Writing in Biology

Today in Mammalogy lab, we looked at Order Cetacea, which is in the Superorder Cetartiodactyla. Order Cetacea is one of the most highly specialized orders of mammals, as it contains whales and dolphins, which are completely aquatic. All cetaceans share distance features: they all have telescoping skull bones, which is the stretching and overlapping the skull bones that occurs when the nasals are at the top of the skull; they all have external nares on the top of the skull; they all have compressed cervical vertebrae; they all have dorso-ventrally flattened tails with horizontal flukes; and they all live in the Oceanic zone, which—broadly speaking—is all open oceans. The two suborders in Order Cetacea are Suborder Mysticeti (baleen whales) and Suborder Odontoceti (toothed whales). The main difference in these two Suborders is that, unlike Odontoceti, Mysticeti have no teeth; instead they have a filter-feeding system called a baleen, which they use to filter plankton out of the water to eat. We looked at two families within S. Mysticeti, F. Balaenidae and F. Balaenopteridae. F. Balaenidae are the right whales and bowheads, and are distinguishable by their long baleen and stock bodies, their smooth throats, and their lack of a dorsal fin. F. Balaenopteridae on the other hand are the humpback whales, mink whales, rorquals etc. These have a short baleen, a long and streamlined body, grooves on their throats, and a small dorsal fin.

Our unknown gene’s protein sequence was compared for similarities to other proteins by performing a Protein BLAST with the same algorithm parameters as the previous search. The “nonredundant protein” database was searched. This search strategy was saved. In the output, matches that seem false were noted. Back at the blastp page, the searches were sequentially limited to: Brachypodium, plants, animals, insects, mammals, fungi, bacteria, archaebacteria, saving the search strategies every time. The extent to which our protein appears among living organisms was noted.

Library research of the unknown gene was performed, first by expanding the descriptions of the conserved domains on the NCBI Protein BLAST output. The Phytozome predicted amino acid sequence was then entered into the European Bioinformatics Institute website, and information and publications were found there. Further research was performed on the Strubbelig-Receptor Family 7 (SRF7) and 6 (SRF6) that were highly similar to our unknown gene.

Vertex Pharmaceuticals is a global biotechnology company that continuously invests in scientific innovation to develop transformative medicines for patients living with life-threatening diseases. The company offers a wide variety of summer internship programs within several departments, allowing for interdisciplinary collaboration and opportunities to work alongside first-class innovators in medicine. Scientific research is an essential component in the advancement of healthcare as it can provide important information about disease trends, outcomes of treatment and functional abilities. Vertex Pharmaceuticals has more than a dozen ongoing research programs focused on targeting underlying mechanisms of a variety of serious diseases. 

If there is a new retrovirus that will cause domestic dogs to become extinct, than the smartest move would be to save the Sauki breed of dog. The Saluki is not only one of the oldest breeds dating back 10,000 years, but the breed is genetically very close to wolves. Saving a pregnant Saluki mother and her pups would ensure that the dog species survive this epidemic, and lead way to thriving domestic dog species once again.

    As one of the oldest breeds of dogs in the world, the slim and rugged Saluki was a hunting hound used for thousands of years. With a greyhound-like build, these dogs combine long legs, a relatively narrow body, a small waist and long tail. They are swift and agile sprinters who love the thrill of a chase. Although appearing leggy and slim, these dogs are strong and perfectly balanced, making perfect athletes. This breed is highly adaptable and able to live in almost any climate. Typically breeding with non-salukis was forbidden to allow the Saluki to remain unchanged for thousands of years, however given its closeness to wolves, it is possible this dog could be bred with wolves to preserve the agility and essence of dogs. Being that this breed has thrived for thousands of years and can withstand many climates, Salukis have proven to be a dependable, highly resilient breed that would be able to survive for several more thousand years with this vaccine. Additionally, given the Saluki perfect physique to hunt and run, this would be a great animal that would be easy to train, and could hunt for humans if need be. What if this fatal disease eventually spreads to humans? It would be essential to have an animal that could not only withstand this epidemic, but also help provide food and comfort to humans.

In this experiment, cyclohexene was synthesized via the dehydration of cyclohexanol using 85% phosphoric acid. First, 0.5 mol phosphoric acid and 2.003 g of cyclohexanol formed a mixture and proceeded through fractional distillation. The experimental boiling point was measured to be 68.5℃.

