Writing in Biology

Please download this directory, unzip it, and work with a partner to analyze the data: https://bcrc.bio.umass.edu/data_practice/data_practice_files.tar.gz

Statistics can be applied to a variety of subjects. In statistics, we learned how to read and interpret graphs and other forms of data. Being able to understand and analyze data helps us improve our thinking and analytical skills. Additionally, statistics helps us design effective methods for data collection, analyze that data correctly, and share that data effectively. While it may differ, data analysis is used in many fields and has become an important skill for many jobs.

The main thing I remember from statistics are the probability tests. These tests allows us to see if the data we have has any significance. If the data is significant, that means the results were not just due to chance. Learning how to carry out these tests taught me the importance of sample size, paying attention to detail, and interpreting data. Additionally, outliers can affect the results. These tests are often used in scientific papers, so it is important to understand what those tests mean.

In our example the population is increasing. When lambda is 1 the population remains stable. When it is below 1 the population is decreasing, and when lambda is above 1 the population is increasing. So in our table we know that the population is increasing. Looking at Figure 10.8 B we see that the population size is growing. From year 1 to year 5 it increased by 1037.3 individuals. Our lambda increased by .21 from year 2 to year 5. From year 2 to the next year was the biggest increase in lambda. After the first initial jump lambda continued to increase just by less every year. If we continued our table, we would notice that lambda would eventually reach a constant assuming our survival and fecundity rates remain constant.

The cytoskeleton has diverse functions, owing to the diverse structure of the proteins and filaments that form it. The interactions between these proteins result in emergent properties that add yet another layer to these diverse functions. Two major proteins in the cytoskeleton are actin and tubulin, which comprise microtubules and microfilaments respectively. Actin and tubulin have different structures and functions, and interact with each other to create emergent properties. One characteristic that is extremely different in tubulin and actin is their stiffness; microtubules made of tubulin are much more stiff than microfilaments made of actin. When these two proteins are added together in high concentrations, they interact sterically, and as a result, conform to the “reptation” or “tube” model. Each filament is spatially restricted to a tube-like area, which is formed by the constraining filaments around it. In order to relax and decrease the straining forces on it, the filament reptates, (sliding curvilinearly) out of its tubular space. There are other methods by which the filaments can partially relax, such as bending fluctuations.The interactions that occur in cells between actin and tubulin are integral to cellular function. Interactions between these proteins provide controlled, structured support of the cytoskeleton. They also are also important in cytokinesis and cell motility. Another key trait of microtubule-actin interactions is their ability to reinforce each other’s strength and elasticity. When interacting with the supporting actin network around it, a microtubule can withstand much larger forces without buckling than it would be able to withstand alone. Learning the interactions of these filaments has several different potential applications. In material engineering, tweaking the ratio of softer, more flexible rods (such as actin) to stiffer rods (such as tubulin) could help one discover the ideal ratio to be used to synthesize a material that is light yet durable. Combinations of actin and tubulin also provide the possibility for increased control over large-scale mechanics. 

In addition to Hotez’s work in providing a healthier community, he did research as to why poverty has been linked to a high disease rate. There are three main reasons as to why neglected diseases have caused an outbreak in poor developments are conflict, poverty, and climate. The most interesting idea that was brought to my attention during this presentation was the fact that when a nation is in conflict, such as a war, the healthcare system crashes. This causes a surge in diseases that had not been present in many years. I never thought to connect the presence of diseases to the political conflicts that were occuring in a nation.

        In later years, a new set of global goals were published. There were seventeen goals, in which one obtained the improvement of healthcare. Although the number of goals that mentioned healthcare decreased, it was more specific in addressing the concerns that needed to be improved. Ultimately, poverty related neglected diseases are an important dilemma that needs more attention and funding in order to improve healthcare worldwide.

It's really interesting that fusion proteins can be expressed. I assumed that Abl did something to the protein that it fused with in the cytosol, like affect its noncovalent bonding and consequently change its conformation/function. But, this implies that the fusion protein is expressed so the mutation begins at the DNA before transcription.

Does the Abl kinase act as a phosphatase? It states that one of its functions is to inhibit tyrosine kinases. Maybe it acts as a competitor for phosphorylation as a mechanism of inhibition instead?  

This is fascinating because I assumed that all SH2 domains functioned as phosphotyrosine binding partners. But in the case of Abl, it seems that the SH2 domain functions to bind to the SH3 domain and thereby maintain its autoinhibition. If the SH2 domain is not able to bind to a phosphorylated tyrosine, then its normal function will no longer work.

