Engineering the gut microbiome & microfluidics . Week 8
Homework
Part 1: Design a milli-fluidic device for microbial cell-culture
In this homework, we will useĀ Autodesk Fusion 360, a 3D CAD software, to design a 3D printed micro/milli fluidic device. Please install the software using the followingĀ instruction.
For inspiration, visitĀ Metafluidic, an open repository for fluidic devices. Details on how to use software tools will be discussed in recitation on Wed 4/28 @5p ET.
idea 1:
- neurones...
- gut - plastic
- fetal bovine serum...
Part 2: Design experimental conditions for...a microbial cross-feeding interaction?
- Find a research or journal article where researchers cultivate 2 or more microbial strains. What technology are they utilizing? How scalable is this approach to more than 2 strains? How do they address issues related to requiring multiple media?
- Propose a technology for culturing 2 or more strains. How might you innovate in this area given the paper you reviewed?
- One of the great challenges in microbiology currently is culturing āunculturableā microbes. Propose a methodology for how you might explore this significant space of uncultured microbes.
- Review an article on an artificial gut-on-a-chip technology. What scientific hypotheses are they testing with this in vitro tool? Could you propose an upgrade or innovation to their technique to enable the exploration of other scientific hypotheses? Provide an example of at least one hypothesis you would explore with your proposed system.
- One of the biggest challenges in public health is quickly detecting new disease outbreaks. How would you go about adaptively responding to new outbreaks? Biobots is using qPCR, so you need to know what you are looking for. How might you develop a technology with a more general view? Some example approaches include microfluidics and point-of-care sequencing, but what else? In particular, are there ways to look for RNA viruses like the flu and SARS-CoV2?
- Extra credit: In the hardware class you designed a fluidic device. Please either use this device as a starting point, or provide a sketch design of a fluidic device that could be used in the gut-on-a-chip system you are proposing in question 4.
interesting microbes:
- Brockarcheota - archea - newly discovered phylum which . they use some new metabolism.
Vector Designing
We were also asked to design a plasmid with a function that would be corresponding with our final project. Since I have been reconsidering overall feasibility of my project I had a hard time in figuring out what I would like to design. What function I would like to my plasmid have.
I started with learning about vector design. And also I read the article "Materials design by Synthetic Biology".
Important parts in designing plasmid:
ori - origin of replication
selection marker -
Kinds of vectors:
...
expression vectors -
...
Very interesting would be design a vector for metagenomics
Bibliography:
On Microfluidics:
- ...