Perfect Paragraph

Overall, each of the figures followed the same formatting style, with one large photo on the left and two smaller photos on top of each other to the right. However besides that similarity, most of the other characteristics of the complete figures are contrasting. The overall resolution and lighting of each of the photos were significantly different. The resolution of Figure 1 seemed blurrier and the lighting appeared overexposed compared to the sharp resolution of Figure 2. Figure 1 contained even, white spacing between each of the panels while Figure 2 had a more significant gap between panel B and C. This links to the sizing of B and C, where the panels in Figure 1 were horizontal in contrast to Figure 2 where the panels were vertical. The letters that marked each panel in Figure 1 were black letters with no background. In comparison, the letters that marked each panel in Figure 2 were black letters with a white square background and a black border. The overall ordering of the panels were switched, therefore A from Figure 1 matches with B from Figure 2.

There are many factors which could have contributed to the differences between the original and replicate figure. The clear difference in lighting could have multiple factors. The time of day could have been different, which would lead to differences in light color, intensity, and the direction of the rays on the plant in the pictures. If the replicate was taken later in the day or early in the morning, that could explain the low light intensity. Weather could also be causing these differences, as the original was taken on a day clear enough for the sun to brightly illuminate everything, the replicate could have been taken on an overcast day which limits light intensity. A difference in camera would also lead to the variation in light, color, focus, and quality of the two figures. A combination of these factors could have also been affecting the different outcomes of the photographs. Unspecific directions in the methods section could have led to different subjects being examined as in panels B, C, and D. Since there was no specifications of the angle the pictures should be taken at, or the distance from the subject this could account for the differences in those features. Not knowing they should have their fingers holding the branch, the individual doing the replicate would not have known to have their fingers included in panel C. If specification was not the problem, lack of thorough reading could have also resulted in the differences, especially when considering two different plants were photographed. 

Genotyping is a common technique learned in the genetic lab used to figure out the genotype of animals form their DNA. A proper genotyping is done in three distinct steps. The first is DNA extraction, the second is PCR, and the third is gel electrophoresis. The first step is DNA extraction. This is typically done using silicon columns. In this method, the lysis buffer and proteinase k is added to the tissue and incubated. The tube is then spun so that the supernatant can be removed without contamination. When this is done, the supernatant is then put into a spin column. It is then spun. This allows for the DNA to bind to the silicon and the rest of the supernatant to be separated from the DNA. The column is then washed using a wash buffer to remove any impurities and the column is then put into a new collection tube and eluted. The eluted solution contains DNA. The DNA is then put into another tube, and buffer, forward primer, reverse primer, MgCl2, and taq Polymerase are added. This is then heated and cooled at the optimal temperature for the gene, allowing for the duplication of the desired DNA. The resulting solution is then put into a well of the gel, and the gel is then ran using electricity. The resulting gel is able to show whether the gene is present or not. However, every gene is different in how it shows in the gel. One of the things that can be done if there is a relatively large amount of soft tissue is to skip on DNA extraction and just boil the tissue at 95 degrees in NaOH, adding tris HCl after. This is a more crude way of extracting DNA however, it is effective in some tissues, such as mouse ear, and often saves time. 

A recent story about a man on an airplane that was saved by a celebrity doctor has given rise to the news of a parasite (tick) that can make you allergic to red meats. "The "hygiene" hypothesis, now several decades old, suggests that with no parasites to fight, the immune system doesn't know when to quit and ends up targeting allergens." The symbiosis between parasites and humans is not well understood. Common allergens such as peanuts, bees, pets, and trees can be detected within the immune system while parasites are not. The fact that our bodies do not deal with every parasite suggests that the body purposely does not hurt specific parasites by turning this response off. Another theory could be that parasites have unique methods to alter their host's immune system. The relationship between a parasite-fighting immune system and the cause of an allergen must come down to similarity within the molecule composition and protein structure. "Using blood serum from parasite-infected people in Ghana, experimental studies finally revealed the first known example of a pollen-like protein present in a parasitic worm that gets targeted by IgE." The results reveal that immunotherapy may prove to be useful as long as the allergen-causing protein.

https://www.smithsonianmag.com/science-nature/why-do-humans-have-allergies-parasite-infections-trigger-180957101/?no-ist

