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Math Modeling Pages

2008-07-09T16:20:12Z

AaLewis: /* Created Kinetic Law for Double Promoter */

This is the place for math modelers to post ideas, papers, examples and computer programs.

==Created Kinetic Law for Double Promoter==
''As of 7/3/08''

[[Image:Created_Kinetic_Law2.JPG]]

Link to ETH Zurich 2007 iGEM page for constants
http://parts.mit.edu/igem07/index.php/ETHZ/Engineering

The following units should be used (we think) for the expression above which gives the level of transcription for any doubly-regulated promoter.
Pay close attention to the units of molecules as it is critical that we have molecules of the correct schtuff.

[pro] is in molecules of promoter

[rep] is in molecules of repressor

[act] is in molecules of activator

K b is in molecules of mRNA per (second * molecules of promoter) which makes sense for the basal rate (Yea!!)

K 1 is the same units as K b 

K 2 is in 1/molecules of repressor (making the first denominator unitless)

K m is in molecules of activator (so that addition in denominator of second fraction is well-defined)

Note that the units of the overall product are molecules of mRNA per second, as needed. Note also that we want K 2 in the denominator of the first fraction to have the units described above and substituting (K 2 ) 2 as discussed durring "MWSU to Davidson" week would mess up the units on K b which would lead to serious problems with the model. If we need different numbers numerically in the two terms, we will need to go to K 3 as a separate constant but preserve the units by making K 3 have the same units as K 2 .

== Km Values for Models ==
''LIST OF Km Values'' 
*Km of '''3OC12 for LasR''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/LuxR.pdf Egland and Greenberg, 2000]) 
*Km of '''3OC6 for LuxR''' is 100 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Urbanowski_04.pdf Urbanowski et al., 2004]) 
*Km of '''LasR* for operator/promoter''' is 11 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Schuster_04.pdf Schuster et al, 2004]) 
*Km of '''LuxR* for operator/promoter''' is 10 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Kapland_Greenberg_87.pdf Kaplan and Greenberg, 1987]) 
*Km of '''cI dimer for OR1 and OR2''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/King_93.pdf King et al., 1993]) 
*Km of '''Mnt tetramer for binding to half operator/promoter''' is 50 nM and '''binding whole operator''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Berggrun_01.pdf Berggrun and Sauer, 2001]) 
*Km of '''Lsr for its binding site''' is X nM (no data available) 
*Km of '''AI-2 for LsrR''' is X nM (no data available) 
*Km of '''IPTG for LacI''' is 1.3 µM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gibert_Muller_hill_66.pdf Gilbert and Muller-Hill, 1966]) 
*Km of '''LacI for its binding site''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gilbert_Muller_Hill_67.pdf Gilbert and Muller-Hill, 1967]) 
*Km of '''LacI-I12 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-X86 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-I12_X86 for its binding site''' is 0.001 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*'''Half life of molecules in ''E. coli'':''' 2 minutes for mRNA; 1 molecule is 1 nM concentration ([http://www.bio.davidson.edu/courses/synthetic/papers/lsr_thesis_07.pdf Fang Ph.D. Thesis, 2007]); translation rate 15 amino acids per second and transcription is 40 nt per second (from ''Genes VII'' by Lewin).

==SimBiology (from MATLAB)==

We are attempting to create an accurate model of all the biological processes which will be present in the XOR gate when it is activated. Listed are some of the possible reactions we have come up with thus far, along with a short explanation of each of the reactions' respective functions.
 
(1) A -> A_RNA + A (Leak, Transcription) - Before the model is activated, we must account for a small portion of Transcription to naturally occur.
 
(2) B -> B-RNA + B - Same as (1)
 
(3) X_R + AI <-> XA (Receptor-Ligand Binding) - This is where LuxR and AI-1 bind to create the protein.
 
(4) S_R + PA <-> SP - Where LasR and pAI-1 bind
 
(5) XA + A -> A_RNA (Transcription) - The LuxR-AI-1 protein encodes into the pLux + Las- DNA and transcribes into the mRNA.
 
(6) SP + B -> B_RNA - The LasR-pAI-1 encodes into the pLas + Lux- DNA and transcribes into the mRNA
 
(7) A_RNA -> A_RNA + LuxI (Translation) - The mRNA is translated into the desired protein, LuxI.
 
(8) B_RNA -> B_RNA + LuxI - Same as (7)
 
(9) SP + A_RNA -> SP (Repressor) - The LasR-pAI-1 protein encodes onto the pLux + Las- DNA and represses the LuxR-AI-1 protein, inhibiting transcription of the mRNA.
 
(10) XA + B_RNA -> XA - The LuxR-AI-1 protein encodes onto pLas + Lux- DNA and represses the LasR-pAI-1 protein, inhibiting transcription of the mRNA.
 
(11) A_RNA -> null (Degradation) - After being translated, it will eventually degrade.
 
(12) B_RNA -> null - Same as (11)
 
(13) LuxI -> null - Same as (11)
 
(14) LuxI -> AI (*) - Protein LuxI is known to bind with AI-1.
 
[[Image:Xor_model.jpg]]

== Models ==

'''Aaron's Idea'''

''Workin' In, Workin' Out''

[[Image:Hash map.JPG]]

== Papers ==
[http://www.rfc-archive.org/getrfc.php?rfc=1319 MD2 Message-Digest Algorithm]

==Logical negation==

[[Logical negation]] is an [[logical operation|operation]] on one [[logical value]], typically the value of a [[proposition]], that produces a value of ''true'' if its operand is false and a value of ''false'' if its operand is true.

The truth table for '''NOT p''' (also written as '''~p''' or '''¬p''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:40%"
|+ '''Logical Negation'''
|- style="background:paleturquoise"
! style="width:20%" | p
! style="width:20%" | ¬p
|-
| F || T
|-
| T || F
|}
==Logical conjunction==

[[Logical conjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are true.

The truth table for '''p AND q''' (also written as '''p ∧ q''', '''p & q''', or '''p<math>\cdot</math>q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Conjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p · q
|-
| T || T || T
|-
| T || F || F
|-
| F || T || F
|-
| F || F || F
|-

|}

 

In ordinary language terms, if both ''p'' and ''q'' are true, then the conjunction ''p'' ∧ ''q'' is true. For all other assignments of logical values to ''p'' and to ''q'' the conjunction ''p'' ∧ ''q'' is false.

It can also be said that if ''p'', then ''p'' ∧ ''q'' is ''q'', otherwise ''p'' ∧ ''q'' is ''p''.

[[Logical disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' [[if and only if]] both of its operands are false.

The truth table for '''p OR q''' (also written as '''p ∨ q''', '''p || q''', or '''p + q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p + q
|-
| T || T || T
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

Stated in English, if ''p'', then ''p'' ∨ ''q'' is ''p'', otherwise ''p'' ∨ ''q'' is ''q''.

==Exclusive disjunction==

[[Exclusive disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if one but not both of its operands is true.

The truth table for '''p XOR q''' (also written as '''p + q''', '''p ⊕ q''', or '''p ≠ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Exclusive Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ⊕ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

For two propositions, '''XOR''' can also be written as (p = 1 ∧ q = 0)∨ (p = 0 ∧ q = 1).

This is the most efficient way of making an XOR with simple opperations.

[[Image:XOR5.jpg]]

[[Image:XOR.jpg]]

This diagram is the biological representation to: (A'∨B')∧(A∨B)

[[Image:XOR_using_AND_and_NOT_only.jpg]]

The picture above illustrates an XOR gate using only the operations of AND and NOT. While complicated, it appears to be the easiest way to perform an XOR operation with only AND and NOT. There are other ways but seem to involve even more operations. A minimum of 3 ANDs and 4 NOTs appears to be optimal, but is not guaranteed.

[[Image:XOR2.jpg]]

[[Image:XOR3.jpg]]

[[Image:XOR4.jpg]]

==Logical NAND==

The [[logical NAND]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' if and only if both of its operands are true. In other words, it produces a value of ''true'' if and only if at least one of its operands is false.

The truth table for '''p NAND q''' (also written as '''p | q''' or '''p ↑ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NAND'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↑ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || T
|}
 

==Logical NOR==

The [[logical NOR]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are false. In other words, it produces a value of ''false'' if and only if at least one of its operands is true. ↓ is also known as the [[Peirce arrow]] after its inventor, [[Charles Peirce]], and is a [[Sole sufficient operator]].

The truth table for '''p NOR q''' (also written as '''p ⊥ q''' or '''p ↓ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NOR'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↓ q
|-
| T || T || F
|-
| T || F || F
|-
| F || T || F
|-
| F || F || T
|}
 

*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

Math Modeling Pages

2008-07-08T15:23:33Z

AaLewis: /* Created Kinetic Law for Double Promoter */

This is the place for math modelers to post ideas, papers, examples and computer programs.

==Created Kinetic Law for Double Promoter==
''As of 7/3/08''

[[Image:Created_Kinetic_Law2.JPG]]

== Km Values for Models ==
''LIST OF Km Values'' 
*Km of '''3OC12 for LasR''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/LuxR.pdf Egland and Greenberg, 2000]) 
*Km of '''3OC6 for LuxR''' is 100 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Urbanowski_04.pdf Urbanowski et al., 2004]) 
*Km of '''LasR* for operator/promoter''' is 11 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Schuster_04.pdf Schuster et al, 2004]) 
*Km of '''LuxR* for operator/promoter''' is 10 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Kapland_Greenberg_87.pdf Kaplan and Greenberg, 1987]) 
*Km of '''cI dimer for OR1 and OR2''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/King_93.pdf King et al., 1993]) 
*Km of '''Mnt tetramer for binding to half operator/promoter''' is 50 nM and '''binding whole operator''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Berggrun_01.pdf Berggrun and Sauer, 2001]) 
*Km of '''Lsr for its binding site''' is X nM (no data available) 
*Km of '''AI-2 for LsrR''' is X nM (no data available) 
*Km of '''IPTG for LacI''' is 1.3 µM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gibert_Muller_hill_66.pdf Gilbert and Muller-Hill, 1966]) 
*Km of '''LacI for its binding site''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gilbert_Muller_Hill_67.pdf Gilbert and Muller-Hill, 1967]) 
*Km of '''LacI-I12 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-X86 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-I12_X86 for its binding site''' is 0.001 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*'''Half life of molecules in ''E. coli'':''' 2 minutes for mRNA; 1 molecule is 1 nM concentration ([http://www.bio.davidson.edu/courses/synthetic/papers/lsr_thesis_07.pdf Fang Ph.D. Thesis, 2007]); translation rate 15 amino acids per second and transcription is 40 nt per second (from ''Genes VII'' by Lewin).

==SimBiology (from MATLAB)==

We are attempting to create an accurate model of all the biological processes which will be present in the XOR gate when it is activated. Listed are some of the possible reactions we have come up with thus far, along with a short explanation of each of the reactions' respective functions.
 
(1) A -> A_RNA + A (Leak, Transcription) - Before the model is activated, we must account for a small portion of Transcription to naturally occur.
 
(2) B -> B-RNA + B - Same as (1)
 
(3) X_R + AI <-> XA (Receptor-Ligand Binding) - This is where LuxR and AI-1 bind to create the protein.
 
(4) S_R + PA <-> SP - Where LasR and pAI-1 bind
 
(5) XA + A -> A_RNA (Transcription) - The LuxR-AI-1 protein encodes into the pLux + Las- DNA and transcribes into the mRNA.
 
(6) SP + B -> B_RNA - The LasR-pAI-1 encodes into the pLas + Lux- DNA and transcribes into the mRNA
 
(7) A_RNA -> A_RNA + LuxI (Translation) - The mRNA is translated into the desired protein, LuxI.
 
(8) B_RNA -> B_RNA + LuxI - Same as (7)
 
(9) SP + A_RNA -> SP (Repressor) - The LasR-pAI-1 protein encodes onto the pLux + Las- DNA and represses the LuxR-AI-1 protein, inhibiting transcription of the mRNA.
 
(10) XA + B_RNA -> XA - The LuxR-AI-1 protein encodes onto pLas + Lux- DNA and represses the LasR-pAI-1 protein, inhibiting transcription of the mRNA.
 
(11) A_RNA -> null (Degradation) - After being translated, it will eventually degrade.
 
