projects in need of doing
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Projects in need of doing
Rui Alves
Metabolic Reconstruction
Rui Alves
To do
• Literature analysis– Semi done– Needs to implement
• FREQUENCY ANALYSIS• CO-OCCURENCE ANALYSIS• A GOOD DATA BASE STRUCTURE TO KEEP
TRACK OF PREVIOUS SEARCHES AND USE THEM
• A GOOD VISUALIZATION TOOL
You would learn
• Literature analysis– PHP– APACHE– MAYBE JAVA AND C
To Do
• Phylogenetic analysis– 60% done– Needs to improve the database structure– Needs to implement a web front to connect
the database to a browser
You would learn
• Literature analysis– PHP– APACHE– HTML– MYSQL
To Do
• MODELLING & DOCKING– IMPLEMENT A METASEARCH TOOLS TO
USE EXISTING MODELLING SERVERS– SAME FOR DOCKING– IMPLEMENT IN HOUSE WAY OF RUNNING
ROBETTA – WEB INTERFACE
You would learn
• Literature analysis– PHP– APACHE– HTML– C
To Do
• INTEGRATIVE ARCHITECTURE– DESIGN ARCHITECTURE TO INTEGRATE
ALL DATA
You would learn
• Literature analysis– PHP– APACHE– HTML– C
To Do
• BIOLOGICAL APPLICATION, ALLWAYS
REWARDS
• CO-AUTORSHIP IN PAPERS DESCRIBING THE WORK
• THERE MAY BE SOME MONEY FOR ONE PART TIME JOB FOR A FEW MONTHS, DEPENDING ON HOW THE MINISTRY ALLOWS THE ADMINISTRATION OF THE PROJECTS
Design Principles in Signal Transduction
Rui Alves
To Do
• Compare MAPK pathways to TCS
• Compare different types of TCS
• Compare different types of MAPKS
TCS MAPK
You would learn
• MATHEMATICA
• MATHEMATICAL MODELLING
REWARDS
• CO-AUTORSHIP IN PAPERS DESCRIBING THE WORK
Modeling the life cycle of the lac operon
Rui Alves
To Do
• Start working with stochastica approximations to analyze demand theory not only in gene expression but also in protein modules
You would learn
• MATHEMATICA
• MATHEMATICAL MODELLING
• Mathematically Controlled Comparisons
• Theoretical ecology
REWARDS
• CO-AUTORSHIP IN PAPERS DESCRIBING THE WORK
• Possibility of going abroad if funding can be secured
The lac operon
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAP
RNAPol
Maintenance of the lac operon as a function of life style
Can one understand, quantitatively, which are the boundaries for selection of the lac operon so that bacteria do not lose this operon through random drift?
The lac operon
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
Mike has done the analysis, with the simplifying assumptions that no glucose was ever in the medium (i.e. CAP is always on) and considering only the regulator mutants and building and analyzing a model of bacterial growth
Determining the mutant to wild type ratios as a function of time
, ,
, ,
w ww w
P P w w P P P
m m w w m m m
X X
X X X
X X X
2
, ,
2
, ,
/ /( ) / ( / ) /
/ /( ) / ( / ) /
P w w PP P w
w
P P ww P P w
m w w mm m w
w
m m ww m m w
dX dt X dX dt Xd R dt d X X dt
X
R
dX dt X dX dt Xd R dt d X X dt
X
R
, ,,
, ,
, ,,
, ,
0
0
P w P wP P P ww P
ww P P ww P P
m w m wm m m ww m
ww m m ww m m
R t Exp t R
R t Exp t R
Bacteria Cycle between environments with high (H) and low
(L) Lac
,,
,
,
,
1
, ,
,
,
,
1
HP w H H
P i P P wwH Hww P P
LP w
L Lww P P
P i
L L LP P ww P w
L Lww P P
HP w
H Hww P P
R C Exp CD
R C
Exp C D
Parameter values are a function of the environment and of the
genotype
Hwg 1(1 )H H H H
ww w w P w m
L Hww ww
g m m
0.0125
Hw P P
Hw m m m
m
m
9 1 16 10
10
30
60
P
m
m
mutations res generation
res
res
res
Selection boundaries for the lac operon
0.0001 0.001 0.01 0.1 1
LogD1
100
10000
1. 106