This facet of Abl 1b coincides with its cancerous tendencies. If the kinase activity is deregulated then the implications for the cell as a whole are not good. Cancerous cell utilize these kinds of mutations for grow and proliferate. Without normal regulation, the kinase can promote this. Therefore, it makes sense that the Abl 1b mutant is commonly a part of the cell that when mutated can lead to cancer.

Since Gab/Grb2 fulfill such a large role in the cell, it makes sense that its deregulation by Bcr-Abl results from the mutation. Gab/Grb2 bind to epidermal growth factor receptors (EGFR) which is a commonly mutated in various forms of cancer. Furthermore, because Gab2 serves a number of other functions in the cell like being the binding site for the assembly of SHP2 and potentially coordinating STAT5, its deregulation can have serious consequences for the longevity of the cell.

I took Resource Economics 212 to fulfill my statistics requirement. We learned about common statistical notation. For example P(A) stands for probability of event A. P(A U B) stands for the probability that A OR B will happen, whereas P(A ∩ B) stands for the probability that BOTH A and B will happen. P(A I B) is the probability of event A, given that event B occurred. We also learned about standard deviation, which tells you, on average, how much the values as a whole are different from the average, i.e. determining whether they all right around the middle, or are there a lot on the lower end and a lot on the higher end that just average out to a middle value.  We learned how to calculate permutations and combinations as well. Permutations are the number of different ways a set of things from a group of things can be arranged, paying attention to their order, while combinations are also a set selected from a group but not paying attention to the order.

The cellular cytoskeleton has a large number of functions, due to the varying structure of cytoskeletal proteins and filaments, and their various interactions. Two major proteins in the cytoskeleton are actin and tubulin, which comprise microtubules and microfilaments respectively. Actin and tubulin have different structures and functions, and interact with each other to create emergent properties. They have very different stiffnesses. When together in high concentrations, they have steric interactions that conform to the “reptation” or “tube” model. Each filament is spatially restricted to a tube-like area, which is formed by the constraining filaments around it. To relax and decrease the straining forces on it, it reptates, (sliding curvilinearly) out of its tubular space. There are other methods by which the filaments can partially relax, such as bending fluctuations. The interactions that occur in cells between actin and tubulin provide controlled, structured support of the cytoskeleton. Their interactions are also important in cytokinesis and cell motility. Microtubule strength is also reinforced by the presence of supporting actin; they can withstand greater forces without buckling in the presence of actin than they can on their own. Studying the interactions of these filaments has different potential applications. Potentially, one could learn to identify an ideal ratio of soft to rigid rods to be used in the synthesis of a material that effectively combines light weight with durability. Combinations of actin and tubulin also provide the possibility for increased control over large-scale mechanics. Previous research studies have shown that actin is compressible in the presence of microtubules, and that low concentrations of microtubules added to cross-linked actin cause strain-stiffening in the actin, as opposed to the normal strain-softening that usually occurs in cross-linked actin. These previous studies, however, were limited in a few ways. The parameter space of the composite matter was limited, so differences between varying concentrations and ratios of actin and tubulin were not measured to be contrasted. The studies also measured large-scale strain and micro-scale strain, but not mesoscale strain which would be more useful based on the mesh size of actin and tubulin. These studies also used microtubules that were pre-polymerized before they were added to the actin, which oftentimes encourages actin bundling, preventing the possibility of a truly isotropic composites. In contrast, the study “Co-Entangled Actin-Microtubule Composites Exhibit Tunable Stiffness and Power-Law Stress Relaxation”methodically varies the relative concentrations of tubulin and actin and characterizes mesoscale mechanics of the filaments by displacing optically trapped microspheres by 30 µm at a rate that is very high compared to the normal relaxation rate of the filaments, and measuring the restoring force that the composite applies to the sphere. These measurements disrupt the equilibrium of the composite and allow exploration for possible buckling, rupture, and rearrangement. 

Looking back at my statistics 240 course, I realize that I remember a lot of key concepts but some of the details of calculation are a blur.  For example, I know all of the basic measures including mean, median, mode. I recall that significance in a set of data is a way to determine if an effect was actually observed. Also, confidence intervals are essentially a measure of how confident you can be that the obtained result could be repeated. A confidence interval of .9 indicates 90% confidence and .99 indicates 99% confidence. If you have a very large sample and a high confidence interval then you can more readily rely on the validity of the results. In addition, a given sample size must have a minimum of thirty participants for its results to be considered significant (n=30). All of these concepts can be related to the normal distribution. When conducting an experiment, you want to prove that your hypothesis actually generated a result. By using statistical analysis, you can provide a numeric confirmation that a difference was observed between an original condition and the experimental condition. Since it has been awhile since I took the course, I’m not currently confident with all of the calculations pertaining to these concepts. Luckily, these are things that I could open up my old notebook and refresh myself on.