IGEM:Melbourne/2008/ProjectIdeas

From OpenWetWare

< IGEM:Melbourne | 2008(Difference between revisions)
Jump to: navigation, search
Current revision (23:29, 3 January 2008) (view source)
 
(25 intermediate revisions not shown.)
Line 1: Line 1:
[[IGEM:Melbourne/2008|Return to Melbourne Homepage]]
[[IGEM:Melbourne/2008|Return to Melbourne Homepage]]
-
== Detection of allergens in food ==
+
==[[/Allergens|Detection of allergens in food]]==
*the presence of certain alergen promote the expression of GFP.
*the presence of certain alergen promote the expression of GFP.
*must be fast reaction. ie. detection on the spot.
*must be fast reaction. ie. detection on the spot.
Line 10: Line 10:
*setup a basic ALU(arithmetic logic unit), from pre-designed gates
*setup a basic ALU(arithmetic logic unit), from pre-designed gates
*biological clock; counts up in seconds or minutes (not countdown like peking07-hopcount), something similar but not elegant enough has been done by [http://parts2.mit.edu/wiki/index.php/Harvard_2006#A_Circadian_Oscillator_for_E.coli Harvard2006]
*biological clock; counts up in seconds or minutes (not countdown like peking07-hopcount), something similar but not elegant enough has been done by [http://parts2.mit.edu/wiki/index.php/Harvard_2006#A_Circadian_Oscillator_for_E.coli Harvard2006]
 +
*Circuit from Cellular Autonoma: one bacterial cell could produce simple circuit or fancy pattern.
==Biological Manufacturing==
==Biological Manufacturing==
Line 18: Line 19:
*[http://en.wikipedia.org/wiki/PID_controller PID control] similar but more elaborate to [http://parts.mit.edu/igem07/index.php/Valencia/Controller Valencia2007]
*[http://en.wikipedia.org/wiki/PID_controller PID control] similar but more elaborate to [http://parts.mit.edu/igem07/index.php/Valencia/Controller Valencia2007]
-
 
+
== [[In vivo sensors, processors and actuators]] ==
-
== In vivo sensors and actuators ==
+
Bacteria have remarkable abilities to sense, process and actuate. These attributes of bacteria are potentially useful in designing and fabricating them for therapeutic purposes. One good example is here. [http://www.technologyreview.com/TR35/Profile.aspx?Cand=T&TRID=601]
Bacteria have remarkable abilities to sense, process and actuate. These attributes of bacteria are potentially useful in designing and fabricating them for therapeutic purposes. One good example is here. [http://www.technologyreview.com/TR35/Profile.aspx?Cand=T&TRID=601]
-
In his quest to build tumor killing bacteria, he articulated some steps useful for building synthetic biological systems.
+
'''[[/more|(more...)]]'''
 +
 
 +
== cell-cell interaction ==
 +
* something similar to peking 2007 one..
 +
* group A bacteria undergo conjugation certain number of times before expressing a promotor
 +
* the promotor promotes the expression in group B bacteria of some other protein.
 +
* after undergoing conjugation certain number of times, group B bacteria express a repressor which inhibites the expresion of promotor from group A bacteria thus negative feedback.
 +
* a system with timing and quatity control
 +
 
 +
== Radiation-proof E.coli ==
 +
*Express the DNA repair system (enzymes) of radiodurans in e.coli ?
 +
 
 +
== Gold mining bacteria ==
 +
*Bacteria that uptake gold particles in solution possibly using transporters from alfalfa or other plants used in phytomining. For the purpose of making money.
-
1) Define spatial and temporal environments that the bacteria encounter.
+
==[[/Desal|Bacterial desalination]]==
 +
Bacteria that uptake salt from water for the purpose of a more cost effective method of desalination. Investigations into archaea probably needed.
-
2) Identify processes that satisfy the environmental constraints and promote environmental progression.
+
== HIV rapid diagnostic test ==
 +
A rapid diagnostic test for HIV using bacteria that express CD4 and CCR5 coupled with an amplification signal (such as used in Brown university 2007).
-
3) Identify modules that satisfy these requirements.
+
== HIV sink ==
 +
Bacteria that express CD4 and CCR5 to act as a sink within the body thus lowering the viral load of HIV. Immunogenicity must be removed as was done with Bactoblood (UC Berkeley 2007).
-
4) Build a minimal system from parts.
+
== Remote controlled locomotive micromachine ==
 +
A remote control locomotive micro machine using bacterial flagella as the driver. The bacteria with flagella could possibly adhere to the micro machine using adhesins.
-
5) If required, go back to 2), re-build and add complexity.
+
== Bacterial kettle ==
 +
Hyperthermophilic bacteria or archaea treated with uncouplers e.g. DNP, used to boil water for power generation.
 +
== Bacterial TV ==
 +
A television screen composed of bacteria that release the different colors of fluorescent proteins to form an image.
-
Of course, unless the chassis has no system that is already running, the systems that are being built here are done in the existence of a host system, which perform
+
== Bacterial Bioremediation ==
 +
Bacteria that fix or modify harmful contaminants in soil (i.e. cyanide, petrochemicals) after a spill/industrial activity.
-
1) DNA replication
+
==[[/BiologicalClock|A Feasible implementation of Bacteria Counter using a '''Binary Counting Approach]]'''==
-
2) Transcription
 