    Two functional tests were used to determine which functional groups were present. In the first test, bromine in dichloromethane was added to cyclohexene product in a vial and into another separate vial containing cyclohexane. The vial containing the cyclohexene observed no change in color, which concludes that the compound contained an alkene because the reaction between bromine and alkene formed colorless dibromide. On the other hand, alkanes react slower with bromine by free radical mechanism initiated by light, which explains the color change of red-brownish. In the second test with 1% potassium permanganate and 10% sulfuric acid, the vial containing cyclohexene had no color change, however a brown precipitate was observed after all the drops were administered. The precipitate formed was manganese dioxide, which forms between reactions of potassium permanganate and alkenes. Lastly, the vial with cyclohexane turned purple because the potassium permanganate did not react with alkanes.

The topic that has intrigued me the most so far in the semester is Chapter 12 on Predation. This chapter included the several types of trophic interactions in which one species consumes another species. We categorized the different types of predator-prey relationships into carnivory, herbivory, and parasitism, and investigated the effects of selective pressures that the predator and prey species have on each other. This subject interests me because it is a basic topic I have been taught since Middle School in biology, however it is far more complex than I originally thought, so I am excited to continue to learn further details. There is an issue currently about rodent pesticides having not only a drastic effect on rodent populations but this also causing harm to the predator birds. I will be working with predator birds this summer, and the ones who are impacted by the decline in rodents, so it will be interesting to apply what I am learning about selective pressures and populations dynamics to this field.

Learning about predation has changed my view on ecology because I did not realize the extent that species can adapt in response to selective pressures. Herbivores and predators exert selective pressures on prey such as armor exterior, appearing toxic, physical defenses, or mimicry. But then predators and herbivores adapt to overcome prey defenses through physical features (snakes can unhinge jaw, eat anything), toxins, mimicry (crypsis), or detoxification. So it is interesting to see the reason certain species have particular phenotypes is because of these predation selective pressures.

Using the spinach leaves, we extracted the chloroplasts and observed the rate of photosynthesis in various concentrations of water, with a control group in DI water, and two experimental groups- one in tap water, the other in salt water. The rate of the light-dependent reactions was monitored by comparing the absorbance of light in a spectrophotometer at 600 nanometers. As the DCPIP used in the experiment is reduced, the absorbance of light decreases since the first stage of photosynthesis involves the extraction of electrons from water by light energy. Knowing this, if the concentration of water increases within the plant cell, then the rate of the light-dependent reactions should increase as plants require water in the first step of photosynthesis. If our hypothesis is correct, the data would reveal that the chloroplasts exposed to tap water have a significantly lower absorbance over time than the chloroplasts exposed to salt water, where the concentration of H2O is less.

Epilepsy is the fourth most common disorder of the Central Nervous System. It occurs in patients of all ages but is most commonly experienced in childhood or late adulthood (Shaikh et al., 2018). It is characterized by recurrent, spontaneous episodes of excessive electrical discharge, in the brain, called seizures. (Cunliffe, 2015). The effects of epilepsy range from temporary loss of consciousness, or abnormal motor activity observed in minor involuntary movements, to whole-body convulsions (Cunliffe et al., 2012). Problems could also be psychological in nature, experienced by patients as anxiety and depression (Shaikh et al., 2018). Persistent, prolonged seizures often cause further damage to the CNS, affecting not just the quality of life for patients but also for their carers, thus revealing the far-reaching effects of the disorder. While brain abnormalities and the manifestation of brain lesions, such as brain tumors, do play roles in triggering epileptic symptoms, many forms of epilepsy are due to genetic factors (Reid et al., 2009). About 1% of the general population suffers from epilepsy but one-third of patients are unable to benefit from available treatment due to the nature of their disorder (Cunliffe et al., 2015). Some patients are unable to respond to anti-epileptic drugs (AEDs) due to some level of pharmacoresistance while others experience adverse side effects. This necessitates the exploration of new pathways through which epilepsy may occur and development of novel therapies to combat epilepsy with greater efficacy.

Enzymes work to speed up the rates of reaction. This is done by lowering the activation energy, or the energy needed to reach the transitition state. Activator increased the acitivity of enzymes while inhibitors decrease the activity of enzymes. Inhibitors can be classified as reversible or irreversible. Reversible inhibitors are changes to the enzyme that are not permanet. They include: competitive, uncompetitive, mixed, and noncompetitive (which are a type of mixed). Competitive inhibitor binds to the same place as the substrate, the active site. Inhibition can be overcome at high substrate concentrations. Vmax is not effected but Km increases. Uncompetitive inhibitors bind to the enzyme-substrate complex and cannot be overcome at high substrate concentration. Vmax and Km both decrease. Mixed and noncompetitive inhibitors can bind to the enzyme or the enzyme-substrate. They decrease the Vmax and do not change the Km. Irreversible inhibitors cannot be removed from the enzyme, instead the whole protein would have to be denatured to undo the changes made.