1. 108
1. 1010
LogCPromoter Ratio= 0.001
Regulator Ratio= 0.001
Selection for inhibitor and promoter elements
The lac operonlacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAPRNAPol
, ,
, ,
w w w
wY Y w Y Y Y
wZ Z w Z Z Z
X X
X X X
X X X
, ,
, ,
, ,
, ,
wI I w I I I
wP P w P P P
wP P w P P P
wCAP CAP w CAP CAP CAP
X X X
X X X
X X X
X X X
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
The lac operon: Selecting an up-promoter
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAPRNAPol
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
, ,wP P w P P PX X X
Gain of function promoter mutant
0.00001 0.0001 0.001 0.01 0.1LogD1
100
10000
1. 106
1. 108
1. 1010
LogC Stronger promoter selected
The lac operon:Selecting a down-promoter
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAPRNAPol
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
, ,wP P w P P PX X X
Loss of function promoter mutant
0.00001 0.0001 0.001 0.01 0.1LogD1
100
10000
1. 106
1. 108
1. 1010
LogCStronger promoter selected
Weaker promoter selected
Maintenance of current promoter
The lac operon: Selecting for less efficient lacZ
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAPRNAPol
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
, ,wZ Z w Z Z ZX X X
Loss of function -Gal
0.00001 0.0001 0.001 0.01 0.1LogD1
100
10000
1. 106
1. 108
1. 1010
LogC
Weaker galactosidase selected
Maintenance of current -Gal plus promoter
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAPRNAPol
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
, ,wY Y w Y Y YX X X
The lac operon: Selecting for less efficient lacY
Loss of permease function mutant
0.00001 0.0001 0.001 0.01 0.1LogD1
100
10000
1. 106
1. 108
1. 1010
LogC
Weaker permease selected
Maintenance of current permease plus -Gal plus
promoter
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAPRNAPol
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
, ,wI I w I I IX X X
The lac operon: Selecting for less efficient lacI
Loss of function inhibitor
0.00001 0.0001 0.001 0.01 0.1LogD1
100
10000
1. 106
1. 108
1. 1010
LogC Maintenance of current repressor protein plus
permease plus -Gal plus promoter
Weaker repressor selected
lacZ (3510) lacY (780) lacA (825)POlacI (1040)
-Gal Permease AcetylaseInhibitor
lacI
CAPRNAPol
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
, ,wCAP CAP w CAP CAP CAPX X X
The lac operon: Selecting for less efficient CAP
Loss of function activator
0.001 0.01 0.1 1LogD1
100
10000
1. 106
1. 108
1. 1010
LogC
Demand for activator OR absence of Glucose
If D~<2x10-4, activator is lost for this particular circuit
Connecting Lac operon demand regulated by Glu and Lac
Demand for LacI
Demand for CAP
Connecting Lac operon demand regulated by Glu and Lac
Demand for LacI
Demand for CAP
Connecting Lac operon demand regulated by Glu and Lac
Demand for LacI
Demand for CAP
Connecting Lac operon demand regulated by Glu and Lac
Demand for LacI
Demand for CAP
Connecting Lac operon demand regulated by Glu and Lac
Demand for LacI
Demand for CAP
Connecting Lac operon demand regulated by Glu and Lac
Demand for LacI
Demand for CAP
Connecting Glu and Lac demand
6
1
1ww w ii
g m
ww
Y Y
Xw
XZ-
XY-
XI-
XCAP-
XP-
XP+
Z Z
P P
P P
I I
CAP CAP
,P w
,P w
,CAP w
,Z w
,Y w
,I w
., .w wg m
6
.,. .1.
1 iii
g m
Bacteria Cycle between environments with high and low Lac and high and low
Glu
,,
,
,
,
, 1 2 3 ,
,
,
,
...