(12) B_RNA -> null - Same as (11)
 
(13) LuxI -> null - Same as (11)
 
(14) LuxI -> AI (*) - Protein LuxI is known to bind with AI-1.
 
[[Image:Xor_model.jpg]]

== Models ==

'''Aaron's Idea'''

''Workin' In, Workin' Out''

[[Image:Hash map.JPG]]

== Papers ==
[http://www.rfc-archive.org/getrfc.php?rfc=1319 MD2 Message-Digest Algorithm]

==Logical negation==

[[Logical negation]] is an [[logical operation|operation]] on one [[logical value]], typically the value of a [[proposition]], that produces a value of ''true'' if its operand is false and a value of ''false'' if its operand is true.

The truth table for '''NOT p''' (also written as '''~p''' or '''¬p''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:40%"
|+ '''Logical Negation'''
|- style="background:paleturquoise"
! style="width:20%" | p
! style="width:20%" | ¬p
|-
| F || T
|-
| T || F
|}
==Logical conjunction==

[[Logical conjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are true.

The truth table for '''p AND q''' (also written as '''p ∧ q''', '''p & q''', or '''p<math>\cdot</math>q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Conjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p · q
|-
| T || T || T
|-
| T || F || F
|-
| F || T || F
|-
| F || F || F
|-

|}

 

In ordinary language terms, if both ''p'' and ''q'' are true, then the conjunction ''p'' ∧ ''q'' is true. For all other assignments of logical values to ''p'' and to ''q'' the conjunction ''p'' ∧ ''q'' is false.

It can also be said that if ''p'', then ''p'' ∧ ''q'' is ''q'', otherwise ''p'' ∧ ''q'' is ''p''.

[[Logical disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' [[if and only if]] both of its operands are false.

The truth table for '''p OR q''' (also written as '''p ∨ q''', '''p || q''', or '''p + q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p + q
|-
| T || T || T
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

Stated in English, if ''p'', then ''p'' ∨ ''q'' is ''p'', otherwise ''p'' ∨ ''q'' is ''q''.

==Exclusive disjunction==

[[Exclusive disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if one but not both of its operands is true.

The truth table for '''p XOR q''' (also written as '''p + q''', '''p ⊕ q''', or '''p ≠ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Exclusive Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ⊕ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

For two propositions, '''XOR''' can also be written as (p = 1 ∧ q = 0)∨ (p = 0 ∧ q = 1).

This is the most efficient way of making an XOR with simple opperations.

[[Image:XOR5.jpg]]

[[Image:XOR.jpg]]

This diagram is the biological representation to: (A'∨B')∧(A∨B)

[[Image:XOR_using_AND_and_NOT_only.jpg]]

The picture above illustrates an XOR gate using only the operations of AND and NOT. While complicated, it appears to be the easiest way to perform an XOR operation with only AND and NOT. There are other ways but seem to involve even more operations. A minimum of 3 ANDs and 4 NOTs appears to be optimal, but is not guaranteed.

[[Image:XOR2.jpg]]

[[Image:XOR3.jpg]]

[[Image:XOR4.jpg]]

==Logical NAND==

The [[logical NAND]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' if and only if both of its operands are true. In other words, it produces a value of ''true'' if and only if at least one of its operands is false.

The truth table for '''p NAND q''' (also written as '''p | q''' or '''p ↑ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NAND'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↑ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || T
|}
 

==Logical NOR==

The [[logical NOR]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are false. In other words, it produces a value of ''false'' if and only if at least one of its operands is true. ↓ is also known as the [[Peirce arrow]] after its inventor, [[Charles Peirce]], and is a [[Sole sufficient operator]].

The truth table for '''p NOR q''' (also written as '''p ⊥ q''' or '''p ↓ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NOR'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↓ q
|-
| T || T || F
|-
| T || F || F
|-
| F || T || F
|-
| F || F || T
|}
 

*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

File:Created Kinetic Law.JPG

2008-07-08T15:06:43Z

AaLewis:

INCORRECT!
SEE CREATED KINETIC LAW2.JPG FOR CORRECT

Math Modeling Pages

2008-07-08T15:03:16Z

AaLewis: /* Created Kinetic Law for Double Promoter */

This is the place for math modelers to post ideas, papers, examples and computer programs.

==Created Kinetic Law for Double Promoter==
''As of 7/2/08''

[[Image:Created_Kinetic_Law2.JPG]]

== Km Values for Models ==
''LIST OF Km Values'' 
*Km of '''3OC12 for LasR''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/LuxR.pdf Egland and Greenberg, 2000]) 
*Km of '''3OC6 for LuxR''' is 100 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Urbanowski_04.pdf Urbanowski et al., 2004]) 
*Km of '''LasR* for operator/promoter''' is 11 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Schuster_04.pdf Schuster et al, 2004]) 
*Km of '''LuxR* for operator/promoter''' is 10 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Kapland_Greenberg_87.pdf Kaplan and Greenberg, 1987]) 
*Km of '''cI dimer for OR1 and OR2''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/King_93.pdf King et al., 1993]) 
*Km of '''Mnt tetramer for binding to half operator/promoter''' is 50 nM and '''binding whole operator''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Berggrun_01.pdf Berggrun and Sauer, 2001]) 
*Km of '''Lsr for its binding site''' is X nM (no data available) 
*Km of '''AI-2 for LsrR''' is X nM (no data available) 
*Km of '''IPTG for LacI''' is 1.3 µM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gibert_Muller_hill_66.pdf Gilbert and Muller-Hill, 1966]) 
*Km of '''LacI for its binding site''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gilbert_Muller_Hill_67.pdf Gilbert and Muller-Hill, 1967]) 
*Km of '''LacI-I12 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-X86 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-I12_X86 for its binding site''' is 0.001 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*'''Half life of molecules in ''E. coli'':''' 2 minutes for mRNA; 1 molecule is 1 nM concentration ([http://www.bio.davidson.edu/courses/synthetic/papers/lsr_thesis_07.pdf Fang Ph.D. Thesis, 2007]); translation rate 15 amino acids per second and transcription is 40 nt per second (from ''Genes VII'' by Lewin).

==SimBiology (from MATLAB)==

We are attempting to create an accurate model of all the biological processes which will be present in the XOR gate when it is activated. Listed are some of the possible reactions we have come up with thus far, along with a short explanation of each of the reactions' respective functions.
 
(1) A -> A_RNA + A (Leak, Transcription) - Before the model is activated, we must account for a small portion of Transcription to naturally occur.
 
(2) B -> B-RNA + B - Same as (1)
 
(3) X_R + AI <-> XA (Receptor-Ligand Binding) - This is where LuxR and AI-1 bind to create the protein.
 
(4) S_R + PA <-> SP - Where LasR and pAI-1 bind
 
(5) XA + A -> A_RNA (Transcription) - The LuxR-AI-1 protein encodes into the pLux + Las- DNA and transcribes into the mRNA.
 
(6) SP + B -> B_RNA - The LasR-pAI-1 encodes into the pLas + Lux- DNA and transcribes into the mRNA
 
(7) A_RNA -> A_RNA + LuxI (Translation) - The mRNA is translated into the desired protein, LuxI.
 
(8) B_RNA -> B_RNA + LuxI - Same as (7)
 
(9) SP + A_RNA -> SP (Repressor) - The LasR-pAI-1 protein encodes onto the pLux + Las- DNA and represses the LuxR-AI-1 protein, inhibiting transcription of the mRNA.
 
(10) XA + B_RNA -> XA - The LuxR-AI-1 protein encodes onto pLas + Lux- DNA and represses the LasR-pAI-1 protein, inhibiting transcription of the mRNA.
 
(11) A_RNA -> null (Degradation) - After being translated, it will eventually degrade.
 
(12) B_RNA -> null - Same as (11)
 
(13) LuxI -> null - Same as (11)
 
(14) LuxI -> AI (*) - Protein LuxI is known to bind with AI-1.
 
[[Image:Xor_model.jpg]]

== Models ==

'''Aaron's Idea'''

''Workin' In, Workin' Out''

[[Image:Hash map.JPG]]

== Papers ==
[http://www.rfc-archive.org/getrfc.php?rfc=1319 MD2 Message-Digest Algorithm]

==Logical negation==

[[Logical negation]] is an [[logical operation|operation]] on one [[logical value]], typically the value of a [[proposition]], that produces a value of ''true'' if its operand is false and a value of ''false'' if its operand is true.

The truth table for '''NOT p''' (also written as '''~p''' or '''¬p''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:40%"
|+ '''Logical Negation'''
|- style="background:paleturquoise"
! style="width:20%" | p
! style="width:20%" | ¬p
|-
| F || T
|-
| T || F
|}
==Logical conjunction==

[[Logical conjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are true.

The truth table for '''p AND q''' (also written as '''p ∧ q''', '''p & q''', or '''p<math>\cdot</math>q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Conjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p · q
|-
| T || T || T
|-
| T || F || F
|-
| F || T || F
|-
| F || F || F
|-

|}

 

In ordinary language terms, if both ''p'' and ''q'' are true, then the conjunction ''p'' ∧ ''q'' is true. For all other assignments of logical values to ''p'' and to ''q'' the conjunction ''p'' ∧ ''q'' is false.

It can also be said that if ''p'', then ''p'' ∧ ''q'' is ''q'', otherwise ''p'' ∧ ''q'' is ''p''.

[[Logical disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' [[if and only if]] both of its operands are false.

The truth table for '''p OR q''' (also written as '''p ∨ q''', '''p || q''', or '''p + q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p + q
|-
| T || T || T
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

Stated in English, if ''p'', then ''p'' ∨ ''q'' is ''p'', otherwise ''p'' ∨ ''q'' is ''q''.

==Exclusive disjunction==

[[Exclusive disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if one but not both of its operands is true.

The truth table for '''p XOR q''' (also written as '''p + q''', '''p ⊕ q''', or '''p ≠ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Exclusive Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ⊕ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

For two propositions, '''XOR''' can also be written as (p = 1 ∧ q = 0)∨ (p = 0 ∧ q = 1).

This is the most efficient way of making an XOR with simple opperations.

[[Image:XOR5.jpg]]

[[Image:XOR.jpg]]

This diagram is the biological representation to: (A'∨B')∧(A∨B)

[[Image:XOR_using_AND_and_NOT_only.jpg]]

The picture above illustrates an XOR gate using only the operations of AND and NOT. While complicated, it appears to be the easiest way to perform an XOR operation with only AND and NOT. There are other ways but seem to involve even more operations. A minimum of 3 ANDs and 4 NOTs appears to be optimal, but is not guaranteed.

[[Image:XOR2.jpg]]

[[Image:XOR3.jpg]]

[[Image:XOR4.jpg]]

==Logical NAND==

The [[logical NAND]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' if and only if both of its operands are true. In other words, it produces a value of ''true'' if and only if at least one of its operands is false.

The truth table for '''p NAND q''' (also written as '''p | q''' or '''p ↑ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NAND'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↑ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || T
|}
 

==Logical NOR==

The [[logical NOR]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are false. In other words, it produces a value of ''false'' if and only if at least one of its operands is true. ↓ is also known as the [[Peirce arrow]] after its inventor, [[Charles Peirce]], and is a [[Sole sufficient operator]].

The truth table for '''p NOR q''' (also written as '''p ⊥ q''' or '''p ↓ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NOR'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↓ q
|-
| T || T || F
|-
| T || F || F
|-
| F || T || F
|-
| F || F || T
|}
 

*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

File:Created Kinetic Law2.JPG

2008-07-08T15:02:29Z

AaLewis:

Math Modeling Pages

2008-07-08T14:20:47Z

AaLewis:

This is the place for math modelers to post ideas, papers, examples and computer programs.

