Writing in Biology

For the treatment regarding the three miRNAs in ovarian cancer associated fibroblasts, I tried to elucidate the downstream targets by which these epigenetic changes of mi-RNAs in CAFs induce epithelial to mesenchymal transition of cancer cells. By reading the literature, I found and described a few pathways. Despite these known pathways, the mechanisms by which mi-RNAs lead to epithelial to mesenchymal transition are likely far more complicated. Mi-RNAs are short, approximately 20 bases in length. Therefore, they are interesting because they often have binding specificity for thousands of genes, meaning they can downregulate the expression for all of these genes. Therefore, there are likely many more pathways that are unknown. Treatment involving mi-RNAs usually evolves from an observational study about miRNA dysregulation, and the reversal of the cancerous phenotype having anti-cancer effects. These studies are sometimes substantial to warrant treatments based on their findings, without figuring out exactly why they work. While it may be startling, proving anti-tumor properties is sometimes enough to garner FDA approval, despite not knowing a mechanism of action. For example, Procarbazine, an FDA approved chemotherapy drug commonly used to treat Hodgkin’s lymphoma, has a mechanism of action that is not fully understood.

Triglycerides are also proposed to have an impact on the development of neuropathy. Triglycerides and obesity correlate with diabetic neuropathy independent of glucose control. Smith and Singleton found that obesity and triglycerides were related to small axon loss whereas hyperglycemia was related to large fiber loss indicating that hypertriglyceridemia and obesity have an independent effect on peripheral neuropathy (8). Wiggin et al analyzed samples from a double-blind placebo clinical trial with Acetyl-L-carnitine (ALC) at two doses.  Since the intervention had no effect, data from three arms (placebo, 1.5 and 3.0 gm doses) were combined.  The investigators found a correlation between elevated triglycerides and mixed small and large myelinated fiber density (MFD).   Further higher triglycerides were associated with those whose neuropathy progressed as evidenced by changes in MFD (9).

           For the work-up, the cooled contents of the rb flask were transferred into a centrifuge tube containing water (1.0 mL, 56.0 mmol). The layers were mixed thoroughly, allowed to resettle, and then the lower aqueous layer was removed into a beaker marked for waste. Saturated aqueous sodium bicarbonate (1.0 mL, 5.4 mmol) was added, the layers were mixed thoroughly the lower aqueous layer was removed into waste.This process was repeated. Saturated aqueous sodium chloride (1.0 mL, 7.9 mmol) was added, the layers were mixed thoroughly, and the lower aqueous layer was removed to waste. The organic layer was transferred into a vial, and five spheres of anhydrous CaCl2 were added to the mixture and swirled until no clumping occurred, then left to stand for about five minutes. The liquid was transferred to a dry, tared vial. The odor was noted, the final mass was measured and recorded,  and IR spectroscopy was performed. 

Metastatic pancreatic adenocarcinoma is driven by cancer stem cells, formation and upregulation of the metastatic niche, EMT, and the largely hypoxic state of the tumor microenvironment (TME). Cancer stem cells are the central drivers of metastasis due to their inherent plasticities and contribute to chemoresistance, functioning of the premetastatic niche, and induction of EMT (Sancho et al. 2016). In the premetastatic niche, extracellular signaling contributes to a TME that facilitates the development of the cancer. EMT allows cancer cells to detach from a tumor site, relocalize, and change their phenotype to a less differentiated state. When tumor growth reaches a critical point, cancerous cells deprive their environments of oxygen, resulting in hypoxia and potential metabolic shifts including the Warburg effect or oxidative phosphorylation (Sancho et al. 2016).

For Ornithology class, we were divided into groups to study bird behavior. Our group became intrigued with the competition of feeding behavior among perching birds and ground foraging birds. The main question that continued to arise was whether there was a competitive relationship between these two groups, the first question being whether perching birds attracted foraging birds or not. As birds perch on a feeder and eat, seeds fall from the feeder to the ground. From this fact, our first goal was to examine if there was a correlation if perching birds being at a feeder leads to ground forager or other unrelated groups to come near the feeder and exhibit interspecie competition. Based on this data, our next question was whether there was a level of competition present among each group and between each group. The number of birds were counted in descrete values to observe how birds interacted with one another.