-
3) Translation
+
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.
-
4) DNA repair
+
We could use the strategy of '''binary counting''' in biological counting 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):
-
5) Protein enzymatic functions
 
-
6) Protein non-enzymatic functions
+
Binary counting (based on 2) is done in the same a way as decimal counting (based on 10, as we do everyday). For example,
-
7) Protein degradation
+
if we want to represent number 3 in binary numbers (bits), <math>3 = 1\times 2 + 1\times 1 = 1\times 2^1 + 1\times2^0 = 11~(base ~2) </math>
-
8) Cell division
+
to represent number 4 in binary, <math>4 = 1\times2^2 + 0\times2^1 + 0\times2^0 = 100~(base ~2)</math>
-
9) Metabolism for energy
+
to represent number 5 in binary, <math>5 = 1\times4 + 0\times2^1 + 1\times1 = 1\times2^2 + 1\times2^0 = 101~(base~ 2)</math>
-
10) others?
+
Binary numbers can represent arbitarily large numbers just as digital numbers, e.g. if we have a binary number 1011011,
-
The above applies to the construction of synthetic system using plasmids, which is what we will likely use. Some potential problems with this approach is cross-talk of newly built system with the host system. The concept of orthogonality [http://www2.mrc-lmb.cam.ac.uk/PNAC/Chin_J/] should be understood here because it can be useful to avoid cross-talk.
 
-
In terms of optimizing some parts for specific functions, the concept of directed evolution is powerful and was applied in the tumor killing bacteria example above. Of course, directed evolution is only possible if positive selection for the part functions is possible.
 
-
The generic approach presented for sensing, processing and actuating responses with bacteria can be tailored for some applications on top of my mind (see below). The study of these applications require our engineer friends to tell us how to study the transfer functions from sensing to processing, what logic devices (eg. Inverters, AND gate, switches, etc) to use for processing, and how to study the transfer function from processing to actuation. Of course, modeling at the level of device and system function will be appreciated too.  
+
{|
 +
|-
 +
!<math>2^6</math>
 +
!<math>2^5</math>
 +
!<math>2^4</math>
 +
!<math>2^3</math>
 +
!<math>2^2</math>
 +
!<math>2^1</math>
 +
!<math>2^0</math>
 +
|-
 +
|1
 +
|0
 +
|1
 +
|1
 +
|0
 +
|1
 +
|1
 +
|} = <math>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>
 +
 +
===Implementing Binary expression on "bacteria counter"===
 +
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=<font color = "red">red</font>
 +
B1=<font color = "green">green</font>, B0=<font color = "blue">blue</font>. 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(time)
 +
|-
 +
|clear 
 +
|clear 
 +
|clear 
 +
|000
 +
|0
 +
|-
 +
|clear
 +
|clear
 +
|<font color = "blue">blue</font>
 +
|001
 +
|1
 +
|-
 +
|clear
 +
|<font color="green">green</font>
 +
|clear
 +
|010
 +
|2
 +
|-
 +
|clear
 +
|<font color="green">green</font>
 +
| <font color="blue">blue</font>
 +
|011
 +
|3
 +
|-
 +
|<font color="red">red</font>
 +
|clear
 +
|clear
 +
|100
 +
|'''4'''
 +
|-
 +
|<font color="red">red</font>
 +
|clear
 +
|<font color="blue">blue</font>
 +
|101
 +
|5
 +
|-
 +
|<font color="red">red</font>
 +
|<font color="green">green</font>
 +
|clear
 +
|110
 +
|6
 +
|-
 +
|<font color="red">red</font>
 +
|<font color="green">green</font>
 +
|<font color="blue">blue</font>
 +
|111
 +
|'''7'''
 +
|}
-
Can we built bacteria to interface with cells other than mammalian cells?
+
So for instance if our colour combination is <font color="red">red</font>, <font color="green">green</font>, <font color="blue">blue</font>, then we know our current time is '''7''', if colour combination is just <font color="red">red</font>, we know it's time '''4'''. Every expression of B(n) depends only on input from B(n-1) plus another toggle control. So the only bacteria determining counting speed is B0 (just like in a stop watch where the counting speed is entirely dependent on the last digit). Maybe we can race the real clock by adjusting the expression rates!
-
1) Perhaps insect cells
+
As we know ALU (Arithmetic Logical Unit) is also based on binary number operation. This idea could be extended to be implemented on binary addition, substitution, multiplication.
-
[[Image:invading_drosophila.jpg]]
 
-
GFP as reporter on our bacteria invading different cell types. If germ cells can be invaded and transgene can be incorporated to the insects, this is a way of transforming them. A suicide gene may be installed, etc.
+
This is just 1 out of the many thoughts we've put. We have the whole bucket of great ideas from other brilliant brainstormers!
-
Can we built bacteria that interface with mammalian cells but do different things than killing tumor?
 