==Created Kinetic Law for Double Promoter==
''As of 7/2/08''

[[Image:Created_Kinetic_Law.JPG]]

== Km Values for Models ==
''LIST OF Km Values'' 
*Km of '''3OC12 for LasR''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/LuxR.pdf Egland and Greenberg, 2000]) 
*Km of '''3OC6 for LuxR''' is 100 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Urbanowski_04.pdf Urbanowski et al., 2004]) 
*Km of '''LasR* for operator/promoter''' is 11 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Schuster_04.pdf Schuster et al, 2004]) 
*Km of '''LuxR* for operator/promoter''' is 10 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Kapland_Greenberg_87.pdf Kaplan and Greenberg, 1987]) 
*Km of '''cI dimer for OR1 and OR2''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/King_93.pdf King et al., 1993]) 
*Km of '''Mnt tetramer for binding to half operator/promoter''' is 50 nM and '''binding whole operator''' is 1 nM ([http://www.bio.davidson.edu/courses/synthetic/papers/Berggrun_01.pdf Berggrun and Sauer, 2001]) 
*Km of '''Lsr for its binding site''' is X nM (no data available) 
*Km of '''AI-2 for LsrR''' is X nM (no data available) 
*Km of '''IPTG for LacI''' is 1.3 µM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gibert_Muller_hill_66.pdf Gilbert and Muller-Hill, 1966]) 
*Km of '''LacI for its binding site''' is 10 pM ([http://www.bio.davidson.edu/courses/synthetic/papers/Gilbert_Muller_Hill_67.pdf Gilbert and Muller-Hill, 1967]) 
*Km of '''LacI-I12 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-X86 for its binding site''' is 0.13 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*Km of '''LacI-I12_X86 for its binding site''' is 0.001 pM (calculated from [http://www.bio.davidson.edu/courses/synthetic/papers/pLac_1980.pdf Schmitz and Galas, 1980]; and [http://www.bio.davidson.edu/courses/synthetic/papers/Scmitz_etal_78.pdf Schmitz et al., 1978]) 
*'''Half life of molecules in ''E. coli'':''' 2 minutes for mRNA; 1 molecule is 1 nM concentration ([http://www.bio.davidson.edu/courses/synthetic/papers/lsr_thesis_07.pdf Fang Ph.D. Thesis, 2007]); translation rate 15 amino acids per second and transcription is 40 nt per second (from ''Genes VII'' by Lewin).

==SimBiology (from MATLAB)==

We are attempting to create an accurate model of all the biological processes which will be present in the XOR gate when it is activated. Listed are some of the possible reactions we have come up with thus far, along with a short explanation of each of the reactions' respective functions.
 
(1) A -> A_RNA + A (Leak, Transcription) - Before the model is activated, we must account for a small portion of Transcription to naturally occur.
 
(2) B -> B-RNA + B - Same as (1)
 
(3) X_R + AI <-> XA (Receptor-Ligand Binding) - This is where LuxR and AI-1 bind to create the protein.
 
(4) S_R + PA <-> SP - Where LasR and pAI-1 bind
 
(5) XA + A -> A_RNA (Transcription) - The LuxR-AI-1 protein encodes into the pLux + Las- DNA and transcribes into the mRNA.
 
(6) SP + B -> B_RNA - The LasR-pAI-1 encodes into the pLas + Lux- DNA and transcribes into the mRNA
 
(7) A_RNA -> A_RNA + LuxI (Translation) - The mRNA is translated into the desired protein, LuxI.
 
(8) B_RNA -> B_RNA + LuxI - Same as (7)
 
(9) SP + A_RNA -> SP (Repressor) - The LasR-pAI-1 protein encodes onto the pLux + Las- DNA and represses the LuxR-AI-1 protein, inhibiting transcription of the mRNA.
 
(10) XA + B_RNA -> XA - The LuxR-AI-1 protein encodes onto pLas + Lux- DNA and represses the LasR-pAI-1 protein, inhibiting transcription of the mRNA.
 
(11) A_RNA -> null (Degradation) - After being translated, it will eventually degrade.
 
(12) B_RNA -> null - Same as (11)
 
(13) LuxI -> null - Same as (11)
 
(14) LuxI -> AI (*) - Protein LuxI is known to bind with AI-1.
 
[[Image:Xor_model.jpg]]

== Models ==

'''Aaron's Idea'''

''Workin' In, Workin' Out''

[[Image:Hash map.JPG]]

== Papers ==
[http://www.rfc-archive.org/getrfc.php?rfc=1319 MD2 Message-Digest Algorithm]

==Logical negation==

[[Logical negation]] is an [[logical operation|operation]] on one [[logical value]], typically the value of a [[proposition]], that produces a value of ''true'' if its operand is false and a value of ''false'' if its operand is true.

The truth table for '''NOT p''' (also written as '''~p''' or '''¬p''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:40%"
|+ '''Logical Negation'''
|- style="background:paleturquoise"
! style="width:20%" | p
! style="width:20%" | ¬p
|-
| F || T
|-
| T || F
|}
==Logical conjunction==

[[Logical conjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are true.

The truth table for '''p AND q''' (also written as '''p ∧ q''', '''p & q''', or '''p<math>\cdot</math>q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Conjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p · q
|-
| T || T || T
|-
| T || F || F
|-
| F || T || F
|-
| F || F || F
|-

|}

 

In ordinary language terms, if both ''p'' and ''q'' are true, then the conjunction ''p'' ∧ ''q'' is true. For all other assignments of logical values to ''p'' and to ''q'' the conjunction ''p'' ∧ ''q'' is false.

It can also be said that if ''p'', then ''p'' ∧ ''q'' is ''q'', otherwise ''p'' ∧ ''q'' is ''p''.

[[Logical disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' [[if and only if]] both of its operands are false.

The truth table for '''p OR q''' (also written as '''p ∨ q''', '''p || q''', or '''p + q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p + q
|-
| T || T || T
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

Stated in English, if ''p'', then ''p'' ∨ ''q'' is ''p'', otherwise ''p'' ∨ ''q'' is ''q''.

==Exclusive disjunction==

[[Exclusive disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if one but not both of its operands is true.

The truth table for '''p XOR q''' (also written as '''p + q''', '''p ⊕ q''', or '''p ≠ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Exclusive Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ⊕ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

For two propositions, '''XOR''' can also be written as (p = 1 ∧ q = 0)∨ (p = 0 ∧ q = 1).

This is the most efficient way of making an XOR with simple opperations.

[[Image:XOR5.jpg]]

[[Image:XOR.jpg]]

This diagram is the biological representation to: (A'∨B')∧(A∨B)

[[Image:XOR_using_AND_and_NOT_only.jpg]]

The picture above illustrates an XOR gate using only the operations of AND and NOT. While complicated, it appears to be the easiest way to perform an XOR operation with only AND and NOT. There are other ways but seem to involve even more operations. A minimum of 3 ANDs and 4 NOTs appears to be optimal, but is not guaranteed.

[[Image:XOR2.jpg]]

[[Image:XOR3.jpg]]

[[Image:XOR4.jpg]]

==Logical NAND==

The [[logical NAND]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' if and only if both of its operands are true. In other words, it produces a value of ''true'' if and only if at least one of its operands is false.

The truth table for '''p NAND q''' (also written as '''p | q''' or '''p ↑ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NAND'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↑ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || T
|}
 

==Logical NOR==

The [[logical NOR]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are false. In other words, it produces a value of ''false'' if and only if at least one of its operands is true. ↓ is also known as the [[Peirce arrow]] after its inventor, [[Charles Peirce]], and is a [[Sole sufficient operator]].

The truth table for '''p NOR q''' (also written as '''p ⊥ q''' or '''p ↓ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NOR'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↓ q
|-
| T || T || F
|-
| T || F || F
|-
| F || T || F
|-
| F || F || T
|}
 

*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

File:Created Kinetic Law.JPG

2008-07-08T14:13:43Z

AaLewis: As of 7/3/08

As of 7/3/08

Contact A Team Member

2008-06-02T14:22:52Z

AaLewis: /* Davidson */

== Davidson ==
'''Biology'''

Dr. Malcolm Campbell

macampbell@davidson.edu

Erin Feeney

erfeeney@davidson.edu

James Barron

james.barron@pipeline.hamptonu.edu

Madeline Parra

maparra@davidson.edu

Pallavi Penumetcha

papenumetcha@davidson.edu

Samantha Simpson

sasimpson@davidson.edu

'''Math'''

Dr. Laurie Heyer

laheyer@davidson.edu

Kelly Davis

kedavis@davidson.edu

Karlesha Roland

karlesha.roland@yahoo.com

Kristi Muscalino

krmuscalino@davidson.edu

== Missouri Western ==
'''Biology'''

Dr. Todd Eckdahl

echdahl@missouriwestern.edu

Bob Cool

rcool@missouriwestern.edu

Xiao Zhu

Xzhu@missouriwestern.edu

Andrew Gordon

ajg714@hotmail.com

'''Math'''

Dr. Jeff Poet

poet@missouriwestern.edu

Aaron Lewis

masterwizard_32@hotmail.com

John Igo

john_igo@hotmail.com

Contact A Team Member

2008-06-02T14:22:07Z

AaLewis: /* Davidson */

== Davidson ==
'''Biology'''

Dr. Malcolm Campbell

macampbell@davidson.edu

Erin Feeney

erfeeney@davidson.edu

James Barron

james.barron@pipeline.hamptonu.edu

Madeline Parra

maparra@davidson.edu

Pallavi Penumetcha

papenumetcha@davidson.edu

Samantha Simpson

sasimpson@davidson.edu

'''Math'''

Dr. Laurie Heyer

laheyer@davidson.edu

Karlesha Roland

karlesha.roland@yahoo.com

Kristi Muscalino

krmuscalino@davidson.edu

== Missouri Western ==
'''Biology'''

Dr. Todd Eckdahl

echdahl@missouriwestern.edu

Bob Cool

rcool@missouriwestern.edu

Xiao Zhu

Xzhu@missouriwestern.edu

Andrew Gordon

ajg714@hotmail.com

'''Math'''

Dr. Jeff Poet

poet@missouriwestern.edu

Aaron Lewis

masterwizard_32@hotmail.com

John Igo

john_igo@hotmail.com

Math Modeling Pages

2008-06-02T14:12:26Z

AaLewis: /* Models */

This is the place for math modelers to post ideas, papers, examples and computer programs.

Presentation on Sudoku (Aaron and John have seen)

http://www.math-cs.ucmo.edu/~hchen/talks/sudoku.pdf

== Models ==

'''Aaron's Idea'''

''Workin' In, Workin' Out''

[[Image:Hash map.JPG]]

== Papers ==
[http://www.rfc-archive.org/getrfc.php?rfc=1319 MD2 Message-Digest Algorithm]

==Logical negation==

[[Logical negation]] is an [[logical operation|operation]] on one [[logical value]], typically the value of a [[proposition]], that produces a value of ''true'' if its operand is false and a value of ''false'' if its operand is true.

The truth table for '''NOT p''' (also written as '''~p''' or '''¬p''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:40%"
|+ '''Logical Negation'''
|- style="background:paleturquoise"
! style="width:20%" | p
! style="width:20%" | ¬p
|-
| F || T
|-
| T || F
|}
==Logical conjunction==

[[Logical conjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are true.

The truth table for '''p AND q''' (also written as '''p ∧ q''', '''p & q''', or '''p<math>\cdot</math>q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Conjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p · q
|-
| T || T || T
|-
| T || F || F
|-
| F || T || F
|-
| F || F || F
|-

|}

 

In ordinary language terms, if both ''p'' and ''q'' are true, then the conjunction ''p'' ∧ ''q'' is true. For all other assignments of logical values to ''p'' and to ''q'' the conjunction ''p'' ∧ ''q'' is false.

It can also be said that if ''p'', then ''p'' ∧ ''q'' is ''q'', otherwise ''p'' ∧ ''q'' is ''p''.

[[Logical disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' [[if and only if]] both of its operands are false.

The truth table for '''p OR q''' (also written as '''p ∨ q''', '''p || q''', or '''p + q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p + q
|-
| T || T || T
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

Stated in English, if ''p'', then ''p'' ∨ ''q'' is ''p'', otherwise ''p'' ∨ ''q'' is ''q''.

==Exclusive disjunction==

[[Exclusive disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if one but not both of its operands is true.

The truth table for '''p XOR q''' (also written as '''p + q''', '''p ⊕ q''', or '''p ≠ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Exclusive Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ⊕ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

For two propositions, '''XOR''' can also be written as (p = 1 ∧ q = 0)∨ (p = 0 ∧ q = 1).

[[Image:XOR.jpg]]

This diagram is the biological representation to: (A'∨B')∧(A∨B)

[[Image:XOR_using_AND_and_NOT_only.jpg]]

The picture above illustrates an XOR gate using only the operations of AND and NOT. While complicated, it appears to be the easiest way to perform an XOR operation with only AND and NOT. There are other ways but seem to involve even more operations. A minimum of 3 ANDs and 4 NOTs appears to be optimal, but is not guaranteed.