CHIKV also known s Chinkungunya is an almost fatal illness. This is spread by a mosquito, like Zika and dengue.  The most common symptoms of this virus are joint pain along with fever symptoms. It can become very severe, as it can lead to headaches, swelling of limbs and even can be fatal. There are recent outbreaks in the United States, but this virus is primarily spread in parts of Africa, the Caribbean’s and India. Researchers from the University of Bristol and the French National Centre for Scientific Research (CNRS) in Grenoble, France, have come together and created a vaccine that can withstand very warm temperatures.  They worked with a synthetic protein scaffold with no genetic material inside that is still extremely stable, even without refrigeration. The greatest part about their discovery is that they can insert harmless bits of the Chikungunya to generate a mimic to further use as a vaccine. Although they are still figuring out the logistics of it, computers and technology have helped them create a digital model of the vaccine. Intriguingly, because of this great beginning to fight again CHIKV, they can now rapidly engineer similar vaccines that can combat many other infectious diseases.

Abstract. Plants adapts to varying climates based on their varying geographical locations. Photosynthetic rates sometimes vary among plants within a habitat, and across habitats... [and are]...correlated with species composition, habitat preference, or growth rates (Guerevitch, 2006). An experiment is conducted to determine the effects of latitude and elevation on vegetation patterns of Vaccinium vacillans. The density of Vaccinium vacillans is measured in 11 4x4m plots within three sites: Mt. Norwottuck, Amherst, Massachusetts,  Plum Creek, Amherst, Massachusetts and at Deer Brook, Swanton, Vermont. Each site is varying in latitude and elevation. It is predicted that a widespread, common species will show parallel changes in abundance as elevation increases and as latitude increases in New England.

In the tropics between 10 degrees north and south of the equator resides a unique biome known as a tropical jungle. At these latitudes, consistent precipitaion rates fall which exceede 2,000 mm or 79 inches annually with two peaks around late april and october. The intertropical convergence zone (ITCZ) controls these peaks. The ITCZ is a region in the tropics with low average pressures due to the high uplift of warm air. Low air pressures generate large amounts of precipitation, as the data collected in this biome suggests. Temperatures don't vary much here, staying relatively stable around 25 degrees Celsius or 80 degrees Fahrenheit year-round. A tropical jungles stable environment, with little change in both precipitation and temperature, allows species to thrive with little to no stress or disturbance. Approximately 50% of the earth's species are present here, even though it covers only 11% of earths vegetation. However, this lack of stress or disturbance and abundance of life creates a competive enviorment requiring each species to develop a niche niche. 

In the agriculture industry, only a handful of companies own the rights of a few strains of genetically modified (GM) crops. This monopoly over the agriculture space results in abusive behavior, such as lawsuits for patent infringment when farmers re-use GM seed (Bowman v. Monsanto). However, with the advent of realtively inexpensive methods of gene editing, this monopolization could soon come to an end. The expensive process of utilizing agrobacterium-mediated transformation of plants is being replaced by the reasonably priced, more percise method of CRISPR editing. Not only is this an economical and more accurate alternative, but CRISPR modification of crops will not necessarily require the GMO label on the final product-a label that bears a negative connotations in the eyes of consumers. Because of this, small agriculture companies and startups such as Inari in Boston, will soon be able to compete with the likes of Bayer Crop Science, who recently completed its aquisition of Monsanto. The addition of competition in such a centralized field is likely to spark innovation and reduce seed prices for farmers, two outcomes that are welcome news in the agricultural space.

The third goal of this lab is to Identify potential variables that must be controlled for the replicability of the study. For the best results, I will be writing my methods using descriptive and explicit language. Specifying the path I took to the proper plant and taking a picture from the proper angle, will be the first part. I will determine a landmark as a starting point and give detailed notes on the pathing I took to find my plant. The photo angles, especially for the ‘distant shot', will have clear steps and notes on my positioning and height. I will also describe where I am in relation to the plant. This will require detail because it can be very easy to step back and take a photograph of the plant with a completely different background. Another variable to control is the time of day. It is important the person replicating my work takes the photos at a similar time of day to match the shadows and lighting. A third factor I can control is how the final figure will be constructed. Careful instructions will be written for each step, beginning from the software used to the final touches. Methods sections may seem dry and unnecessary, however, having proper notes for every step along the way separates an easily replicable experiment from another.