Last summer I received tremendous experience and exposure in the field of oncology, shadowing a pulmonologist. I was able to review malignant CT scans, observe various procedures and sit-in on Thoracic Pulmonology Board meetings at New York Presbyterian – Queens. After gaining experience in the field of oncology both academically and clinically, I am interested in gaining valuable research experience as well.

One pathway for protein misfolding and pathogenesis is improper degradation of proteins. Improper degradation occurs when proteins that are partially functional and can actually benefit cellular processes are degraded despite it being detrimental to the cell. This is seen in the case of cystic fibrosis, where a deletion of a phenylalanine in CFTR leads to partial functionality but is still targeted for degradation by CHIP, a molecular chaperone which ubiquitylates the protein. CFTR is an important membrane channel for the production of mucus, which is why this improper degradation is seen in a large number of cystic fibrosis patients.  Another way in which improper folding can lead to disease is through improper localization. Improper localization occurs when misfolded proteins cannot get to where they need to go, leading to not only a loss-of-function but potential toxicity if aggregated in the wrong place. One example of this is misfolded antitrypsin, which becomes retained in the ER of liver cells and accumulates, preventing synthesis of other proteins resulting in liver damage. Also, since antitrypsin does not get secreted to its proper location, it is unable to inhibit protease activity in the lungs leading to damage in the alveoli and emphysema. Another mechanism for pathogenesis as a result of protein misfolding is dominant-negative mutations. Dominant-negative mutations are characterized by mutant proteins that compromise the function of wild-type proteins, most often in a dimer or quaternary structure. An example of this process is seen in the connective tissue disorder epidermolysis bullosa simplex. When mutant forms of keratin proteins are present, they disrupt the function of the entire keratin composed filament, leading to fragile skin that blisters easily in response to minor friction. Gain of toxic function and amyloid accumulation are two other mechanisms for pathogenesis as a result of misfolding and play a big role in neurodegenerative disorders.

The question whether an organism is intrinsic is a very subjective one. To be intrinsic is to be essential within itself; unlike instrumental which is to be useful to others. In a sense, every living thing has intrinsic value just in the fact that it is living because there is value in life. However, it seems that some organisms may hold more value than others. A good way to determine how high an organism’s value is, might be looking at how long it has existed on this planet and how essential it is for life on this planet. Based on this, single celled organisms like bacteria are the most intrinsic, before them no life existed and without them no life would exist. Bacteria allowed oxygen to accumulate which led to more complex organisms, or prokaryotes, to evolve. The next large step was plants and trees and their appearance seems to jumpstart the evolution of many of the more advanced organisms around today.

In this article, researchers wanted to learn about the conformational changes of Cas9. Conformation changes can be caused by binding of single guide RNA (sgRNA). These researchers wanted to figure out which molecular components of sgRNA caused the conformation change in Cas9 from inactive to active. In order to do that, the researchers removed different parts of the sgRNA to see how much it changed the change in conformation. When they removed the entire target recognition sequence, the sgRNA was unable to find the Cas9 and there was no change in conformation. However, when they only removed pieces of the recognition sequence, there was some conformational change. This showed that the target recognition sequence could still work if there was some pieces missing, although it would not work consistently. In addition to that, they tried removing the hairpins at the 3’ end of the sgRNA. When they removed the hairpins, they observed intermediate levels of conformation change. These intermediate levels of conformation change indicate that there was incoverting from closed to open in the Cas9 sample.

- The researchers in this study are trying to treat the motor problems and issues associated with the Parkinson’s disease. Parkinson’s disease is caused by a lack of dopamine, which is a neurotransmitter in the brain. Dopamine is directly connected to movement, thus a lack of dopamine can cause some motor issues. As stated in article, “a low level of dopamine causes the basal ganglia to severely inhibit target neurons in the thalamus, called an inhibition.”

- Optogenetics is the usage of lights to control specific target neurons in the brain. The scientists found out that when signals from are more active in the basal ganglia, the neurons in the thalamus become hyperactive. This hyperaction causes the muscle stiffness and muscle tremors that are usually seen with parkinson’s patients. However, when they used the light to suppress this hyperactivity, movement in the mice became normal again.

- Based on the results, I think the light treatment did in fact cure the motor issues in the mice with parkinson’s disease. However, this treatment was used only to confirm that this certain hyperactivity of neurons was the cause of the muscle tremors. As a result, this study was more for a research purpose than a treatment purpose.