Fatty acid synthesis is primarily carried out in the cytoplasm of liver cells and involves multiple processes: (1) Acetyl-CoA transport, (2) malonyl-CoA formation, and (3) synthesis cycles. Acetyl-CoA is produced in the mitochondrial matrix and must be transported to the cytoplasm. It is transported indirectly as citrate, which is then converted back to acetyl-CoA once outside. The enzyme acetyl-CoA carboxylase (ACC) then carboxylates the acetyl-CoA to form malonyl-CoA, the direct substrate of fatty acid synthesis. Synthesis is carried out by fatty acid synthase (FAS), an enzyme that acts as a dimer to make two fatty acid chains simultaneously. First, the cysteine amino acid on FAS is primed. Then, sequential cycles of reactions create the fatty acid, each cycle adding two carbons from malonyl-CoA with energy from NADPH. Seven cycles produce a 16-carbon chain, and all fatty acid chains produced by FAS are 16:0. Additional enzymes are then required to elongate and/or desaturate the chain to form other fatty acids. The enzyme desaturase is responsible for adding double bonds, but it is incapable of forming double bonds past the tenth carbon. Therefore, fatty acids with double bonds past the tenth carbon are acquired solely through the diet.

Fatty acid synthesis is mainly carried out in the cytoplasm of liver cells. It is not the reverse of fatty acid oxidation and involves multiple processes: (1) Acetyl-CoA transport, (2) malonyl-CoA formation, and (3) synthesis cycles. Acetyl-CoA is produced in the mitochondrial matrix and must be transported to the cytoplasm. Carbons are transported out to the cytoplasm indirectly as citrate, which is then recreated into acetyl-CoA once outside. The acetyl-CoA is then carboxylated to form malonyl-CoA by the enzyme acetyl-CoA carboxylase (ACC). Malonyl-CoA is the actual direct substrate of fatty acid synthesis. Synthesis is carried out by the enzyme fatty acid synthase (FAS), which acts as a dimer that makes two fatty acid chains at once. First the cysteine amino acid on FAS is primed, and then sequential cycles of reactions create the fatty acid. Each cycle adds two carbons from malonyl-CoA using the energy from NADPH. Seven cycles produce a 16-carbon chain, and all fatty acid chains produced by FAS are 16:0. Elongation and desaturation to create other fatty acids are carried out by additional enzymes. Double bonds are added by the enzyme desaturase; although, human enzymes cannot form double bonds past the tenth carbon. Fatty acids with double bonds past the tenth carbon are acquired solely through diet.

The first biome has a climate diagram similar to that of a tropical rainforest or savanna on Earth, although there are a few key differences. The temperature pattern throughout the year ranges from about 5℃ in the winter months to about 25℃ in the summer months. The precipitation pattern is high throughout the year but drops significantly during the summer months. In a tropical rainforest biome on Earth, there is high precipitation throughout the year but a period of low precipitation in the summer, much like Biome 1 on the mystery planet. Also like Biome 1, the temperature pattern in a tropical rainforest or savanna is relatively constant throughout the year, the values just differ greatly. Based on the temperature values as well as the precipitation pattern, I would expect Biome 1 to be located close to the equator of this planet, provided the planet is farther away from the Sun than Earth is in its solar system, since the temperature range is closer to what would be found in Earth’s more temperate zones. Due to the precipitation pattern, I would expect the vegetation to be similar to the vegetation in Earth’s tropical rainforest biome. However, due to the temperature pattern, I would expect the vegetation to be similar to Earth’s temperate shrubland biome. Therefore, I would expect this biome to have vegetation with lots of foliage due to the precipitation, but I would also expect the vegetation to be able to withstand colder temperatures. Perhaps these plants would have the hardiness of an evergreen tree but the leaves of tropical trees.

The goal of this experiment is to determine whether there is differential expression of the Bradi1g25180 gene between old versus young roots. Seeds were planted in gel and roots were grown for one week. New roots will be defined as the bottom half of the central axis root, while old roots will be defined as the top half of the central axis root. There are eight plants. There will be eight experiments; four of old roots and four of new roots. Each tube will contain either old or young roots from plants 1+2, 3+4, 5+6, or 7+8. The first step is to extract RNA. Once RNA is extracted and quantified using Nanodrop, RT-PCR will be performed. Primers that anneal to exons with an intron in between were made, such that the cDNA product is 261 b.p. long and the gDNA product is 537 b.p. long. This difference will allow us to see differential expression on a gel, because the more cDNA there is, the more RNA was present. High levels of RNA for a gene indicate high expression.

I just did the weekly preparation assignment about poster assessment. The poster that I looked at tried to find a link between google searches for west nile virus and if the virus was present in the area. It was a pretty cool idea, they had an algorithm to predict when and where the next west nile outbreak would be but when they incorporated google trends into the algorithm it became significantly more accurate. The researchers best guess as to why this could be is because if people here about the virus or there are a lot of mosquitoes present people search for the virus. The more people searching it in a specific area is usually fueled by a certain factor. The poster looked very nice overall, it had all of the components that a scientific poster requires. I was not a huge fan of the way that the poster flowed through. It appeared broken up by the two figures in the middle of the poster and the text was in two sections on either side that had little separation. This made it look like there were two massive blocks of text on either side of the poster, that kind of through off the flow when I read it.