1
HP w H H
P i P P wwH Hww P P
LP w
L Lww P P
L L LP P ww P w
L Lww P P
HP w
H Hww P P
R C Exp CD
Exp C D D D
4 fractions of the cycle
The words:
Demand for LacI
Demand for CAP
Highest extend of selection for this type of demand cycle
~99.2%0.8%
~0.005%~0.07%
HL,HH,HL,LL
-4 -2 0 2 4
3
3.2
3.4
3.6
3.8
LogC
LogExtent of selection
HL,HH,HL,LL
0.992 0.993 0.994 0.995 0.996 0.997
3
3.2
3.4
3.6
3.8
LogFraction of low demand
LogExtent of selection
HL,HH,HL,LL
-4 -2 0 2 4
0.992
0.993
0.994
0.995
0.996
0.997
LogC
LogExtent of selection
HL,HH,HL,LL
-4 -2 0 2 4
0.002
0.004
0.006
0.008
LogC
t1
HL,HH,HL,LL
-4 -2 0 2 4
0
0.00001
0.00002
0.00003
0.00004
0.00005
t2
HL,HH,HL,LL
-4 -2 0 2 4
0
0.001
0.002
0.003
0.004
0.005
0.006
0.007
t3
HL,HH,LH,LL
-4 -2 0 2 4
2.8
3
3.2
3.4
3.6
3.8
LogC
LogExtent of selection
0.976 0.978 0.98 0.982 0.984 0.986
2.8
3
3.2
3.4
3.6
3.8
LogFraction of low demand
-4 -2 0 2 4
0.976
0.978
0.98
0.982
0.984
0.986
Low Demand
-4 -2 0 2 4
0.005
0.01
0.015
0.02
LogC
t1
HL,HH,LH,LL
-4 -2 0 2 4
-1
-0.5
0
0.5
1
LogC
t2
-4 -2 0 2 4
0
0.002
0.004
0.006
0.008
0.01
t3
-2.4 -2.2 -2 -1.8 -1.6
2.8
3
3.2
3.4
3.6
3.8
Logt1
LogExtend of Selection
HL,LL,LH,LL
-4 -2 0 2 4
2.8
3
3.2
3.4
3.6
3.8
LogC
LogExtent of selection
-2.4 -2.2 -2 -1.8 -1.6
2.8
3
3.2
3.4
3.6
3.8
Logt1
LogExtend of Selection
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35
2.8
3
3.2
3.4
3.6
3.8
t2
0.65 0.7 0.75 0.8 0.85 0.9 0.95
2.8
3
3.2
3.4
3.6
3.8
LogFraction of low demand
LogExtent of selection
HL,LL,LH,LL
-4 -2 0 2 4
0.65
0.7
0.75
0.8
0.85
0.9
0.95
LogC
Low Demand
-4 -2 0 2 4
0.005
0.01
0.015
0.02
LogC
t1
-4 -2 0 2 4
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
t2
-4 -2 0 2 4
0
0.002
0.004
0.006
0.008
0.01
t3
HH,HL,LL,LH
-4 -2 0 2 4
1.2
1.4
1.6
1.8
2
LogExtent of selection
0.38 0.382 0.384 0.386 0.388 0.39
1.2
1.4
1.6
1.8
2
-4 -2 0 2 4
0
0.2
0.4
0.6
0.8
1
1.2
Low Demand
HH,HL,LL,LH
-4 -2 0 2 4
0.38
0.382
0.384
0.386
0.388
0.39
t3
-4 -2 0 2 4
0.01
0.012
0.014
0.016
0.018
0.02
t2
Sensitivity Analysis
-4 -2 0 2 4
2
2.5
3
3.5
4
LogC
LogExtend of Selectionmiu 5
-4 -2 0 2 4
2
2.5
3
3.5
4
LogC
LogExtend of Selectionmiu 4
-4 -2 0 2 4
2
2.5
3
3.5
4
LogC
LogExtend of Selectionmiu 3
-4 -2 0 2 4
2
2.5
3
3.5
4
LogC
LogExtend of Selectionmiu 2
Sensitivity Analysis
-4 -2 0 2 4
2
2.5
3
3.5
4
LogC
LogExtend of Selectionmiu 1
-4 -2 0 2 4
1.8
2
2.2
2.4
2.6
2.8
3
3.2
LogExtend of Selectionmiu 0
Lambda-cro
-5
0
5-8
-6
-4
-2
0
11.000251.0005
1.000751.001
-5
0
5
-5
0
5-8
-6
-4
-2
0
0.999920.999940.999960.99998
1
-5
0
5
-5
0
5-8
-6
-4
-2
0
11.000251.0005
1.000751.001
-5
0
5
-5-2.5
02.5
5 -10
-8
-6
-4
-2
0
0.166660.1666650.16667
0.166675
-5-2.5
02.5
5
The lac operon
High Lactose Low Lactose
High Gluco
se
Low Gluco
se
High Gluco
se
Low Gluco
se
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