Blogs

The methods project is meant to explore the elements needed to write a sufficient scientific paper, especially the methods section. The goal of the project is to make a multi panel figure of photographs of a flowering plant and a map displaying the plants origin, write a methods section for someone to follow and have someone else follow the methods and recreate the figure.

Green sea turtles are the largest species of hard-shelled turtle normally found in tropical and subtropical waters around the globe.   The principal cause of the historical, worldwide decline of the green turtle is long-term harvest of eggs and adults on nesting beaches and juveniles and adults on feeding grounds. These harvests are cultural and continue in some areas of the world, compromising the efforts made to recover this species.  Incidental capture in fishing gear, primarily in gillnets, but also in trawls, continues to decrease the numbers of wild turtles inhabiting our oceans.

The Central Nervous System (CNS) is responsible for the bodies response to and immense amount of stimuli. A recent study has gone on to map the CNS in a highly dimentional single-cell procedure that has pointed to the fact that the CNS has specialezed and specific immune cell subsets in order to respond to stimuli. The subsets include, but are not limited to, tissue homeostasis, immune defense and neurological diseases. This newly found highly dimmentional procedure has proven very beneficial in mapping part of the brain and CNS that have never been seen or studied before. It has specifically helped in the study of the pathology of the specific subsets of immune cells, present in order to respond to specific stimuli. This new data may lead to immense adavancements in medicine, including treatments of debilitating neurological diseases, by identifying disease mechanisms, biological markers and possible thereapeutic targets. 

In the results, Figure 1 refers to the original figure, and Figure 2 refers to the replicate figure. Figure 1 and Figure 2 look somewhat similar, however they bear differences. The differences observed will be sorted in paragraphs, about the labels, photography differences, and differences in part C of the Figures.

When looking at the labels, in Figure 1, the letters are black and have a white square behind them, while in Figure 2 the letters “A” and “B” are in white font, and the letter “C” is in black font. On the same note, the letters are bigger and less tightly organized in Figure 2. In addition to that, the background of Figure 2 is transparent, while the background of the Figure 1 is white. In Figure 1, there is no empty space in between photos A, B, and C. However, in Figure 2, there is white space between photos A and B, and between photos B and C.

Looking at the photos of the plant and flower itself, in Figure 2, the pictures of the plant and of the flower are brighter than Figure 1. In addition to that, Figure 2 is more blue shifted while Figure 1 has warmer tones to the photos. In Figure 2b, the flower is smaller than the flower in Figure 1b. Lastly, in Figure 2a, the top of the flower pot is less cicular than the top of the pot in Figure 1a.

Overall, this laboratory exercise demonstrates the importance of the use of a primary antibody to gain specific and localized staining of a particular cellular structure when using indirect immunofluorescence. Additionally, the use of direct cellular targets to label specific cellular components is also shown to be useful, especially when comparing cellular structures across cell types.

The fluorescence of control LLC-Pk1 cells was distributed indiscriminately throughout the cellular components due to the absence of primary antibody for the fluorescently tagged secondary antibody to bind to. The lack of affinity for a specific target within or around the cell allowed for the fluorescently tagged secondary antibody to freely bind to any structure or surface that it desired. This resulted in a fluorescent image in which most cellular structures and area surrounding the cells was tagged with fluorescent dye, ultimately brightening much of the area under the cover slip and outputting a low fluorescence intensity in the area of interest (tubulin). The fluorescence of the indirect immunofluorescence stained cells localized specifically to tubulin structures due to the presence of a primary antibody which targeted antigens located on tubulin molecules within the cells. This allowed for multiple secondary antibodies (which possess a high binding affinity for the primary antibodies) to bind to the primary antibodies, achieving a highly amplified fluorescence intensity on only tubulin structures. This is visually represented in Figures 1 and 2, and quantitatively measured in Table 1. Direct targeting of the actin cytoskeleton in LLC-Pk1 cells and NIH 3T3 cells allowed for clear visual distinctions to be seen in the structural composition of the actin cytoskeleton in each cell type. The actin cytoskeleton of the NIH 3T3 cell group is considerably more spread out within the cell, rather than localized to one region of the cell. This is due to the large role that fibroblasts play in maintaining structural integrity of connective tissues in living organisms. These cells must possess qualities of strength and durability throughout the cell, which is provided by the widely distributed actin cytoskeleton. Additionally, fibroblasts are able to migrate as individual cells, so the actin cytoskeleton extending within the branched structure could aid mobility on the cellular level. This structure can be visualized in Figures 3 and 4. Conversely, the actin cytoskeleton of the epithelial cells is more localized around the nucleus of the cell, rather than spread throughout the cell. This can be explained by the epithelial cells inability to migrate as individual cells, so a widely distributed actin cytoskeleton is not necessary. Additionally, the localization of the actin cytoskeleton specifically around the nucleus results from the large role that the actin cytoskeleton plays in cell division by transporting cellular components and preparing the cell to divide. This localization can be seen in Figures 3 and 4.

