Drafts

The level one headings in both articles include the usual of Abstract, Introduction, Materials and Methods, Results, and Discussion. In Olenin’s article, there are level 2 headings within the Introduction such as “Rate of secondary spread within the Baltic Sea”. In Knapp’s article, there are level 2 headings within the Materials and Methods such as “Species Selection.”

Each section is structured with paragraphs. The abstract summarizes the whole article including the results of the scientific study in one paragraph. The introduction introduces terminology needed in order to understand what the article will be talking about. It includes background and the question the article is looking to answer. Materials and Methods describes the procedure that was done for the study. The results report all the main findings. The discussion includes interpretation of the findings. The first paragraph in each section plays a role in introducing background needed to be known by readers in order to understand why the scientists did what they did for the studies and experiments.

There are topic sentences in the paragraphs of the articles. There are logical flows of ideas. The ideas are organized from a big picture into more detailed information in order to understand the topic and research. Once all the details are put together logically, each paragraph ends with a closing sentence to continue on to the next paragraph or section.

One specific paragraph in Non-native species and Rates of Spread that flows exceptionally well is that regarding the New Zealand mud snail, Potamopyrgus antipodarum. First the authors give background on the migration of the mud snail over time, then going into specifics on rates and dates. They then go into the significance of this non-native species and its distinction from others in the area. In Origin Matters, one paragraph that was written very clearly was that regarding the multiple models they used in the experiment. They provided sufficient details and descriptions for a methods paragraph and also clearly stated the purpose for using multiple models in their experiment.

Overall, systems modeling provides a mathematical and holistic view on the dynamic range of effects that various actions may result in. This integrative modeling is an interictal component of achieving the SDGs, due to their highly integrative nature. The development of a modeling system specifically designed to aid in the completion of the SDGs would allow all sectors that impact public health and well-being, both large and small, to be examined and analyzed, providing a comprehensive outlook on a policy’s full impact on the earth and society. Systems modeling provides a heightened level of confidence to policy makers and citizens alike when implementing new systemic changes and allows for the effects of these changes to be explored more deeply before enacting new policies. By testing various policies individually and in combination, policy enactors are able to which policies to put forth in conjunction with others in order to attain the best result, and which aspects to omit.   

Today in my Anthropology Human Anatomy class, we explored the human heart. Here are some of my notes from class:
- walls of atria are very thin, ventricles thicker b/c have to work against gravity, blood enters here goes through pulmonary semilunar valves and through the pulmonary trunk and pulmonary arteries (right and left) to get oxygenated at the lungs
- right ventricle wall (And left) have rigids called Trabeculae carnae (bundles of myocardium)
Function: Their structure is important to their role. Had the inner surface of heart ventricles been flat, suction could occur and this would impair the heart's ability to pump efficiently (source: Google)
- papillary muscles and chordae tendinae attach to cusps of tricupsid valve (and bicupsid valve) that control where the blood goes
Function: papillary muscles contract, shorten and pull and close the valves so that the blood can be shunted where it is supposed to go and not back into the atrias
- Right and Left pulmonary veins from the lungs bring oxygenated blood back to the heart into the left atrium and to the left ventricle and out to the body through the aortas
(heart murmur: a little bit of blood goes back into the atria b/c valves are closing incorrectly)
- the heart contracts (1st!) and relaxes, pressure change, valves open and close with the help of the tendinae
Something that I found interesting was how significant the trabeculae carnae are to the rhythmic and normal pumping of the heart. If someone was born with less than average trabeculae carnae in the ventricles, would their entire body adjust to that throughout its developmental stages or would there be health complications in the individuals life? Would they have smaller than average ventricles? How affected would the circulatory system be to a more than average amount of trabeculae carnae? I wonder if there are any case studies that exhibit these kind of abnormalities.

