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.
Tuesday, September 17, 2013
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0. Prior to reading I knew the basics of OoC based on class discussions and readings.
ReplyDelete1. Learning about the marketable potentials for OoC are interesting such as L’Oreal using the OoC as a allergen test to replace mice.
2. The article mentions HepatoPac, a liver platform, that claims cells in the system can remain functional for 4-6 weeks, is that a realistic time frame to study the effects of a drug? Literature I found regarding bioreactors made by FiberCell Systems has kept cells alive in culture for over 6 months with no visible changes in morphology or alterations to biomarkers. Also one of the images in the paper shows sections with bone marrow, tumor, and liver and the OoC does not seem to provide the 3D nature of a real tumor so how accurate is the OoC to study metastasis?
3. A presentation on potentials of OoC? Advantages and Limitations?
4. I think the article highlighted best that there is potential but still work that needs to be done before the OoC makes the bounds from in vitro to animal models.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_9A_Class_06_Article_17_2013_09_17
0. Knew: Common organs on chips.
1. Learned: Artery on a chip.
2. Pressing: Middle column page 31: Modeling the lungs' "muscles." Normallly one would think of the muscles of breathing (diaphragm, intercostals). Here they are not thinking of skeletal muscles (striated muscles) but rather the smooth muscles that line the bronchi.
3. Presentation: Current state of OoC in different research groups. What has been done and what has not been done?
4. Thoughts: To what extent are the various research groups cooperating? To what extent are they computing? To what extent are efforts being duplicated?
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_9A_Class_06_Article_17_2013_09_17
0. Knew: Common organs on chips.
1. Learned: Artery on a chip.
2. Pressing: Middle column page 31: Modeling the lungs' "muscles." Normallly one would think of the muscles of breathing (diaphragm, intercostals). Here they are not thinking of skeletal muscles (striated muscles) but rather the smooth muscles that line the bronchi.
3. Presentation: Current state of OoC in different research groups. What has been done and what has not been done?
4. Thoughts: To what extent are the various research groups cooperating? To what extent are they computing? To what extent are efforts being duplicated?
0. Knew the reasons for making organs and animals on chips.
ReplyDelete1. Learned that a vast community, composed of both corporate and academic research centers is working to advance tissue modeling technology. Some of the efforts spring from previous attempts to grow organs for transplantation. Fact that more "finicky" cell types are necessary for more accurate modeling. For tissues 3mm thick, a circulatory system is needed
2. Questions: I was struck by the fact that PDMS is not mentioned (though alluded to in the second to last paragraph). What problems caused a shift from silicon / plastic wafers to PDMS? Would returning to these technologies reduce some of the absorption problems seen in PDMS? The article mentions corporate and academic centers. To what extent does collaboration and data-sharing occur?
3. Presentation topic: Academic versus commercial research centers
4. It was interesting to read commentary of various experts. We have read several of their papers but it is interesting to see how they portray their work to a more general audience.
SysBio13 Asgn_9A_Class_06_Article_17_2013_09_17
ReplyDelete0. Knew: General information about OoC such as the current lung, difficulty of a blood flow, and difficulties around removing a fluid sample.
1. Learned: More about how the chips are being used currently and the variety of techniques that have been used. I did not realize the diversity in the field and projects.
2. Questions: In "from animals to organs" it discusses a crafted collagen structure that is representative of the villi; why are the actual cells that produce this structure not used? Why can reconstituted tissue live for months rather than weeks?
3. Presentation: 96 well plate techniques - benefits/drawbacks in comparison to OoC
4. Thoughts: Looking forward to discussion, especially on the two insets. Just cells: how "cells could be used without chips" and more about how "cells must be adapted to culture conditions"; The real McCoy: this is very different than anything we have discuss, not just cells but a whole artery.
0. General setup of OoC's, what's we're trying to accomplish.
ReplyDelete1. Learned the history of the chips, what various people have done so far. Artery on a chip
2. This is something we've addressed in class and something the paper touches on, but how do we create the smallest of vasculature in our organs? we'll probably need some kind of vasculature to make truly 3D organs.
3. Providing nutrients to the organs
4. Would it be better to focus on trying to refine the resolution of 3D printers (smaller blood vessels) or trying to use the bodies natural ability to create blood vessels (understanding the control mechanisms)?
0. Knew: Work on OoC’s discussed in class
ReplyDelete1. Learned: The surmounting importance of the liver in drug metabolism
2. Pressing: What sort of engineered portions of an OoC are admissible, if reappropriated vessels have to be used for fluid transport to maintain relevance, what other portions should adopt native cells/structures instead of fabricated devices?
3. Presentation: Stem cell differentiation housed inside an OoC
4. Thoughts: I thought it was a good synopsis on current works produced and the future directions of work on OoC’s
0. Knew: General knowledge of OoC's.
ReplyDelete1. Learned: About whole organs on chips (e.g. artery)
2. Pressing ?: Can arteries on a chip be useful in integrated OoC?
4. Thoughts: It was a nice review. The "Real McCoy" seems like it doesn't have much future to me, but maybe I'm crazy.
0 Knew: general knowledge of OoCs, some of the organs in development, and some of the challenges
ReplyDelete1 Learned: I learned that this idea is new but commercially applicable platforms have already been developed. This article also articulated again the goal of obtaining the most information from the simplest system possible.
2 Pressing: What's this "Just Cells"? What kind of platform are they growing on? Surely they must have some kind of scaffold. On p. 664 when they discuss "skeletal muscle in multi-well plates," how is this any different than classic cell culture? Is there flow between the wells?
3 Presentation: OoCs to improve animal trials
4 Thoughts: I thought it was interesting (the real McCoy) to think about chips helping to make animal studies more effective. But how else could "the real McCoy" be used?
SysBio13 Asgn_9A_Class_06_Article_17_2013_09_17
ReplyDelete0. OoC as a platform to fill the gap between petridish&animal experiment and human clinical trial.
1. A. another advantage of OoC is the highly controllable environment.
b. alternative usage of OoC to test allergic reaction to drugs.
2. Why the iPS (induced pluripotent stem) cells are more advantageous? Is this advantage just apply to gut cells or also apply to other cells?
3. Network of OoC company or research institute.
4. This paper provides lots of the challenges and limitation for the OoC, nonetheless it gives lots of alternative examples for the application of OoC.
0. Knew: A living system on a chip is the next step in improving drug screening.
ReplyDelete1. Learned: I forgot about the importance of the gut in drug absorption. It seems disproportionately important to the amount that we've talked about it.
2. Questions: Why did Wikswo get the grant when he wasn't in this paper?
3. Presentation: What are other people specializing in with OoCs?
4. Thoughts: We haven't emphasized the gut and Wikswo's funding is from DARPA. I guess that means that the government is not very concerned with a food based biological/chemical attack.
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