One example of recent modern evolution lies in the Tibetan highlands. At high altitudes oxygen availability is reduced which contributes to altitude sickness, marked by fatigue, insomnia, and nausea. People who are not acclimated or well adapted to life at high altitude suffer serious health issues. “Individuals from low-altitude populations who move to live at high altitude suffer from a number of potentially lethal diseases specifically related to the low levels of oxygen and struggle to reproduce at these altitudes. The hypoxia of altitude would thus have exerted substantial evolutionary selective pressure (Cynthia Beall et al., 2010).”  However, Tibetan highlanders can comfortably reside at elevations above 4,000m or 13,200 ft. The adaptations in tibetan populations that allow them to live at high altitude originates from the EPAS1 gene. This gene encodes for a transcription factor used in the induction of genes regulated by oxygen. The protein is induced when oxygen levels fall and controls the production of red blood cells. Tibetans actually produce fewer red blood cells than their lowland counterparts. An increase in blood cells is only beneficial to a certain point in delivering oxygen to tissues. Having too many red blood cells will make the blood too viscous to efficiently oxygenate tissues. Therefore, the changes in the EPAS1 gene ultimately make Tibetans less likely to overproduce red blood cells at high altitudes. The version of the EPAS1 gene found in tibetans varies from the versions of the gene found in any extant human population, it is unique and seems to be adapted to this specific environment.

My methods project needs some work. I felt extremely rushed to create the methods for my partner so it wasn't really good for my partner to follow my directions. It was very interesting to see how my partner took my direction and made the legend. Also, because the directions or what I did was not clear, my partner's and my legend were off. I had 4 pictures and my partner had 3 which was the biggest difference. Overall, it was fun to follow the direction and try to create replication of my partner’s without giving the final product until the end. I found it amusing how we chose the same exact plant in the same exact place without discussing about it. Presenting in the class went smooth and it was interesting to see how different and similar everyone's were.

So I had the first exam for Chem 262 (organic chem 2). It was on spectroscopy, spin-spin splitting, rule of 13, degrees of unsaturation formula, and functional group characteristics. I studied for hours and hours with couple of my friends and I still did terrible on it which I was pretty bummed about. But we all got an email from the professor saying that the class average was way lower than he expected it to be. So luckily for us, it will be scaled heavily. I get chemical shifts and NMR spectrum part but it is extremely hard to draw the structure when given other information. The fact that it was not all multiple choice and the fact that we had to actually draw the structure itself made the exam way harder.

I have been learning about some interesting and incredible science facts. Few I found were pretty cool like the fact that water can boil and freeze at the same exact time blows my mind. Also, when cat falls from anywhere, they always land on their feet because of physics and gravity. This blows my mind because the fact that they can say always is crazy. Lastly, you'd be better off surviving a grenade on land rather than underwater. I would assume that you'd be more safe underwater but apparently it is more dangerous.