The results for the agrose gel electrophoresis showed a successful DNA extraction and purification. In RNase treatments there were no RNA bands as should be the case. In comparison, the DNA only samples showed RNA present as expected. The DNA ran to the end of the gel as expected. However, the Nanodrop results did not agree with the gel electrophoresis results. It is unclear why there were difference between the two quantification methods. Perhaps there were errors in the Nanodrop quantification.  

The molecular absorbance spectroscopy via Nanodrop showed very different results. In regard to concentration, DNA1, DNA1 with RNase and DNA2 with RNase all showed concentrations around 150ng/µL. However, DNA2 showed concentration of only 91.3ng/µL. This low concentration could be due to errors when making dilutions or perhaps when using the Nanodrop itself. DNA1 and DNA2 had 260/280 values of 2.07 and 2.04 respectively. 260/280 values over ~1.8 suggest that there is a high concentration of RNA in the sample. For DNA1 with RNase and DNA2 with RNase, values for 260/280 were recorded at 2.95 and 3.45. These results would suggest that the two RNase treatments would have more RNA present than the original samples. This result does not agree with the gel electrophoresis results. In the gel electrophoresis it was clear that the RNase treatments did not have RNA present. Perhaps the presence of RNase interfered with the Nanodrop, or there were issues with the computer. DNA1 and DNA2 had 260/230 values of 1.65 and 1.51. 260/230 values below ~2.0-2.2 suggest that carb carryover occurred. Perhaps not all of the carbohydrates which should have been removed via KAOc were indeed removed. DNA1 with RNase and DNA2 with RNase had 260/230 values of -1.43 and -0.73. These values are under the ~2.0-2.2 range, however, they are negative which could mean something else has occurred. The 260/230 value is a ratio, so a negative value may indicate something other than carb carryover. The negative values could also be another possible error with the Nanodrop.

Lanes three and five of the agrose gel electrophoresis show three bands in each lane. The band at the top of the gel is the DNA, which is electrically charged and ran up to the positive end of the gel. The two bans lower in the lanes show RNA present in the sample. In lanes four and six there is one band at the top of the gel but no bands below. The band at the top is again the DNA which ran to the positively charged end of the gel. These two lanes were treated with RNase, which explains why there are no other bands in the gel. The RNase enzyme appears to have successfully broken down the RNA in the treatment samples.

Two separate DNA samples were made in this process. Each sample was then quantified using two different methods: molecular absorbance spectroscopy using a Nanodrop, and 0.9% Agrose gel electrophoresis. Along with the two DNA samples, a RNase treatment was made and quantified from each DNA sample. The RNase treatments were then compared to their respective DNA samples with both quantification methods.

After DNA had been extracted and degradation prevented, the DNA sample had to be purified. Protens, carbohydrates, and lipids were all present in solution and had to be removed for a pure DNA sample. Because carbohydrates and proteins are insoluble in solutions containing high concentration of potassium acetate, KOAc was used to separate these macromolecules. The macromolecules formed a pellet when in KOAc solution which was then removed. To rid the solution of lipids, an alcohol solution of isopropanol was used which formed the DNA into a pellet separate from the lipids. The pellet was then separated from the lipid solution and rinsed with EtOH.

The purpose of this experiment was to extract, purify and quantify the DNA of Brachypodium distachyon a common grass species. The extraction and purification process involved three steps; breaking up tissue and cells, preventing DNA degradation and removing unwanted molecules. To break up the tissue and cells of B. distachyon, mechanical grinding was first performed using a ball mill to break up the extracellular matrix. Chemical disruption was performed next using the detergent sodium dodecyl sulfate (SDS) with metal chelation using ethylene diamine tetra-acetic acid (EDTA). The final step in breaking up tissues and cells was heat disruption to release the DNA which was done on a hot bock set to 65°C. After DNA had been extracted from B. distachyon tissue, it was essential to prevent the enzyme DNase from degrading the free DNA. Preventing DNase from breaking down the extracted DNA was done with the already added EDTA. DNase requires Mg⁺⁺ as a cofactor; by using EDTA to chelate with Mg⁺⁺ prevents DNase from acting.