-
Can you use your imagination to think of others?
+
I just thought about a practical problem we would have which is that if we have many copies of B2B1B0 and the different copies express asynchronously, e.g. one set is expressing 100 while another set is expressing 011 just 1 time behind, then this will cause us problems reading the outcomes. how could we resolve this? If we implement this idea in ALU (binary addition, etc) will this problem still occur?

Current revision

Return to Melbourne Homepage

Contents

Detection of allergens in food

  • the presence of certain alergen promote the expression of GFP.
  • must be fast reaction. ie. detection on the spot.
  • cell-free medium and can be stored in bottles under normal condition.

Biological Circuits

  • variable resistors, capaceitors, a catalog of resistors ...
  • setup a basic ALU(arithmetic logic unit), from pre-designed gates
  • biological clock; counts up in seconds or minutes (not countdown like peking07-hopcount), something similar but not elegant enough has been done by Harvard2006
  • Circuit from Cellular Autonoma: one bacterial cell could produce simple circuit or fancy pattern.

Biological Manufacturing

  • Bacterial cells to assist in production of things like biofuels/fertilisers/etc.
  • Cheap and easy production of pharmaceuticals.

Biological Control

In vivo sensors, processors and actuators

Bacteria have remarkable abilities to sense, process and actuate. These attributes of bacteria are potentially useful in designing and fabricating them for therapeutic purposes. One good example is here. [1] (more...)

cell-cell interaction

  • something similar to peking 2007 one..
  • group A bacteria undergo conjugation certain number of times before expressing a promotor
  • the promotor promotes the expression in group B bacteria of some other protein.
  • after undergoing conjugation certain number of times, group B bacteria express a repressor which inhibites the expresion of promotor from group A bacteria thus negative feedback.
  • a system with timing and quatity control

Radiation-proof E.coli

  • Express the DNA repair system (enzymes) of radiodurans in e.coli ?

Gold mining bacteria

  • Bacteria that uptake gold particles in solution possibly using transporters from alfalfa or other plants used in phytomining. For the purpose of making money.

Bacterial desalination

Bacteria that uptake salt from water for the purpose of a more cost effective method of desalination. Investigations into archaea probably needed.

HIV rapid diagnostic test

A rapid diagnostic test for HIV using bacteria that express CD4 and CCR5 coupled with an amplification signal (such as used in Brown university 2007).

HIV sink

Bacteria that express CD4 and CCR5 to act as a sink within the body thus lowering the viral load of HIV. Immunogenicity must be removed as was done with Bactoblood (UC Berkeley 2007).

Remote controlled locomotive micromachine

A remote control locomotive micro machine using bacterial flagella as the driver. The bacteria with flagella could possibly adhere to the micro machine using adhesins.

Bacterial kettle

Hyperthermophilic bacteria or archaea treated with uncouplers e.g. DNP, used to boil water for power generation.

Bacterial TV

A television screen composed of bacteria that release the different colors of fluorescent proteins to form an image.

Bacterial Bioremediation

Bacteria that fix or modify harmful contaminants in soil (i.e. cyanide, petrochemicals) after a spill/industrial activity.

A Feasible implementation of Bacteria Counter using a Binary Counting Approach

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 counting 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), 3 = 1\times 2 + 1\times 1 = 1\times 2^1 + 1\times2^0 = 11~(base ~2)

to represent number 4 in binary, 4 = 1\times2^2 + 0\times2^1 + 0\times2^0 = 100~(base ~2)

to represent number 5 in binary, 5 = 1\times4 + 0\times2^1 + 1\times1 = 1\times2^2 + 1\times2^0 = 101~(base~ 2)

Binary numbers can represent arbitarily large numbers just as digital numbers, e.g. if we have a binary number 1011011,


26 25 24 23 22 21 20
1 0 1 1 0 1 1
= 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)

Implementing Binary expression on "bacteria counter"

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(time)
clear clear clear 000 0
clear clear blue 001 1
clear green clear 010 2
clear green blue 011 3
red clear clear 100 4
red clear blue 101 5
red green clear 110 6
red green blue 111 7

So for instance if our colour combination is red, green, blue, then we know our current time is 7, if colour combination is just red, we know it's time 4. Every expression of B(n) depends only on input from B(n-1) plus another toggle control. So the only bacteria determining counting speed is B0 (just like in a stop watch where the counting speed is entirely dependent on the last digit). Maybe we can race the real clock by adjusting the expression rates!

As we know ALU (Arithmetic Logical Unit) is also based on binary number operation. This idea could be extended to be implemented on binary addition, substitution, multiplication.


This is just 1 out of the many thoughts we've put. We have the whole bucket of great ideas from other brilliant brainstormers!


I just thought about a practical problem we would have which is that if we have many copies of B2B1B0 and the different copies express asynchronously, e.g. one set is expressing 100 while another set is expressing 011 just 1 time behind, then this will cause us problems reading the outcomes. how could we resolve this? If we implement this idea in ALU (binary addition, etc) will this problem still occur?

Personal tools