[[Image:XOR2.jpg]]

[[Image:XOR3.jpg]]

[[Image:XOR4.jpg]]

==Logical NAND==

The [[logical NAND]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' if and only if both of its operands are true. In other words, it produces a value of ''true'' if and only if at least one of its operands is false.

The truth table for '''p NAND q''' (also written as '''p | q''' or '''p ↑ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NAND'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↑ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || T
|}
 

==Logical NOR==

The [[logical NOR]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are false. In other words, it produces a value of ''false'' if and only if at least one of its operands is true. ↓ is also known as the [[Peirce arrow]] after its inventor, [[Charles Peirce]], and is a [[Sole sufficient operator]].

The truth table for '''p NOR q''' (also written as '''p ⊥ q''' or '''p ↓ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NOR'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↓ q
|-
| T || T || F
|-
| T || F || F
|-
| F || T || F
|-
| F || F || T
|}
 

*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

Math Modeling Pages

2008-06-02T14:10:15Z

AaLewis: /* Models */

This is the place for math modelers to post ideas, papers, examples and computer programs.

Presentation on Sudoku (Aaron and John have seen)

http://www.math-cs.ucmo.edu/~hchen/talks/sudoku.pdf

== Models ==
[[Image:Hash map.JPG]]

== Papers ==
[http://www.rfc-archive.org/getrfc.php?rfc=1319 MD2 Message-Digest Algorithm]

==Logical negation==

[[Logical negation]] is an [[logical operation|operation]] on one [[logical value]], typically the value of a [[proposition]], that produces a value of ''true'' if its operand is false and a value of ''false'' if its operand is true.

The truth table for '''NOT p''' (also written as '''~p''' or '''¬p''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:40%"
|+ '''Logical Negation'''
|- style="background:paleturquoise"
! style="width:20%" | p
! style="width:20%" | ¬p
|-
| F || T
|-
| T || F
|}
==Logical conjunction==

[[Logical conjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are true.

The truth table for '''p AND q''' (also written as '''p ∧ q''', '''p & q''', or '''p<math>\cdot</math>q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Conjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p · q
|-
| T || T || T
|-
| T || F || F
|-
| F || T || F
|-
| F || F || F
|-

|}

 

In ordinary language terms, if both ''p'' and ''q'' are true, then the conjunction ''p'' ∧ ''q'' is true. For all other assignments of logical values to ''p'' and to ''q'' the conjunction ''p'' ∧ ''q'' is false.

It can also be said that if ''p'', then ''p'' ∧ ''q'' is ''q'', otherwise ''p'' ∧ ''q'' is ''p''.

[[Logical disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' [[if and only if]] both of its operands are false.

The truth table for '''p OR q''' (also written as '''p ∨ q''', '''p || q''', or '''p + q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p + q
|-
| T || T || T
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

Stated in English, if ''p'', then ''p'' ∨ ''q'' is ''p'', otherwise ''p'' ∨ ''q'' is ''q''.

==Exclusive disjunction==

[[Exclusive disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if one but not both of its operands is true.

The truth table for '''p XOR q''' (also written as '''p + q''', '''p ⊕ q''', or '''p ≠ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Exclusive Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ⊕ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

For two propositions, '''XOR''' can also be written as (p = 1 ∧ q = 0)∨ (p = 0 ∧ q = 1).

[[Image:XOR.jpg]]

This diagram is the biological representation to: (A'∨B')∧(A∨B)

[[Image:XOR_using_AND_and_NOT_only.jpg]]

The picture above illustrates an XOR gate using only the operations of AND and NOT. While complicated, it appears to be the easiest way to perform an XOR operation with only AND and NOT. There are other ways but seem to involve even more operations. A minimum of 3 ANDs and 4 NOTs appears to be optimal, but is not guaranteed.

[[Image:XOR2.jpg]]

[[Image:XOR3.jpg]]

[[Image:XOR4.jpg]]

==Logical NAND==

The [[logical NAND]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' if and only if both of its operands are true. In other words, it produces a value of ''true'' if and only if at least one of its operands is false.

The truth table for '''p NAND q''' (also written as '''p | q''' or '''p ↑ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NAND'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↑ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || T
|}
 

==Logical NOR==

The [[logical NOR]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are false. In other words, it produces a value of ''false'' if and only if at least one of its operands is true. ↓ is also known as the [[Peirce arrow]] after its inventor, [[Charles Peirce]], and is a [[Sole sufficient operator]].

The truth table for '''p NOR q''' (also written as '''p ⊥ q''' or '''p ↓ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NOR'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↓ q
|-
| T || T || F
|-
| T || F || F
|-
| F || T || F
|-
| F || F || T
|}
 

*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

Math Modeling Pages

2008-06-02T14:06:48Z

AaLewis:

This is the place for math modelers to post ideas, papers, examples and computer programs.

Presentation on Sudoku (Aaron and John have seen)

http://www.math-cs.ucmo.edu/~hchen/talks/sudoku.pdf

== Models ==
[[Image:Hash_map.jpg]]

== Papers ==
[http://www.rfc-archive.org/getrfc.php?rfc=1319 MD2 Message-Digest Algorithm]

==Logical negation==

[[Logical negation]] is an [[logical operation|operation]] on one [[logical value]], typically the value of a [[proposition]], that produces a value of ''true'' if its operand is false and a value of ''false'' if its operand is true.

The truth table for '''NOT p''' (also written as '''~p''' or '''¬p''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:40%"
|+ '''Logical Negation'''
|- style="background:paleturquoise"
! style="width:20%" | p
! style="width:20%" | ¬p
|-
| F || T
|-
| T || F
|}
==Logical conjunction==

[[Logical conjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are true.

The truth table for '''p AND q''' (also written as '''p ∧ q''', '''p & q''', or '''p<math>\cdot</math>q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Conjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p · q
|-
| T || T || T
|-
| T || F || F
|-
| F || T || F
|-
| F || F || F
|-

|}

 

In ordinary language terms, if both ''p'' and ''q'' are true, then the conjunction ''p'' ∧ ''q'' is true. For all other assignments of logical values to ''p'' and to ''q'' the conjunction ''p'' ∧ ''q'' is false.

It can also be said that if ''p'', then ''p'' ∧ ''q'' is ''q'', otherwise ''p'' ∧ ''q'' is ''p''.

[[Logical disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' [[if and only if]] both of its operands are false.

The truth table for '''p OR q''' (also written as '''p ∨ q''', '''p || q''', or '''p + q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p + q
|-
| T || T || T
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

Stated in English, if ''p'', then ''p'' ∨ ''q'' is ''p'', otherwise ''p'' ∨ ''q'' is ''q''.

==Exclusive disjunction==

[[Exclusive disjunction]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if one but not both of its operands is true.

The truth table for '''p XOR q''' (also written as '''p + q''', '''p ⊕ q''', or '''p ≠ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Exclusive Disjunction'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ⊕ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || F
|}
 

For two propositions, '''XOR''' can also be written as (p = 1 ∧ q = 0)∨ (p = 0 ∧ q = 1).

[[Image:XOR.jpg]]

This diagram is the biological representation to: (A'∨B')∧(A∨B)

[[Image:XOR_using_AND_and_NOT_only.jpg]]

The picture above illustrates an XOR gate using only the operations of AND and NOT. While complicated, it appears to be the easiest way to perform an XOR operation with only AND and NOT. There are other ways but seem to involve even more operations. A minimum of 3 ANDs and 4 NOTs appears to be optimal, but is not guaranteed.

[[Image:XOR2.jpg]]

[[Image:XOR3.jpg]]

[[Image:XOR4.jpg]]

==Logical NAND==

The [[logical NAND]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''false'' if and only if both of its operands are true. In other words, it produces a value of ''true'' if and only if at least one of its operands is false.

The truth table for '''p NAND q''' (also written as '''p | q''' or '''p ↑ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NAND'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↑ q
|-
| T || T || F
|-
| T || F || T
|-
| F || T || T
|-
| F || F || T
|}
 

==Logical NOR==

The [[logical NOR]] is an [[logical operation|operation]] on two [[logical value]]s, typically the values of two [[proposition]]s, that produces a value of ''true'' if and only if both of its operands are false. In other words, it produces a value of ''false'' if and only if at least one of its operands is true. ↓ is also known as the [[Peirce arrow]] after its inventor, [[Charles Peirce]], and is a [[Sole sufficient operator]].

The truth table for '''p NOR q''' (also written as '''p ⊥ q''' or '''p ↓ q''') is as follows:

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:lightcyan; font-weight:bold; text-align:center; width:45%"
|+ '''Logical NOR'''
|- style="background:paleturquoise"
! style="width:15%" | p
! style="width:15%" | q
! style="width:15%" | p ↓ q
|-
| T || T || F
|-
| T || F || F
|-
| F || T || F
|-
| F || F || T
|}
 

*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

File:Hash map.JPG

2008-06-02T14:03:08Z

AaLewis: Aaron's idea for hash code

Aaron's idea for hash code

Contact A Team Member

2008-06-02T13:53:01Z

AaLewis: /* Missouri Western */

== Davidson ==
'''Biology'''

'''Math'''

Dr. Laurie Heyer

laheyer@davidson.edu

Karlesha Roland

karlesha.roland@yahoo.com

Kristi Muscalino

krmuscalino@davidson.edu

== Missouri Western ==
'''Biology'''

Dr. Todd Eckdahl

echdahl@missouriwestern.edu

Bob Cool

rcool@missouriwestern.edu

Xiao Zhu

Xzhu@missouriwestern.edu

Andrew Gordon

ajg714@hotmail.com

'''Math'''

Dr. Jeff Poet

poet@missouriwestern.edu

Aaron Lewis

masterwizard_32@hotmail.com

John Igo

john_igo@hotmail.com

Contact A Team Member

2008-06-02T13:51:49Z

AaLewis: /* Missouri Western */

== Davidson ==
'''Biology'''

'''Math'''

Dr. Laurie Heyer

laheyer@davidson.edu

Karlesha Roland

karlesha.roland@yahoo.com

Kristi Muscalino

krmuscalino@davidson.edu

== Missouri Western ==
'''Biology'''

Bob Cool

rcool@missouriwestern.edu

Xiao Zhu

Xzhu@missouriwestern.edu

Andrew Gordon

ajg714@hotmail.com

'''Math'''

Dr. Jeff Poet

poet@missouriwestern.edu

Aaron Lewis

masterwizard_32@hotmail.com

John Igo

john_igo@hotmail.com

Contact A Team Member

2008-06-02T13:48:30Z

AaLewis: /* Davidson */

== Davidson ==
'''Biology'''

'''Math'''

Dr. Laurie Heyer

laheyer@davidson.edu

Karlesha Roland

karlesha.roland@yahoo.com

Kristi Muscalino

krmuscalino@davidson.edu

== Missouri Western ==
'''Biology'''

Bob Cool

rcool@missouriwestern.edu

Xiao Zhu

Xzhu@missouriwestern.edu

Andrew Gordon

ajg714@hotmail.com

'''Math'''

Aaron Lewis

masterwizard_32@hotmail.com

John Igo

john_igo@hotmail.com

Contact A Team Member

2008-06-02T13:45:41Z

AaLewis: /* Missouri Western */

== Davidson ==
'''Biology'''

'''Math'''

== Missouri Western ==
'''Biology'''

Bob Cool

rcool@missouriwestern.edu

Xiao Zhu

Xzhu@missouriwestern.edu

Andrew Gordon

ajg714@hotmail.com

'''Math'''

Aaron Lewis

masterwizard_32@hotmail.com

John Igo

john_igo@hotmail.com

Contact A Team Member

2008-06-02T13:43:11Z

AaLewis:

== Davidson ==
'''Biology'''

'''Math'''

== Missouri Western ==
'''Biology'''

'''Math'''

Aaron Lewis

masterwizard_32@hotmail.com

John Igo

john_igo@hotmail.com

Davidson/Missouri Western iGEM2008

2008-06-02T13:36:24Z

AaLewis:

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
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==[[Contact A Team Member]]==

==[[Wet Lab Pages]]==

==[[Math Modeling Pages]]==

== Las/Rhl cell signaling system ==
'''Responsible''': Robert Cool, Alicia Allen, and Erin Feeney

'''Las System'''

