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.
Juan Gnecco
ReplyDeleteAsgn_2C/Presentation 04
0: Foundation of OoC, potential and future goals. Very similar to EBM 2014 review.
1. About the current technology in terms of electronics applicable to the chips used for measurements. Also, many of the physical challenges that must be faced and/or considered.
2. It seems to me that access to this developing technology is often limited by competitive interests and therefore limit the opporunity for interdiciplinary work thus slowing down the process of development. is this true?
3. Introduction, challenges, and concept behind the organ on chips as well as the current status of developement from several groups.
4. Very challenging subject, but interesting to know the progess it is slowly making to overcome challenges and develop new technologies.
James Pino
ReplyDeleteAsgn_2C
0:Knew: Basic information about OoC
1:Learned: The challenges of studying biology (in depth).
2:Pressing: Is it possible to solve a Leibniz of PDEs?
3:Presentation: Class presentation about systems biology and the use of OoC along with challenges and approaches to overcome these.
4:Thoughts: 184 slides is a lot to summarize. Biology is an amazing puzzle, which probably is never going to be solved. This is what makes is amazing. I suppose if we did "solve" it, then we would be a god of some sort? The complexity is amazing.
Kate Jones
ReplyDeleteAssignment 2C/ Presentation 04
0. Knew: I knew that the complexity of human biology poses a major obstacle to modeling using organs on chips. I also knew that though the organs on chips are developed individually, the goal is to link the organs to model a human.
1. Learned: Many of the challenges in modeling and developing organs on chips are somewhat contradictory. As the graph shows, the ideal model has to balance cost, size, and failure rate. However, this leads to a challenge in developing a model that suits a particular researchers needs.
2. Pressing ?: Many of the challenges presented seem to be contradictory. If you oversimplify the model, it will not be as useful for example. How do researchers establish a ranking of importance of size, cost, etc when developing the model?
3. Presentation: Cost is an interesting factor. Will the money that goes into research and development as well as the cost of each individual device eventually balance the amount of money saved in drug trials and other applications?
4. Thoughts: A lot of the challenges presented are from the perspective of the scientists. However, as we've discussed, a potential application of organs on chips is personalized medicine. The needs of the consumer may be different than that of the developer, and that might pose an interesting obstacle in research and development. For example, an average consumer may be more concerned with cost than with size.
Tim Lee
ReplyDeleteAsgn_2C/Presentation 04
0. Knew: Basic principles about Organs on a Chip and the extreme complexity of human biology.
1. Learned: The rich history of great minds progressing our knowledge of human biology one step at a time. Learned that even the most advanced minds came to the conclusion that the human body might simply be too complex to fully understand.
2. Pressing: From my understanding of Organs on a Chip, the extent to which the project can be successful depends on our knowledge of the human body and the parameters we impose on the chip. If so many of the great minds in the past admitted that human biology is too complex for our understanding, at what point can we make the project practical for clinical use? When and how can we be sure if the project is far along enough to say what happens on the chip will happen exactly to the person?
3. Presentation: History and overview of human biology as well as introduction into conveying the complexity of human biology we are about to delve into and the Organs on a Chip project.
4. Thoughts: There are a plethora of obstacles to complete this project but I am excited to learn more about how we've grown our understanding of the human body through the project. It seems like to me that our quest is to learn more and apply what we learned, not to solve science.
0. Knew: The basics on how Ooc might be useful and revolutionary.
ReplyDelete1. Learned: The many challenges that stand in the way of this revolution, and how they may be overcome.
2. Pressing ?: What type of cells will be used for each organ? Would organoids be a more realistic choice?
3. Presentation: About the promise and challenges of Ooc and micro-physiological systems.
4. Thoughts: How well does a mono-layer of any type of cell mimic a organ it composes? If there is more than one type of cell or stem cells are used to mimic the organ, how well does it work?
Mark Vander Roest
ReplyDeleteAssignment 2C
0. Knew: The complexity of systems biology and how it presents a major challenge to recreating it in OoC.
1. Learned: Certain challenges associated with biology in particular, including fluid volumes, reaction scale, fluid based measurements, etc.
2. Pressing ?: What are the predictions for what will solve existing biological problems first? Reductionist cellular strategies, OoC, computational biology, etc?
3. Complexity of systems biology, challenges and approaches to realizing the goal of interconnected OoCs, homunculi.
4. Thoughts: How could we even scratch the surface of systems biology in a one semester class? Are there any organs or areas that we will focus on?
Cami Johnson
ReplyDeleteAssignment 2C/Presentation 04
0. Knew: Organs-on-a-chip could be a more useful drug testing model than currently used methods, but there are many challenges to overcome in the field.
1. Learned: More about the specific ways in which the problems with organs-on-a-chip can be overcome and what particular tools are necessary. One of the things I learned in the previous article was the difficulty of simply gaining any quantitative knowledge from the devices, considering the small volume of fluid available, and in this presentation I learned what will most likely be the best analytical instrument, ion mobility-mass spectrometry (IM-MS).
2. Pressing ?: The presentation states that organs-on-a-chip may become utilized commonly when the cost is roughly $100, but is it possible to achieve that with such a complex system? Can these devices ever be made inexpensive and disposable?
3. Presentation: The presentation described the necessity of a new method for drug testing, as well as detailed some of the particulars of designing and assembling an organ- or human-on-a-chip.
4. Thoughts: A quote from the presentation that I thought was really interesting was "If the human brain were so simple that we could understand it, we would be so simple that we couldn't." This really poses the ultimate question of whether or not we will ever really be able to fully understand human biology. Regardless, I think organs-on-a-chip could provide us more information, even if we can't ever know it all.
Selene van der Walt
ReplyDelete0. Knew: There is only so much investigation you can do to a life form before you kill that life form, as the Bohr quote explains. ‘Life on plastic’ is not realistic.
1. Learned: The benefits of post-reductionist thinking when applied to biology. The ‘hairball’ of protein interactions and how that defines biology today.
2. Pressing ?: How else can microfluidics be used to improve biological research?
3. Presentation: The complexity of biological systems and the problems this presents for designing OoC systems.
4. Thoughts: Does the scaled down nature of OoC present problems or limitations for applications such as drug testing? Does the fact that the cells are in a single layer and not in their normal configuration in an organ effect their behavior?
Cameron Togrye
ReplyDeleteAsgn_2C/Presentation 04
0.Knew: The means by which fluid volumes were controlled in OOC's via the action of peristaltic valves and pumps.
1. Learned: I was surprised to learn the ion mobility- mass spectrometry could provide bioinformatic data in microseconds using 100 nL of fluid, scales which would be neccessary considering the minute volume scales OOC's operate with.
2. Pressing: Does the PDMS which the peristaltic pumps and valve compress and decompress in movement ever wear down from his process? Also, how can we be sure that the valve fully closes off a channel from the compression of the passage?
3. Presentation: Comparison of the various methods used by the teams across the nation developing OOC's.
4. Thoughts: I think one major issue that confronts the development of OOC's is the heterogeneity of even specific organs. Many organs have wide varieties of cells which compose them, and how can this variety be mirrored in OOC's? Also, how do epigenetics play a role in OOC's?