User:Di Wu
About Me
Di Wu. I graduated with an Honours degree in Comp Sci at Monash University, right now doing a second degree in Cell Biology major at Melbourne. I hope you will enjoy our iGEM project!
Current Work
I'm currently working at the St. Vincent's Institute of Medical Research as a UROP student. My focus is on Cancer Structural Biology, under the supervision of Professor Michael Parker. The main idea is to use crystallography to analyse structures of cancer causing/related proteins and find ways to inhibit them.
Oh, and I can't just walk away without telling you about my other interests, which is on insects! I'll put some photos and vidoes clips of my favourate insect pets. I bet you'll enjoy them.
Reserch Interests
- Cancer, Cancer Stem Cell, cell cycle, signalling regulation
- Biomedical informatics
- And off course our Melbourne iGEM!
Contact
ever_wudi@yahoo.com, diw@student.unimelb.edu.au
A Feasible implementation of Bacteria Counter
Hi Friends,
I know we are at the stage of brainstorming. I just thought about a feasible way of implementating a "bacteria counter", just to put it here in case I forgot, not intending to confuse or distract anyone. If not feeling like to read it now, just skip it or come back later. The "bacteria counter" not only can be used for "biological clock" but also could be used for related topics which we might come up later. Just as a proposed idea.
We could use the strategy of binary counting in biological systems. Before I start, I shall give a very brief idea (and that's all we need to know) on binary counting (I'm sure some people already knew this via mathematics, computer science, physics, engineering etc):
Binary counting (based on 2) is done in the same a way as decimal counting (based on 10, as we do everyday). For example,
if we want to represent number 3 in binary numbers (bits), [math]\displaystyle{ 3 = 1\times 2 + 1\times 1 = 1\times 2^1 + 1\times2^0 = 11~(base ~2) }[/math]
to represent number 4 in binary, [math]\displaystyle{ 4 = 1\times2^2 + 0\times2^1 + 0\times2^0 = 100~(base ~2) }[/math]
to represent number 5 in binary, [math]\displaystyle{ 5 = 1\times4 + 0\times2^1 + 1\times1 = 1\times2^2 + 1\times2^0 = 101~(base~ 2) }[/math]
Binary numbers can represent arbitarily large numbers just as digital numbers, e.g. if we have a binary number 1011011,
| [math]\displaystyle{ 2^6 }[/math] | [math]\displaystyle{ 2^5 }[/math] | [math]\displaystyle{ 2^4 }[/math] | [math]\displaystyle{ 2^3 }[/math] | [math]\displaystyle{ 2^2 }[/math] | [math]\displaystyle{ 2^1 }[/math] | [math]\displaystyle{ 2^0 }[/math] |
|---|---|---|---|---|---|---|
| 1 | 0 | 1 | 1 | 0 | 1 | 1 |
= [math]\displaystyle{ 1\times2^6 + 0\times2^5 + 1\times2^4 + 1\times2^3 + 0\times2^2 + 1\times2^1 + 1\times2^0 = 64 + 0 + 16 + 8 + 0 + 2 + 1 = 91~(base~10) }[/math]
Ok, so how can we implement this in bacteria systems? Say we have 3 bacteria: B2 B1 B0, each with its own characteristic colour (or other traits) when its expression is turned on, e.g. B2=red
B1=green, B0=blue. Also, each B(n) needs the expression outcome only from B(n-1) plus a toggle control to express its own gene. Then we can read off the current number just by
reading the color combinations (or other characteristic traits). For example,
| B2 | B1 | B0 | Binary | Decimal |
|---|---|---|---|---|
| clear | clear | clear | 000 | 0 |
| clear | clear | blue | 001 | 1 |
| 010 | 2 | |||
| 011 | 3 | |||
| 100 | 4 | |||
| 101 | 5 | |||
| 110 | 6 | |||
| 111 | 7 |
B2 B1 B0 Binary Decimal clear clear clear 0 0 0 0 clear clear blue 0 0 1 1 clear green clear 0 1 0 2 clear green blue 0 1 1 3 red clear clear 1 0 0 4 red clear blue 1 0 1 5 red green clear 1 1 0 6 red green blue 1 1 1 7
So for instance if our colour combination is red, green and blue, then we know our current time is 7, if colour combination is just red, we know it's time 4. We could just control the expression rate of B0 to control how fast our counter counts up (because every B(n) expression only depends on input from B(n-1) and the terminal one is B0), and maybe we can race the real clock by adjusting the expression rates!
This is just 1 of the topics we've thought. We have the whole bucket of great ideas from brillian brainstormers!