'''Signal Molecule''': An AHL called PAI-1 (N-3-oxododecanoyl-l-hsl)(3-oxo-C12-hsl)

'''Bacterial species''': Pseudomonas aeruginosa gram(-) possibly E.coli (see article 3)

'''Receiver protein''': LasR

'''Effect of binding''': TXN activation of virulence genes, lasA, lasB, apr, toxR

'''Synthase''': LasI enzyme

'''Target Genes''': lasI, lasA, lasB, apr, toxR

'''Regulation''': unknown

'''References'''

"Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes"

JP Pearson, EC Pesci and BH Iglewski
[http://jb.asm.org/cgi/reprint/179/18/5756?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&titleabstract=las&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT]

"Regulation of Pseudomonas Quinolone Signal Synthesis in Pseudomonas aeruginosa"

Dana S. Wade, M. Worth Calfee, Edson R. Rocha, Elizabeth A. Ling, Elana Engstrom, James P. Coleman, and Everett C. Pesci
[http://jb.asm.org/cgi/content/full/187/13/4372?view=long&pmid=15968046 2]

Posttranscriptional Control of Quorum-Sensing-Dependent Virulence Genes by DksA in Pseudomonas aeruginosa

Florence Jude,Thilo Köhler,Pavel Branny,Karl Perron,Matthias P. Mayer,Rachel Comte, and Christian van Delden
[http://jb.asm.org/cgi/content/full/185/12/3558?view=long&pmid=12775693 3]

Pending: [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1447470]

'''Rhl System'''

 
'''Signal Molecule''': An AHL called PAI-2, Plasminogen activator inhibitor-2, N-butanoyl-homoserine lactone (C4HSL)

'''Bacterial species''': Pseudomonas aeruginosa, gram(-)

'''Receiver Protein''': Rhl R

'''Effect of Binding''': activation of Rhamnosyl Transferase, then making RL (rhamnolipid)

'''Synthase''': RhlA and RhlB

'''Target Genes''': pqsABCDE and phnAB

'''Regulation''': unknown

'''References'''

[http://jb.asm.org/cgi/reprint/189/13/4827 background information on Las and Rhl]

[[Image:Las_rhl.gif]]

'''Parts Needed''':

LasR + pro/term

RhlR + pro/term

RhlI + pro/term

pqsABCDE + pro/term

pqsR

pqsH + pro/term

phnAB

LasI

RBS

== Lux cell signaling system ==

'''Responsible:''' Andrew Gordon and Pallavi Penumetcha

'''Signal molecule:''' ''N''-acyl-homoserine lactone (AHL) Generic term for a variety of species specific hormone-like molecules

'''Bacterial species:''' discovered in ''Vibrio fischeri'' known to work in ''E. coli''

'''Receiver protein:''' LuxR protein receives signal from AHL; also has some control over transciption of luciferase

'''Signal molecule synthase:''' LuxI; also has some control over transciption of luciferase

'''Additional Information:''' "Quorum Quenching" aiiA (intracellular) lactonase reduces AHL concentration

[[Image:800px-Luxrreceiverschematic.png]]

'''Resources'''

[http://partsregistry.org/Lux Lux Operon Pathway]

[http://partsregistry.org/AHL AHL signaling molecules by species; some are specific to gram pos but may affect gram negs]

'''References'''

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=522112 Quorum Quenching to control Lux Pathway]

'''Parts Needed''':

LuxR + pro/term

RBS

LuxI + pro/term

LuxI sender

== The ainS Quorum Sensing System??? ==

'''References'''

[http://www.medmicro.wisc.edu/labs/mcfall_ruby_papers/pdf/2003/Lupp_Ruby_2003_MolMicro.pdf Synergy of Lux and Ain]

[http://www.medmicro.wisc.edu/labs/mcfall_ruby_papers/pdf/2004/Lupp_Ruby_Jun2004_JBacteriol.pdf Ain induction of Lux]

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1112039 Layers of Signaling]

[http://www.medmicro.wisc.edu/labs/mcfall_ruby_papers/pdf/2003/Lupp_Ruby_2003_MolMicro.pdf Sequential Induction]

== Lsr (AI-2) cell signaling system ==

'''Responsible''': Kelly Davis, Xiao Zhu

'''Signal molecule''': AI-2 (furanosyl borate diester in V. harveyi, a variety of other molecules in other species), all are derived from DPD [http://www.biomedcentral.com/content/pdf/1471-2148-4-36.pdf]

'''Bacterial species''':

lsrA,B,C,D,F,G,R,K: Escherichia coli HS, SMS-3-5, str. K12 substr. MG1655, and substr. DH10B.

lsrE:Escherichia coli str. K12 substr. MG1655

LuxS:Escherichia coli HS, SMS-3-5, APEC O1, str. K12 substr. MG1655, substr. DH10B, and UTI89.

'''Receiver protein''': LsrR protein receives signal from sensor protein

'''Signal molecule synthase''': Pfs enzyme, then LuxS autoinducer synthase

'''Target genes''': lsr operon, including ABC transporter and LsrK kinase

'''Regulation''': LsrR represses the lsr operon, derepression by phospho-AI-2; cAMP-CRP is shown to bind to a cAMP receptor protein (CRP) binding site located in the upstream region of the lsr promoter and works with the LsrR repressor to regulate AI-2 uptake.

'''Note:''' AI-2 is synthesized and secreted during exponential growth and is imported in stationary phase when glucose becomes limiting. In the presence of glucose, AI-2 is not imported because the lsr operon is not transcribed due to camp-CAP mediated repression. Both glycerol and G3P(glycerol 3-phosphate) repress lsr transcription, while the majority repression comes from G3P. DHAP represses lsr transcription by a cAMP-CAP-independent mechanism involving LsrR.

'''Parts Needed:'''

LsrR pro/term

LsrK

LsrACDB (transport)

LsrFGE (catabolic)

LuxS

Pfs enzyme (?)

http://gcat.davidson.edu/GcatWiki/images/b/b8/N654260305_1291548_2335.jpg

'''Note:'''

lsrB encodes the periplasmic AI-2 binding protein

lsrC & lsrD encode the channel proteins

lsrA encodes the ATPase that provides energy for AI-2 transport

lsrF is similar to genes specifying aldolases

lsrG encodes a protein with an unknown function.

[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5591389&ordinalpos=26&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum tam: trans-aconitate 2-methyltransferase, also known as lsrE or yneD] [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=6061192&ordinalpos=10&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum yneE:conserved inner membrane protein]

[[Image:Har.JPG]]
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=55669965 R-THMF]
http://gcat.davidson.edu/GcatWiki/images/8/8c/S-DPD.gif
http://www.nature.com/nrmicro/journal/v3/n5/images/nrmicro1146-f2.gif

http://gcat.davidson.edu/GcatWiki/images/c/c9/Grl.jpg

DHAP: dihydroxyacetone phosphate.

http://gcat.davidson.edu/GcatWiki/images/9/9b/Grlw.jpg

'''References'''

[http://iai.asm.org/cgi/reprint/IAI.00550-07v1.pdf Global Effects of the Cell-to-Cell Signaling Molecules Autoinducer-2, Autoinducer-3, and Epinephrine in a luxS Mutant of Enterohemorrhagic Escherichia Coli]

[http://www.rsc.org/delivery/_ArticleLinking/DisplayHTMLArticleforfree.cfm?JournalCode=CC&Year=2005&ManuscriptID=b509396a&Iss=38 Shows how AI-2 is formed]

[http://www.jstor.org/sici?sici=0027-8424(20031125)100%3C14549%3ACCAB%3E2.0.CO%3B2-B&cookieSet=1 Signaling explained with graphics of AI-2 pathways]

[http://web.ebscohost.com/ehost/detail?vid=1&hid=116&sid=edfbf2f7-b0c8-40c3-8227-1cc94f134972%40sessionmgr108 Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium]

[http://www.microbialcellfactories.com/content/pdf/1475-2859-1-5.pdf Review of AI-2 and other systems]

[http://jb.asm.org/cgi/content/full/189/16/6011?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&titleabstract=AI+2+LsrR&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture]

[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22733&blobtype=pdf E. coli produces a signal that can substitute for AI-2]

[http://jb.asm.org/cgi/content/full/187/1/238?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&titleabstract=quorum+sensing+AI-2&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Regulation of Uptake and Processing of the Quorum-Sensing Autoinducer AI-2 in Escherichia coli]

'''Resources'''

[http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=5586283 lsrK gene in Entrez]

[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=6062136&ordinalpos=9&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum#summary lsrR gene in Entrez]

[http://BioCyc.org/ECOLI/substring-search?type=NIL&object=lsr lsr genes in EcoCyc]

== Fec cell signaling system ==
Responsible: Xiao Zhu, James Barron (DC)

'''Ferric Dicitrate Transport System'''
The inducer, ferric citrate, binds to an outer membrane transport protein, FecA, and without further transport elicits a signal that is transmitted across the outer membrane (by FecA), the periplasm, and the cytoplasmic membrane (by FecBCDE and FecR) into the cytoplasm. Signal transfer across the three subcellular compartments is mediated by the outer membrane transport protein (FecA) that interacts in the periplasm with a cytoplasmic transmembrane protein (FecR). FecR is required for activation of a sigma factor (FecI) which belongs to the extracytoplasmic function (ECF)sigma factor family.
 
Only iron not iron complex enters the cytoplasm. FecA is the TonB energy transducing system-dependent.
 
'''Signaling Molecule:''' FeC (ferric dicitrate)
 
'''Bacteria species:''' E.coli, Pseudomonas putida, P. aeruginosa, Serratia marcescens, Klebsiella pneumoniae, Aerobacter aerogenes, Bordetella pertussis, B. bronchseptica, B. avium, and Ralstonia solanacearum.
 
'''Receptor Protein: ''' FecA
 
'''Effect of binding:''' the conformational changes that FecA undergoes when binding to ferric citrate:The alpha helix in loop 7 unravels, and the loop moves by up to 11 angstroms ; Loop 8 moves up to 15 angstroms.
http://www.rsc.org/ej/CS/2007/b617040b/b617040b-f13.gif
 
'''Sensor Producer:''' N/A
 

 
Harvard iGEM'07 team worked with Fec system, the results were not favorable. [http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing :We believe that overexpression of the Fec system killed the cells, possibly by disturbing the cell membranes.]
 
Regulation of the FecI-type ECF sigma factor by transmembrane signaling
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4834NW4-1&_user=2665120&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=23ac72561c82e74caa6a61b622c3501a]
 
[http://pathway.gramene.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-2261 More detailed information about Fec]
 
[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=215624&blobtype=pdf Exogenous Induction of the Iron Dicitrate Transport System of Escherichia coli K-12]
 
[http://jb.asm.org/cgi/content/full/183/1/162 Control of the Ferric Citrate Transport System of Escherichia coli:Mutations in Region2.1 of the FecI ECF Sigma Factor Suppress Mutations in the FecR Transmembrane Regulatory Protein]
 
[http://jb.asm.org/cgi/content/full/189/19/6913 Docking of the Periplasmic FecB Binding Protein to the FecCD Transmembrane Proteins in the Ferric Citrate Transport System of Escherichia coli]
 
[http://jb.asm.org/cgi/content/abstract/185/6/1870 Interactions between the Outer Membrane Ferric Citrate Transporter FecA and TonB: Studies of the FecA TonB Box]

== Signal molecules ==

[[Image:QSsignals.gif|QSsignals.gif]]

'''Gram (-) bacteria use:'''

3-oxo-C6-HSL, N-(3-oxohexanoyl)-L-homoserine lactone, an AHL

DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione

HHQ, 2-heptyl-4(1H)-quinolone, an AQ

'''Gram (+) bacteria use:'''

DPD, the AI-2 precursor, 4,5 dihydroxy-2,3-pentanedione

A-Factor, 2-isocapryloyl-3-hydroxymethyl--butyrolactone

PQS, pseudomonas quinolone signal, 2-heptyl-3-hydroxy-4(1H)-quinolone

DSF, ‘diffusible factor’, cis-11-methyl-2-dodecenoic acid

3OH-PAME, hydroxyl-palmitic acid methyl ester;

AIP-1, staphylococcal autoinducing peptide 1

== E. coli Signaling ==

"As yet no AHL-producing Escherichia coli or Salmonella strains have been identified, although both organisms possess an AHL receptor (SdiA) of the LuxR protein class and respond to AHLs produced by other bacteria." [http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Williams 2007]

== Cell signaling resources ==
[http://partsregistry.org/Featured_Parts:Cell-Cell-Signaling Featured parts in iGEM registry]

[http://en.wikipedia.org/wiki/Cell_signaling Wikipedia entry]

[http://mic.sgmjournals.org/cgi/reprint/153/12/3923 Quorum sensing, communication and cross-kingdom signalling in the bacterial world]

[http://www.molbio.princeton.edu/index.php?option=content&task=view&id=27 Bonnie Bassler lab at Princeton]

[http://www.nottingham.ac.uk/quorum/ One-Stop Shopping for QS from Nottingham]

[http://journals.royalsociety.org/content/w26732234707/?p=c1685368363e450faabedd3ee8fd60dc&pi=3 Special Issue: Bacterial conversations: talking, listening and eavesdropping]

[http://library.albany.edu/science/whatsnew_dialogs.htm Dialogs with Bacteria: Quorum Sensing]

[http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellSignaling.html General Types of Cell Signaling: Bacteria on Steroids?]

