Drafts

Climate change, specifically global warming, has been associated with increases in atmospheric CO₂ levels. Fixation of this airborne carbon dioxide and subsequent removal from the atmosphere is possible, though impractical due to little or no economic incentive. Hepburn et al. counter this position with viable utilization of captured CO₂ that yield decent economic return. Some of these utilities include chemicals (methanol, urea, plastics), fuels (methanol/methane), microalgae products (biofuels, biomass, aquaculture feed), and concrete and various building materials¹. In addition to these ventures, Hepburn et al. also lay out the probability of re-release of carbon dioxide from these various applications¹.

(1) Hepburn, C., Adlen, E., Beddington, J. et al. The technological and economic prospects for CO₂ utilization and removal. Nature 575, 87–97 (2019) doi:10.1038/s41586-019-1681-6

Alcohol-related liver disease can result in alcoholic hepatitis, a diseased and inflamed state of the liver. In mice, the gut microbiome produces toxins that contribute to liver damage in response to ethanol. Duan et al. identified a two-unit exotoxin cytolysin, excreted by Enterococcus faecalis as a cause of injury to the liver¹. In patients with alcohol-related liver disease, Duan et al. also found increased numbers of E. faecalis in these patients' microbiomes¹. Analyzing this further, Duan et al. used E. faecalis targeting bacteriophages in humanized mice with ethanol-induced liver disease¹. They found that through this treatment, ethanol-induced liver disease was abolished in these test subjects, though more comprehensive testing must be performed to determine the true efficacy of this treatment.

(1) Duan, Y., Llorente, C., Lang, S. et al. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature (2019) doi:10.1038/s41586-019-1742-x

Embryosis is the formation of an embryo. There are two main steps to this process: blastulation, and gastrolation. The begining of this process is the sperm and egg cell fusion to form a zygote. This is when the genetic material merges and all cells are pluripotent. Next there is clevage, compaction, and differentiation forming the blastocyte. The overall size of the blastocyte is not much bigger than the zygote because of compaction. There are many more cells in the blastocyte because of clevage, and some differentiation between the inner cell mass and surrounding cells. Gastrolation is the formation of three distinct layers in the blastocyte which will differentiate. The top layer is the ectoderm, the middle layer is the mesoderm, and the bottom layer is the endoderm. The ectoderm differentiates into the nervous system and the skin. The mesoderm differentiates into the muscles; the endoderm differentiates into the internal organs. This process is virtually the same for all mamals. The outcome is very different because of the genetic information fused, resulting in a wide range of organisms.

Dio lox sites are double inverted orientation lox sites. This is a mechanism used by neurobiologists to insert different genes intot the brain of model organisms. The lox sites surround a gene that you want to insert. The gene is in nonsense orientation, meaning it will not be expressed unless it is in the presence of CRE recombinase which is able to flip the gene in certain circumstances. If there are dio lox sites (in the presence of CRE recombinase), then this is a two step process to perminantly flip the transgene into the sense direction to be expressed. The first step is one set of lox sites are brought togehter by the CRE recombinase. One of the lox sites the CRE is acting on will be inserted to the other side of the transgene and the transgene will be flipped. This leaves three lox sites on one side of the transgene, and one lox site on the other side. Of the tree lox sites on one side, two are in a pair and facing the same direction. These lox site pairs, in the presense of CRE will be spliced out of the gene sequence. The splicing of the lox sites from the gene sequence leaves two lox sites from different pairs in each sequence of DNA (one splices, and one with the transgene). Ultimately, this is a perminant change to the DNA because lox sites from different pairs cannot work together, the CRE will not recognize them as a pair. Therefore, the perminant flip will allow for the expression of the transgene in the cells that express CRE recombinase.

Hunger and body weight are negative feedback loops regulated by the brain. The cycles are controlled by leptin and grellin hormones. Leptin POMC neurons signal for satiety by producing alphaMSH. AGRP neurons signals for hunger. The leptin hormone is produced by fat stores and excites the POMC neurons, signals for satiety. Leptin activates AGRP neurons, signaling for hunger. This corresponds with the hunger-sateity curve. When energy is high, fat stores release leptin to signal sateity. When energy is low, the gut releases ghrelin to signal hunger. This allows the brain to regulate when we eat based on energy and food stores.

To accomplish this, we followed the protocol from ThermoFisher titled, “ER-Tracker™ Dyes for Live-Cell Endoplasmic Reticulum Labeling”.  Initially we incubated the plate of cells at 370C for 30 minutes. Following the incubation period, the cells were again rinsed with PBS and given media without CO2. The resultant cells appeared to over-fluoresce in unexpected locations so we repeated the procedure. We decided to incubated for 20 minutes in the staining mixture to prevent the overfluorescense. The cells incubated for 20 minutes appeared to clearly mark parts of the ER. These distinct sections of the ER marked by the tracker did not seem to distinctly overlap with the portions of the ER marked by the plasmid. However, we can confidently say that the plasmid marked the ER, just not the same aspects as the ER tracker did.

We nucleofected Sec61 beta plasmid labeled with mCherry into LLC-Pk1 cells in order to mark the endoplasmic reticulum. To verify that the plasmid marked the ER, we planned to use an ER tracker to stain the ER. Unfortunately, both the ER tracker and our labelled cells fluoresced mCherry. We thus chose to stain parental LLC-Pk1 cells with the ER tracker, with the understanding that if we stained our nucleofected cells with the marker, it would be difficult to distinguish between fluorescence signal from the plasmid or the tracker. We compared the overall ER morphology from each set of cells to determine if they mark relatively the same location.

Chemistry is at the heart of all bodily processes. Understanding these processes and how they work is crucial for finding solutions to medical problems. Even something as minor as heartburn can be broken down into acid-base chemistry. When you take Tums, the active ingredient is calcium carbonate (CaCO3), which can neutralizer the overproduced stomach acids and protect the lining of the esophagus from damage. Pharmaceutical drugs rely on knowledge of chemical processes and biological pathways in order to produce the desired effect. Usually, there are many processes happening at once and sometimes drugs have other, undesired side effects along with the desired ones. Trying to minimize secondary effects plays a major part in designing pharmaceutical drugs, and often can become a big problem when trying to get a drug into production. It is hard to minimize other effects often because the unwanted effects could be happening due to a multitude of reasons. This is why getting a drug to be approved for human consumption and mass-produced can be a very long process.

I have always wondered how the alcohol and tobacco industries promote their products. Is it through person to person? Or social media? Maybe both? These two industries are also largely on social media promoting their topics, and this is where they have a large similarity. In a study called “Booze and Butts”, scientists discovered 14 of 73 (19%) magazine covers featured alcohol; 581 of 1558 (37%) magazine articles mentioned alcohol; 119 of 444 (27%) tobacco ads showed alcohol images; and 57 of 695 (8%) non-tobacco ads portrayed alcohol. There is no better way to enlarge the industries than putting these products on a magazine cover, as psychology has said that a person is more likely to buy it if they have seen it in a famous magazine/movie/show etc. 

Performing this experiment could lead us to results that will benefit farmers and society from an agricultural standpoint. If the results turn out as predicted and seeds with no seed coat germinate faster, we could apply this information to crop production. The application of the seed coat removal technique in agriculture could benefit people economically and environmentally. If the results do not turn out as predicted, i.e. the seeds fail to germinate or it has no effect on germination rates, this will help us understand crop production further to make better decisions in the future. We could then conclude if the seed coat is or is not important for success rates of plants and crops, and use this information to our advantage in the future of agriculture.