The Systems Biology of COVID-19 and the SARS-CoV-2 virus. The class will build a foundation that includes the emergence of complexity, simple biological subsystems, their reductionist and equivalent toy and organ-chip models, and the measurements required to specify model architecture and parameters. Applications to biology, physiology, medicine, chemical and biological defense, pharmacology, drug discovery, and toxicology. UGrad: PHYS 240 01 and BME 290B; Grad: PHYS 326 and BME 395C.
Brian Evans
ReplyDelete23/Endothelial heterogeneity
0. Knew: I was familiar with the systems biology foundation that was used as a backdrop to explain endothelial cell heterogeneity (i.e. multistability, plasticity, robustness, basins, attractors, etc.)
1. Learned: I gained understanding through the metaphors that are abundantly used to describe endothelial cell heterogeneity. The authors present familiar concepts in a new way that added depth to my understanding of dynamic systems. I also learned the term canalyzation.
2. Pressing ?: What is the biology behind "stabilizing the alternating (salt and pepper) pattern of tip and stalk cells"? They explain it in the paper but it is still unclear to me...
3. Presentation: Canlayzation in biology
4. Thoughts: I really enjoyed this paper and thought it rounded out my understanding of dynamic systems and epigenetics. It was also extremely helpful to have concrete examples for each of the concepts that were covered.
Will Matloff
ReplyDelete23 / Endothelial Heterogeneity
0. Knew: Genetic regulatory networks, multistability, attractors.
1. Learned: The distinction between nature and nurture.
2. Pressing?: Is the hypothesis of the existence of "dynamical modules" reasonable?
3. Presentation topic: Probabilistic boolean network models
4. Thoughts: This was a great paper. It covered many of the same topics of the Huang papers, but had many examples besides differentiation.
Erica Curtis
ReplyDelete23/Endothelial Heterogeneity
0. Knew: Prevalence of endothelial cell heterogeneity.
1. Learned: Two metaphors can be used to describe endothelial cell heterogeneity; input/output and nature v. nurture which seem to be mutually exclusive definitions. In reality, this is not true. A non-linear dynamic approach balances these metaphors with the concept of multistability, characterized by memory, robustness, and plasticity.
2. Pressing ?: Are there examples where nurture dominates nature? Is it really nature if you are knocking out genes? Is it accurate to say that nature is genotype and a combination of nature and nurture defines phenotype?
3. Presentation: Examples of Vascular-Bed Therapies that are either detrimental or inefficient due to endothelial cell heterogeneity.
4. Thoughts: I enjoyed this paper as it integrated the metaphorical/theoretical and technical aspects for an informative and enjoyable read.
Ayeeshik Kole
ReplyDelete23/Endothelial heterogeneity
0. Knew: I knew all the systems biology terminology and concepts. This provided me with a good framework in reading the paper. I wasn't that aware of endothelial heterogeneity being so huge though.
1. Learned: I learned about canalyzing and also what the nature-nurture metaphor means. I also got a better grasp of the specific emergent properties that Boolean models are unable to explain.
2. Pressing ?: Can some cells demonstrate more plasticity than robustness? Can you control this balance by knocking out genes?
3. Presentation: 'Salt and pepper' patterns in biology
4. Thoughts: I thought this paper was very thorough and covered all of the bases. However, in doing so, it was hard to get through. I'm not sure how much of it an endothelial biologist would read.
Zach Eagleton
ReplyDelete23/Enothelial heterogeneity
0 Knew: Systems bio concepts including the non-linear dynamics. Boolean Logic.
1 Learned: Canalyzation and how it can affect studies.
2 Pressing ?: Is boolean modeling currently the best simplification? Can we use the results of multiple simplified models to get the bigger picture.
3 Presentation: Weibel-Palade bodies
4 Thoughts: I thought this paper had good biological examples for the dynamical systems we have gone over in class. I also thought the small world model brought into context how vast the problem is if any one protein can affect almost any other protein in the system. The font on the graphs needs to be changes as well.
Lucas Hofmeister
ReplyDelete23/ Aird Heterogeneity
0. Knew: the endothelium is extremely diverse and there are many diseases associated with dysfunction of ECs
1. Learned: The implications of the fact that the endothelium "does not march blindly to the tune of the microenviroment" This is an important idea for experiments when we want the endothelium to march blindly to our inputs
2. Pressing ?: how can we scale heterogeneity? Aird says that we can figure out the upper limit of heterogeneity by establishing the number of robust attractors caused by the dominant cues in the tissue. I'm assuming that we need to have different local environments for each organ, but really we need to be digging into even smaller heterogeneities. Right now we are at least on the level of shear stress. how much more is possible.
3. Presentation: noise amplification in linear models. how reductionist strategies effect noise
4. Thoughts: I like the way that Aird frames this in terms of nature vs. nurture and then breaks that down systematically until we are left with a much more dynamic systems biology viewpoint. I think this is a great way to convince people that this is meaningful and worthwhile. I also really like the statement that for systems with feedback we need to know that baseline dynamics in order to predict the effect of a perturbation.
Erasing memory destroys heterogeneity!