[http://www.samsi.info/200405/compbio/workinggroup/cell/Eungdamrong_Iyengar_Biology_of_the_Cell_96_355_2004.pdf Modeling Cell-Signaling Networks]

[http://journals.royalsociety.org/content/m5hgygq1t6daxy72/fulltext.pdf Quorum Sensing and the Population Control of Virulence]

== Davidson Journal Club ==

[http://www.bio.davidson.edu/courses/synthetic/papers/Stochastic_Cells.pdf Stochasticity and Gene Expression --- Dr. Campbell]

[http://gcat.davidson.edu/iGEM08/cryptography_graph.pdf Hash Function --- Dr. Heyer]

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

''Engineering and Epidemic''

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

''Half-Adder Logic Gate''

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

''Project 1: Protein Scaffolds as a Molecular Breadboard''

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

''Biological diode''

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

'''Duke University'''

''Bacterial Communication With Light''

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc -

'''University of Cambridge'''

''BOL: Bacteria OnLine''

They talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Cambridge

'''Tokyo Tech'''

''Pareto's Principle: An Ant Society''

The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation". Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

http://parts.mit.edu/igem07/index.php/Tokyo_Tech

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

'''Harvard'''

''Quorum Sensing''

Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.

http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

'''Chiba'''

''Communication Unit''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.

http://parts.mit.edu/igem07/index.php/Chiba/Communication

'''Brown'''

''Cellular Lead Sensor''

-no useful information

http://parts.mit.edu/igem07/index.php/Brown

'''Colombia-Israel (ORT Ebin High School)'''

''A Microbial Biosensor Device''

No description left...

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''Edinburgh'''

''Division PoPper'' and ''Self Flavouring Yoghurt''

- This team is working on a project that is looking into a form of cell communication

- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication."

- Could not find where on this page this info came from, but it was included with this link:
''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.''

http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21

'''Imperial'''

''Infector Detector''

-no useful information, but really interesting project...

http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)

'''Middle East Technical University'''

Chase simulator

This project was not completed, but has some interesting information on E. coli cells triggering a response in nearby E. coli cells.
http://parts.mit.edu/igem07/index.php/Chase_Simulator

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Math Modeling Pages

2008-05-28T13:35:47Z

AaLewis: /* Papers */

This is the place for math modelers to post ideas, papers, examples and computer programs.

Presentation on Sudoku (Aaron and John have seen)

http://www.math-cs.ucmo.edu/~hchen/talks/sudoku.pdf

== Papers ==
*[http://www.doc.ic.ac.uk/~nd/surprise_96/journal/vol4/cs11/report.html#Introduction%20to%20neural%20networks Neural Network Models]
*[http://www.facweb.iitkgp.ernet.in/~niloy/PRESENTATION/ACRI_presentation_97.ppt Cellular Automata Based Authentication]
*MD5 Paper
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1762088 Stochastic model of E. coli AI-2 quorum signal circuit reveals alternative synthesis pathways] Describes a Stochastic Petri Net (SPN) model of AI-2 (Lux), provides XML code and rate constants.

How to break MD5 and other Hash functions.. A paper written by Xiaoyun Wang and her co-authors about how to break MD5 – i.e. how to make collisions occur
http://www.infosec.sdu.edu.cn/uploadfile/papers/How%20to%20Break%20MD5%20and%20Other%20Hash%20Functions.pdf
Nostradamus attack – i.e. the bit about predicting who will become president by exploiting MD5
http://www.win.tue.nl/hashclash/Nostradamus/

The following was taken from http://www.freesoft.org/CIE/RFC/1321/4.htm

MD5 Algorithm Description
We begin by supposing that we have a b-bit message as input, and that we wish to find its message digest. Here b is an arbitrary nonnegative integer; b may be zero, it need not be a multiple of eight, and it may be arbitrarily large. We imagine the bits of the message written down as follows:
m_0 m_1 ... m_{b-1}
The following five steps are performed to compute the message digest of the message.

Step 1. Append Padding Bits
The message is "padded" (extended) so that its length (in bits) is congruent to 448, modulo 512. That is, the message is extended so that it is just 64 bits shy of being a multiple of 512 bits long. Padding is always performed, even if the length of the message is already congruent to 448, modulo 512.
Padding is performed as follows: a single "1" bit is appended to the message, and then "0" bits are appended so that the length in bits of the padded message becomes congruent to 448, modulo 512. In all, at least one bit and at most 512 bits are appended.

Step 2. Append Length
A 64-bit representation of b (the length of the message before the padding bits were added) is appended to the result of the previous step. In the unlikely event that b is greater than 2^64, then only the low-order 64 bits of b are used. (These bits are appended as two 32-bit words and appended low-order word first in accordance with the previous conventions.)
At this point the resulting message (after padding with bits and with b) has a length that is an exact multiple of 512 bits. Equivalently, this message has a length that is an exact multiple of 16 (32-bit) words. Let M[0 ... N-1] denote the words of the resulting message, where N is a multiple of 16.

Step 3. Initialize MD Buffer
A four-word buffer (A,B,C,D) is used to compute the message digest. Here each of A, B, C, D is a 32-bit register. These registers are initialized to the following values in hexadecimal, low-order bytes first):
word A: 01 23 45 67
word B: 89 ab cd ef
word C: fe dc ba 98
word D: 76 54 32 10

3.4 Step 4. Process Message in 16-Word Blocks
We first define four auxiliary functions that each take as input three 32-bit words and produce as output one 32-bit word.
F(X,Y,Z) = XY v not(X) Z
G(X,Y,Z) = XZ v Y not(Z)
H(X,Y,Z) = X xor Y xor Z
I(X,Y,Z) = Y xor (X v not(Z))
In each bit position F acts as a conditional: if X then Y else Z. The function F could have been defined using + instead of v since XY and not(X)Z will never have 1's in the same bit position.) It is interesting to note that if the bits of X, Y, and Z are independent and unbiased, the each bit of F(X,Y,Z) will be independent and unbiased.
The functions G, H, and I are similar to the function F, in that they act in "bitwise parallel" to produce their output from the bits of X, Y, and Z, in such a manner that if the corresponding bits of X, Y, and Z are independent and unbiased, then each bit of G(X,Y,Z), H(X,Y,Z), and I(X,Y,Z) will be independent and unbiased. Note that the function H is the bit-wise "xor" or "parity" function of its inputs.
This step uses a 64-element table T[1 ... 64] constructed from the sine function. Let T[i] denote the i-th element of the table, which is equal to the integer part of 4294967296 times abs(sin(i)), where i is in radians. The elements of the table are given in the appendix.
Do the following:
/* Process each 16-word block. */
For i = 0 to N/16-1 do
/* Copy block i into X. */
For j = 0 to 15 do
Set X[j] to M[i*16+j].
end /* of loop on j */

/* Save A as AA, B as BB, C as CC, and D as DD. */
AA = A
BB = B

CC = C
DD = D

/* Round 1. */
/* Let [abcd k s i] denote the operation
a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 7 1] [DABC 1 12 2] [CDAB 2 17 3] [BCDA 3 22 4]
[ABCD 4 7 5] [DABC 5 12 6] [CDAB 6 17 7] [BCDA 7 22 8]
[ABCD 8 7 9] [DABC 9 12 10] [CDAB 10 17 11] [BCDA 11 22 12]
[ABCD 12 7 13] [DABC 13 12 14] [CDAB 14 17 15] [BCDA 15 22 16]

/* Round 2. */
/* Let [abcd k s i] denote the operation
a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 1 5 17] [DABC 6 9 18] [CDAB 11 14 19] [BCDA 0 20 20]
[ABCD 5 5 21] [DABC 10 9 22] [CDAB 15 14 23] [BCDA 4 20 24]
[ABCD 9 5 25] [DABC 14 9 26] [CDAB 3 14 27] [BCDA 8 20 28]
[ABCD 13 5 29] [DABC 2 9 30] [CDAB 7 14 31] [BCDA 12 20 32]

/* Round 3. */
/* Let [abcd k s t] denote the operation
a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 5 4 33] [DABC 8 11 34] [CDAB 11 16 35] [BCDA 14 23 36]
[ABCD 1 4 37] [DABC 4 11 38] [CDAB 7 16 39] [BCDA 10 23 40]
[ABCD 13 4 41] [DABC 0 11 42] [CDAB 3 16 43] [BCDA 6 23 44]
[ABCD 9 4 45] [DABC 12 11 46] [CDAB 15 16 47] [BCDA 2 23 48]

/* Round 4. */
/* Let [abcd k s t] denote the operation
a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
/* Do the following 16 operations. */
[ABCD 0 6 49] [DABC 7 10 50] [CDAB 14 15 51] [BCDA 5 21 52]
[ABCD 12 6 53] [DABC 3 10 54] [CDAB 10 15 55] [BCDA 1 21 56]
[ABCD 8 6 57] [DABC 15 10 58] [CDAB 6 15 59] [BCDA 13 21 60]
[ABCD 4 6 61] [DABC 11 10 62] [CDAB 2 15 63] [BCDA 9 21 64]

/* Then perform the following additions. (That is increment each
of the four registers by the value it had before this block
was started.) */
A = A + AA
B = B + BB
C = C + CC
D = D + DD

end /* of loop on i */

Step 5. Output
The message digest produced as output is A, B, C, D. That is, we begin with the low-order byte of A, and end with the high-order byte of D.
This completes the description of MD5. A reference implementation in C is given in the appendix.

Summary
The MD5 message-digest algorithm is simple to implement, and provides a "fingerprint" or message digest of a message of arbitrary length. It is conjectured that the difficulty of coming up with two messages having the same message digest is on the order of 2^64 operations, and that the difficulty of coming up with any message having a given message digest is on the order of 2^128 operations. The MD5 algorithm has been carefully scrutinized for weaknesses. It is, however, a relatively new algorithm and further security analysis is of course justified, as is the cas Differences Between MD4 and MD5
The following are the differences between MD4 and MD5:
1. A fourth round has been added.
2. Each step now has a unique additive constant.
3. The function g in round 2 was changed from (XY v XZ v YZ) to (XZ v Y not(Z)) to make g less symmetric.
4. Each step now adds in the result of the previous step. This promotes a faster "avalanche effect".
5. The order in which input words are accessed in rounds 2 and 3 is changed, to make these patterns less like each other.
6. The shift amounts in each round have been approximately optimized, to yield a faster "avalanche effect." The shifts in different rounds are distinct.

== Engineering agar ==
[http://www.biotech.iastate.edu/lab_protocols/EvoAntiResBact.html A lab for showing antibiotic resistance across Amp concentration gradient]

Davidson/Missouri Western iGEM2008

2008-04-07T19:29:46Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

''Engineering and Epidemic''

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

''Half-Adder Logic Gate''

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

''Project 1: Protein Scaffolds as a Molecular Breadboard''

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

''Biological diode''

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

'''Duke University'''

''Bacterial Communication With Light''

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc -

'''University of Cambridge'''

''BOL: Bacteria OnLine''

They talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Cambridge

'''Tokyo Tech'''

''Pareto's Principle: An Ant Society''

The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation". Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

http://parts.mit.edu/igem07/index.php/Tokyo_Tech

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

'''Harvard'''

''Quorum Sensing''

Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.

http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

'''Chiba'''

''Communication Unit''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.

http://parts.mit.edu/igem07/index.php/Chiba/Communication

'''Brown'''

''Cellular Lead Sensor''

-no useful information

http://parts.mit.edu/igem07/index.php/Brown

'''Colombia-Israel (ORT Ebin High School)'''

''A Microbial Biosensor Device''

No description left...

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''Edinburgh'''

''Division PoPper'' and ''Self Flavouring Yoghurt''

- This team is working on a project that is looking into a form of cell communication

- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication."

- Could not find where on this page this info came from, but it was included with this link:
''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.''

http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21

'''Imperial'''

''Infector Detector''

-no useful information, but really interesting project...

http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Davidson/Missouri Western iGEM2008

2008-04-07T19:28:37Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

''Engineering and Epidemic''

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

''Half-Adder Logic Gate''

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

''Project 1: Protein Scaffolds as a Molecular Breadboard''

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

''Biological diode''

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

'''Duke University'''

''Bacterial Communication With Light''

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc -

'''University of Cambridge'''

''BOL: Bacteria OnLine''

They talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Cambridge

'''Tokyo Tech'''

''Pareto's Principle: An Ant Society''

The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation". Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

http://parts.mit.edu/igem07/index.php/Tokyo_Tech

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

'''Harvard'''

''Quorum Sensing''

Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.

http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

'''Chiba'''

''Communication Unit''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.

http://parts.mit.edu/igem07/index.php/Chiba/Communication

'''Brown'''

''Cellular Lead Sensor''

-no useful information

http://parts.mit.edu/igem07/index.php/Brown

'''Colombia-Israel (ORT Ebin High School)'''

''A Microbial Biosensor Device''

No description left...

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''Edinburgh'''

''Division PoPper'' and ''Self Flavouring Yoghurt''

- This team is working on a project that is looking into a form of cell communication

- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication."

Could not find where on this page this info came from, but it was included with this link:
''- The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.''

http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21

'''Imperial'''

''Infector Detector''

- -no useful information, but really interesting project...

- http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007)

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Davidson/Missouri Western iGEM2008

2008-04-07T19:07:06Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

''Engineering and Epidemic''

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

''Half-Adder Logic Gate''

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

''Project 1: Protein Scaffolds as a Molecular Breadboard''

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

''Biological diode''

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

'''Duke University'''

''Bacterial Communication With Light''

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc -

'''University of Cambridge'''

''BOL: Bacteria OnLine''

They talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Cambridge

'''Tokyo Tech'''

''Pareto's Principle: An Ant Society''

The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation". Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

http://parts.mit.edu/igem07/index.php/Tokyo_Tech

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

'''Harvard'''

''Quorum Sensing''

Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.

http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

'''Chiba'''

''Communication Unit''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.

http://parts.mit.edu/igem07/index.php/Chiba/Communication

'''Brown'''

''Cellular Lead Sensor''

-no useful information

http://parts.mit.edu/igem07/index.php/Brown

'''Colombia-Israel (ORT Ebin High School)'''

''A Microbial Biosensor Device''

No description left...

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''University of Waterloo''' (2007) Half-Adder Logic Gate
- -no useful information

'''Edinburgh'''
- http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21 + The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.
- -This team is working on a project that is looking into a form of cell communication +
- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication." +

'''Imperial'''
- http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007) Project 1 Protein Scaffolds as a Molecular Breadboard
- -no useful information, but really interesting project...

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Davidson/Missouri Western iGEM2008

2008-04-07T19:03:12Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

''Engineering and Epidemic''

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

''Half-Adder Logic Gate''

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

''Project 1: Protein Scaffolds as a Molecular Breadboard''

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

''Biological diode''

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

'''Duke University'''

''Bacterial Communication With Light''

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc -

'''University of Cambridge'''

''BOL: Bacteria OnLine''

They talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Cambridge

'''Tokyo Tech'''

''Pareto's Principle: An Ant Society''

The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation". Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

http://parts.mit.edu/igem07/index.php/Tokyo_Tech

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

'''Harvard'''

''Quorum Sensing''

Was developing a luxL luxR quorum sensing system using OHHL. Lux quorum-sensing works like a system of sender and receiver.

http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

'''Chiba'''

''Communication Unit''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.

http://parts.mit.edu/igem07/index.php/Chiba/Communication

'''Brown'''

''Cellular Lead Sensor''

-no useful information

http://parts.mit.edu/igem07/index.php/Brown

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''University of Waterloo''' (2007) Half-Adder Logic Gate
- -no useful information

'''Edinburgh'''
- http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21 + The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.
- -This team is working on a project that is looking into a form of cell communication +
- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication." +

'''Imperial'''
- http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007) Project 1 Protein Scaffolds as a Molecular Breadboard
- -no useful information, but really interesting project...

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Davidson/Missouri Western iGEM2008

2008-04-07T18:50:38Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

''Engineering and Epidemic''

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

''Half-Adder Logic Gate''

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

''Project 1: Protein Scaffolds as a Molecular Breadboard''

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

''Biological diode''

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

'''Duke University'''

''Bacterial Communication With Light''

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc -

'''University of Cambridge'''

''BOL: Bacteria OnLine''

They talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Cambridge

'''Tokyo Tech'''

''Pareto's Principle: An Ant Society''

They say, “Bistability and cell-cell communication are necessary to realize our model of ‘Balanced differentiation’.”

http://parts.mit.edu/igem07/index.php/Tokyo_Tech

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

''Harvard'' was developing a luxL luxR quorum sensing system using OHHL.
http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

''Chiba''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.
http://parts.mit.edu/igem07/index.php/Chiba/Communication

''Tokyo-tec''h:The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation".Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

- http://parts.mit.edu/igem07/index.php/Bay_Area_RSI + Virginia Tech (2007) Engineering and Epidemic
- -no useful information +

*The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

- http://parts.mit.edu/igem07/index.php/Brown
- -no useful information

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''University of Waterloo''' (2007) Half-Adder Logic Gate
- -no useful information

'''Edinburgh'''
- http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21 + The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.
- -This team is working on a project that is looking into a form of cell communication +
- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication." +

'''Imperial'''
- http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007) Project 1 Protein Scaffolds as a Molecular Breadboard
- -no useful information, but really interesting project...

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Davidson/Missouri Western iGEM2008

2008-04-07T18:42:30Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

''Engineering and Epidemic''

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

''Half-Adder Logic Gate''

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

''Project 1 Protein Scaffolds as a Molecular Breadboard''

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

''Biological diode''

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - bacterial communication with light.

http://parts.mit.edu/igem07/index.php/Cambridge - they talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Tokyo_Tech - They say, “Bistability and cell-cell communication are necessary to realize our model of ‘Balanced differentiation’.”

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

''Harvard'' was developing a luxL luxR quorum sensing system using OHHL.
http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

''Chiba''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.
http://parts.mit.edu/igem07/index.php/Chiba/Communication

''Tokyo-tec''h:The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation".Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

- http://parts.mit.edu/igem07/index.php/Bay_Area_RSI + Virginia Tech (2007) Engineering and Epidemic
- -no useful information +

*The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

- http://parts.mit.edu/igem07/index.php/Brown
- -no useful information

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''University of Waterloo''' (2007) Half-Adder Logic Gate
- -no useful information

'''Edinburgh'''
- http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21 + The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.
- -This team is working on a project that is looking into a form of cell communication +
- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication." +

'''Imperial'''
- http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007) Project 1 Protein Scaffolds as a Molecular Breadboard
- -no useful information, but really interesting project...

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Davidson/Missouri Western iGEM2008

2008-04-07T18:39:49Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''

Engineering and Epidemic

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''

Half-Adder Logic Gate

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''

Project 1 Protein Scaffolds as a Molecular Breadboard

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''

Biological diode

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - bacterial communication with light.

http://parts.mit.edu/igem07/index.php/Cambridge - they talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Tokyo_Tech - They say, “Bistability and cell-cell communication are necessary to realize our model of ‘Balanced differentiation’.”

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

''Harvard'' was developing a luxL luxR quorum sensing system using OHHL.
http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

''Chiba''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.
http://parts.mit.edu/igem07/index.php/Chiba/Communication

''Tokyo-tec''h:The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation".Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

- http://parts.mit.edu/igem07/index.php/Bay_Area_RSI + Virginia Tech (2007) Engineering and Epidemic
- -no useful information +

*The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

- http://parts.mit.edu/igem07/index.php/Brown
- -no useful information

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''University of Waterloo''' (2007) Half-Adder Logic Gate
- -no useful information

'''Edinburgh'''
- http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21 + The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.
- -This team is working on a project that is looking into a form of cell communication +
- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication." +

'''Imperial'''
- http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007) Project 1 Protein Scaffolds as a Molecular Breadboard
- -no useful information, but really interesting project...

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

Davidson/Missouri Western iGEM2008

2008-04-07T18:39:11Z

AaLewis: /* iGEM 2007 Useful Information */

<center>
Davidson College - Missouri Western State University
</center>
<center>

iGEM 2008
</center>

== iGEM 2007 Useful Information ==
'''Virginia Tech'''
Engineering and Epidemic

The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

http://parts.mit.edu/igem07/index.php/Virginia_Tech

'''University of Waterloo'''
Half-Adder Logic Gate

The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.

http://parts.mit.edu/igem07/index.php/Waterloo

'''UCSF'''
Project 1 Protein Scaffolds as a Molecular Breadboard

Using synthetic protein scaffolds to control information flow of a kinase pathway in eukaryotic cells.

http://parts.mit.edu/igem07/index.php/UCSF

'''Tianjin'''
Biological diode

In this project, we try to construct a biological device to imitate the function of the diode, one of the most significant parts in the electric integrate circuit. The flow of molecular signal AHL is considered as the current of electric circuit. The generator, amplifiers, blocks and detector cells are constructed with the parts provided by MIT and then are equipped in series in order to establish the cellular and molecular biological diode. Our device, which is a combination of technologies from the field of computer science, molecular biology and chemical engineering, is a breakthrough for the application of mature techniques of chemical engineering to the field of synthetic biology.

http://parts.mit.edu/igem07/index.php/Tianjin

http://parts.mit.edu/igem07/index.php/Duke/Projects/bc - bacterial communication with light.

http://parts.mit.edu/igem07/index.php/Cambridge - they talk a little about making a bacterial internet, I have no idea what they mean.

http://parts.mit.edu/igem07/index.php/Tokyo_Tech - They say, “Bistability and cell-cell communication are necessary to realize our model of ‘Balanced differentiation’.”

'''Quorum Sensing'''
[http://www.nottingham.ac.uk/quorum/index.htm See this quorum sensing web page]

''Harvard'' was developing a luxL luxR quorum sensing system using OHHL.
http://parts.mit.edu/igem07/index.php/Harvard#Quorum_Sensing

''Chiba''

Something about cell to cell communication involving LuxL, LuxR, and AHL. Hard to understand because they did not translate into English very well.
http://parts.mit.edu/igem07/index.php/Chiba/Communication

''Tokyo-tec''h:The goal of our project is to make a bacterial society that follows Pareto's principle as an ant society does. On the other word, we try to construct a bacterial system which takes "balanced differentiation".Bistability and cell-cell communication are necessary to realize our model of "Balanced differentiation".

- http://parts.mit.edu/igem07/index.php/Bay_Area_RSI + Virginia Tech (2007) Engineering and Epidemic
- -no useful information +

*The use of bacteria to model the spread of a disease. It would appear that cell-to-cell communication is a major part of the design of the project. It is unclear how successful the team was in building parts useful to us. Most of the project seems to be on the mathematical modeling side of things.

- http://parts.mit.edu/igem07/index.php/Brown
- -no useful information

- http://parts.mit.edu/igem07/index.php/Colombia-Israel%20(ORT%20Ebin%20High%20School)

'''University of Waterloo''' (2007) Half-Adder Logic Gate
- -no useful information

'''Edinburgh'''
- http://parts.mit.edu/igem07/index.php/Edinburgh#The_Projects.21 + The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome. Useful for long addition in base-2.
- -This team is working on a project that is looking into a form of cell communication +
- "We designed a signal generator device that produces an output in the form of PoPS pulses each time a bacteria undergoes cell division. Therefore it may trigger actions as a function of cell replication." +

'''Imperial'''
- http://parts.mit.edu/igem07/index.php/Imperial + UCSF (2007) Project 1 Protein Scaffolds as a Molecular Breadboard
- -no useful information, but really interesting project...

== iGEM 2006 Useful Information ==
'''UT Austin 2005/2006'''
Project : Edge Detector
Link to parts: http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_UTAustin

Useful information:
They have "black boxed" the light-system and used it as an input for the of the edge detection circuitry.

Edge Detector Circuit and logic. The light sensing machinery from above has been black-boxed and the edge detection circuitry has been added downstream. Red light represses the expression of 2 genes; a biosynthetic gene for a membrane diffusible quorum sensing activator (AHL), and a dominant transcriptional repressor (cI). (Right) The output of the circuit (Z;Beta-galactosidase) is ON only in the presence of X (AHL) and the absence of Y (cI). This can only occur at the light/dark boundary.

Note: Built on 2005’s work. Pretty much the same as 2005.

''' Harvard'''
“Cell Surface Targeting”
http://parts.mit.edu/wiki/index.php/Harvard_2006

Project Overview
“In order to target nanostructures to cells, we developed adaptamers, universal nucleic acid adaptars which can link two substrates.
• Such an interface could also be used to link together entire cells for the study of cell-cell interactions and the linkage of two interacting proteins, in effect creating a nucleic acid enzyme.
• Adaptamers generally depend on aptamers, short sequences of nucleic acid that bind with high specificity and affinity to particular substrates.
• Tahiri-Alaoui et al. created the first aptamer in 2002, consisting of two aptamer sequences linked together by a bulky basepairing region ~100 nucleotides long.
• Our goal was to create an adaptamer that could link together streptavidin and thrombin. Delivery of thrombin to a streptavidin-coated magnetic bead would show the potential for delivery of a macromolecule to a cell surface.
Additionally, we wished to be able to be able to quench adaptamer function through the addition of an adapatamer-disabling oligonucleotide.”

'''The University of Calgary''' 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered ''E. coli'' bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way.
The Receivers express Green Fluorescent Protein in the vicinity of AHSL.
The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place.
Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

'''Berkeley''': networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

'''Mexico''': cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.”
“Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

'''Brown:Bacterial''' Freeze Tag
http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview
2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

'''McGill University Split YFP'''
http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

'''Penn State'''
http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

'''Tokyo'''
http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo.
-1. Inputs
-1. Chemicals
-1. To indicate each square
-1. To be spreaded into all squares.
-1. Outputs
-1. Reporter of SYANAC: GFP
Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.

'''BU 2006'''
Project: build a functioning "Biological Night-Light" system

Link to parts : http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_BU
Goal
Isolate luxCDABE and add the 4 BioBrick restriction sites to the ends of the gene.
Ideas
"Proteins that affect the wavelength of the emitted light, lumazine and yellow fluorescent protein, have been isolated from Photobacterium and Vibrio species, respectively. The lumazine proteins shift the color of the light to wavelengths shorter than 490 nm..." (Meighen 1991) Perhaps we could build a circuit to modulate the emitted wavelength by periodically expressing a carefully-chosen fluoresent protein. Think FRET and BRET.

Let's modify the lux operon so our bacteria can play Conway's Game of Life. In the game, discrete "cells" interact with one another according to four extremely simple rules, which essentially boil down to this: if a cell has too many or too few neighbors it turns off, otherwise it turns/stays on. These rules and the initial state of all the cells often produce systems of fascinating and lifelike complexity. Perhaps we could add a circuit such that LuxI would only be activated in response to a narrow "medium" range of concentrations of its autoinducer (3OC6HSL), not too much or too little. In fact, I think such a circuit has already been built by the Weiss lab and demonstrated with their infamous bullseye.

'''Weiss Lab: Game of Life'''
Link: http://www.princeton.edu/~rweiss/
Note: Weiss Lab build a system that enables cells to “play” Conway’s Game of Life, where cells live or die based on the density of their neighbors. This system exhibits complex global emergent behavior that arises from the interaction of cells based on simple local rules.

Another system is a pulse generator where sender cells communicate to nearby receiver cells, which then respond with a transient burst of gene expression whose amplitude and duration depends on the distance from the senders. In another system, receiver cells have been engineered to respond to cell-cell communication signals from senders.

'''Bangalore NCBS 2006'''
Synchronization of bacterial cell cycles. Use a cell cycle-dependent promoter to drive a LuxI-LuxR based cell-cell signal. Use regulation of replication initiator DnaA to modulate cell cycle in receiver cells. Immediate goals: To determine if candidate promoters oscillate; to regulate DnaA levels
http://parts.mit.edu/wiki/index.php/Workshop

'''Rice University 2006'''
The objective of this project is to engineer Escherichia coli which are able to actively pursue and mark or eliminate another bacterial target. This system can be divided into three components: an input element, a processing element, and a response element. The input element will consist of a quorum sensing circuit which would allow specific detection of the bacterial target. The processing element will facilitate the signaling of this input into controlled responses. A number of different response elements can be conceived, to be used separately or in tandem: 1) integration into the chemotactic pathway of E. coli, allowing for directed mobilization towards the target, 2) reporter response at high pheromone concentrations to allow for visual identification of the target location (e.g., GFP production), and 3) an elimination response to produce molecules which are specifically lethal to the desired target.
http://parts.mit.edu/wiki/index.php/PROJECT_PROPOSAL

'''Cambridge''': http://parts.mit.edu/wiki/index.php/Cambridge_University_2006

The type 1 cell produces 3O-C6-HSL (represented by the small yellow cannon ball) while type 2 produces 3O-C12-HSL (represented by the blue cannon ball).  The type 1 cell responds to 3O-C12 HSL and type 2 responds to 3O-C6 HSL. The response of type 1 cells can be visualized through the expression of RFP. The response of type 2 cells can be visualized through the expression of GFP.

1. Parts used for generating patterns (these are parts whose function Cambridge characterized)
 (a) Constitutively expressed fluorescent proteins:
ECFP: BBa_I13601
GFP: BBa_J04430
EYFP: BBa_I6031
mRFP1: BBa_J04450
(b) Constitutive or auto-induced AHL synthesis:
Lux-sender (auto-inducing): BBa_I15030
Las-sender (constitutive): BBa_I0407
Rhl-sender (constitutive): BBa_I0405
Cin-sender (constitutive): BBa_I0409  
(c) AHL-induced fluorescence response:
Lux-receiver (GFP): BBa_T9002
Lux-receiver (EYFP): BBa_I13263
Las-receiver (EYFP): BBa_I0426
Rhl-receiver (EYFP): BBa_I0424
Cin-receiver (EYFP): BBa_I0428

'''Princeton''': http://parts.mit.edu/wiki/index.php/Princeton:Project_Summary

Mammalian cell-cell signaling using LuxR and LuxI…not applicable

== iGEM 2005 Useful Information ==
'''Caltech'''
http://www.cds.caltech.edu/~murray/synbio/wiki/index.php?title=Main_Page&direction=prev&oldid=52
AND gates used to build an adder (oligo technology, Winfree lab)
http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/5/55/Chen-surf05.pdf

Massive models: http://www.cds.caltech.edu/%7Emurray/synbio/wiki/images/4/44/Ho-surf05.pdf

'''Cambridge'''
http://www.ccbi.cam.ac.uk/iGEM2005/index.php/Main_Page
Used sender/pulse-generator from Princeton to do something?
AHL signal and aTc activated promoter
Important paper in PNAS where this is shown to work:
http://www.princeton.edu/~rweiss/papers/basu-pulse-2004.pdf

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005
Bacterial wire propogates signal of AHL

'''MIT 2005'''
The first way we might build such a system involves the direct communication of an antigen, which can be just about anything, with the cell; this is accomplished by attaching an antibody to the cell in such a way that the binding of an antigen to the antibody initiates a signalling cascade that terminates in PoPs. The main benefit of such a system is that it can stand alone, and is thus a viable solution to problems such as "how do we deploy our biosensor into a lake where it can respond to toxin levels?" The main issue to be dealt with is that this system is in some ways less modular; of course, anyone could just follow our steps and hook up their scFv sequence of choice.
http://openwetware.org/wiki/IGEM:MIT/2005/Direct_communication_of_antigen_and_receiver

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1

'''Penn State'''
http://parts2.mit.edu/wiki/index.php?title=Penn_StateProjectDes

”The idea for our project grew out of one for a "bacterial maze," in which bacteria would use logic to make their way through a microfabricated labrynth. This seemed slightly too difficult, so we linearized the the concept and added transfer of a signal; the idea was then dubbed a "bacterial relay race."
As in a conventional relay race, the signal is to "go," or induce motility of a latter stage participant. This is accomplished by passing a baton. In our case, the participants are E. coli, and the baton is a quorum sensing molecule, 3OC6HSL (we have another strategy that utilizes conjugation rather than quorum sensing to mediate the signal).
In addition to passing the signal, though, the first participant must stop. We explored this option, but settled instead on terminating the first participant. In our design we really do kill the messanger.”

'''Arizona'''
“Water Color”
http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006

Project Details
“The current name of our project is "Water Color." It is a system that selectively expresses one of three florescence proteins. Each of the three florescence proteins will be expressed in the presence of a unique inducer. Each florescent protein will be controlled by a unique repressed promoter. Thus we will have the expression of three flourescent proteins activated by the presence of there respective inducers.
The idea of our project is to have a media with these cells on it so that each cell will be individually activated to shown a certain "color" (in actuallity, express one florescent protein, which may or may not look unique). Thus the media is able to dispaly an image. The spacial resolution with determine how much it will look like an image. A further idea, to be implemented later (time permitting), is to have the ability to "erase" the image. This would be accomplished by repressing all three promoters. Currently, there are no plans to implement this.”

Flowchart of Parts: http://parts.mit.edu/wiki/index.php/University_of_Arizona_2006/Parts_Schedule

'''Harvard'''
http://bio.freelogy.org/wiki/IGEM_2005

'''UC Berkley 2005'''
http://parts2.mit.edu/wiki/index.php/UC_Berkeley_2005

Conjugation is a process through which cells can exchange genetic material on plasmids. Conjugal plasmids (in our case incF and incP plasmids) carry the machinery necessary to transfer themselves in the form of mating pair formation (mpf) and DNA transfer (dtr) genes. Conjugation is under the control of the TraJ regulatory protein, which when expressed induces a cascade that results in the formation of a pore by mpf genes and then subsequent nicking, rolling circle replication and transfer of one strand of the plasmid by the relaxosome complex and other dtr proteins. The relaxosome nicks the plasmid at the OriT region and then covalently attaches one of its subunits to the 5' end of the plasmid DNA, and by doing so it is able to drag the plasmid across the pore formed by the mpf machinery by means of a coupling protein. Upon reaching its destination, the single strand of plasmid DNA is recircularized and a complement strand is synthesized by transferred primases.

Non-mobile synthetic F plasmid: Begins the conjugation signal, which it sends to plasmid B. Also contains the CFP tag which identifies the host cell as "F-type", and always produces mRNA 'key 2' which unlocks RNA lock 2

-1. -B - Non-mobile almost-wild F plasmid: Contains all F-plasmid genes EXCEPT OriTf, TraJf. Plasmid receives and propagates the conjugation signal from TraJf in plasmid 1-A and sends the signal to OriTf in 1-C
1-C - Mobile F plasmid: Contains the OriTf site which receives signal from plasmid 1-B. This plasmid then leaves the host cell and enters the conjugating recipient cell. Holds encrypted message (produce cI --> turn on GFP to signify "message 1 received") secured by RNA lock 1.

2-A Non-mobile synthetic R plasmid: Always produces mRNA 'key1'. Thus when it receives 'lock1' (sent by mobile plasmid 1-C) it can open the latter and produce cI, which will activate plasmid 1-C (turn on GFP, "message 1 received") and simultaneously activate TraJr (start R conjugation cascade)

-1. 2-B Non-mobile almost-wild R plasmid: Just like 1-B, contains all of the wild type R-plasmid EXCEPT OriTr and TraJr. Propagates TraJr signal from 2-A and sends it to OriTr
2-C Mobile R plasmid: Contains the OriTr site, which receives signal from plasmid 2-B. This plasmid then leaves the host cell and submits its message back into cell #1