Nicola Lai @CRS4 Seminar Series 2011

1. A Systems Biology Approach
To Study Metabolic Regulation
In Tissue/Organ Systems
In Health And Disease States
Nicola Lai
Department of Biomedical Engineering
Case Western Reserve University
Dicembre 21, 2011

2. Outline of Presentation
Introduction to Systems Biology
Projects
Experimental approaches to study energy
metabolism at different whole body levels:
Cellular
Tissue-Organ
Whole Body
Integration of experimental data to computational
model to study
O2 transport and metabolism in skeletal muscle (Diabetes)
Fuel Homeostasis: Substrate Utilization (Cystic Fibrosis)
Relation between experimental and computational
models for optimal design of experiments and to
generate hypotheses

3. Systems Biology
Study of the interactions between the components of
biological systems, and how these interactions give
rise to the function and behavior of that system (e.g.,
the enzymes and metabolites in a metabolic pathway)
Organisms
Organs
Tissues Integrative Discover Functional
Systems Biology Properties of the
Cells Approach Biological Systems
Proteins
Genes

4. Systems Approach: Integration
Comprehensive data sets from distinct levels of
biological systems;
It is difficult to relate organ whole-organism
function to cellular and sub-cellular function and
structure properties;
Integration of multi-scale data to build predictive
mathematical models of the system;
Investigate the behavior and relationships of all
elements in a functioning biological system;

5. Cellular Metabolism
All the chemical processes that make it possible for
the cells to continue living
Cell

6. Metabolic Systems
Most metabolic pathways have been
intensely studied;
Little is known in quantitative terms about
their control and integration with other
pathways, as well as their interaction to
regulate physiological variables (e.g., blood,
glucose, muscle ATP) under normal and
stress conditions;
Fell D. Understanding the Control of Metabolism, 1997.

7. Ongoing Research Projects
Title
Systems Biology Investigation of Muscle Exercise Metabolism in Diabetes
Goal
To quantify the key factors responsible for metabolic and mitochondrial
dysfunction in diabetes and elucidate the impact of exercise training on
energy metabolism
Agency
National Institute of Arthritis, Musculoskeletal & Skin Diseases
Title
Systems Biology Approach to Growth Regulation in Cystic Fibrosis
Goal
To investigate the patterns of energy homeostasis (energy utilization and
imbalances) in control and cystic fibrosis (CF) mice using perturbations
including pharmacologic treatment, genetic manipulations and altering
energy balance by diet or exercise
Agency
Institute of General Medical Sciences

8. Systems Biology Approach
1. Choose suitable biological model organism
2. Characterize endocrine-metabolic components
of energy metabolism
3. Generate plausible hypotheses explaining
differences between T2DM and control
4. Develop predictive, quantitative multiscale
models of energy metabolism
5. Perturb systematically system to validate and
refine model and to test hypotheses
6. Generate new experimentally testable
hypotheses

9. Metabolic Characteristics in T2DM
Muscle metabolic functions decline with type 2
diabetes mellitus (T2DM)
Metabolic dysfunction is accompanied by
mitochondrial dysfunction and insulin resistance (IR)
Mitochondrial dysfunction is related to IR, but the
cause-and-effect relationship between them remains
to be defined
The altered metabolic regulation under which insulin
is less effective in inducing glucose utilization is not
completely understood

10. Why study exercise metabolism
Muscle energy metabolism in healthy & disease
state
Detect and prevent pathologies (e.g. Diabetes)
Therapeutic intervention to ameliorate quality of
life in elderly and subjects with metabolic
disorders

11. Experimental Approach
-Exercise
Acute Perturbation / Stimuli -Hypoxia, Hyperoxia
Chronic Stimuli / Conditions -Drugs
-Training, Microgravity
-Diseases
(e.g. Diabetes, Myopathies)
Biological Systems
-Physiological variables
(e.g. Blood flow)
-Metabolic variables
(e.g. Substrates, Enzymes)
System Outputs

12. Whole body response to exercise
Stimulus Response
Physiological
Process

13. Exercise Protocol
WR [watt]
Range (80-200)
Warm up (20) Time
[min]
NT E E
IV ERY
T UP A T
T A VE RY S
RES M NS K R TI VE AS OV
AR CO OR AC CO P C
W RE RE
W

14. Physiological responses to exercise
1.50
Indirect
Calorimetry 1.25
Pulmonary 1.00
VO2 [L min ]
O2 Uptake
-1
0.75
0.50
Bioimpedance
Cardiography 0.25
Cardiac 0.00
0 50 100 150 200 250 300 350 400 450 500
Output [second]
30 12.5
25 NIR
10.0
Spectroscopy
20
7.5
Cdeoxy [mM]
Q [L min ]
Muscle
-1
15
Oxygenation
5.0
10
2.5
5
0 0.0
0 50 100 150 200 250 300 350 400 450 500 0 50 100 150 200 250 300 350 400 450 500
[second] [second]

15. Characterization of the physiological
variable response to stimulus
Mathematical Model
t ≤ t0 +TD Y( t ) = YBL
t > t0 +TD Y( t ) = YBL + A (1 − e( t0 +TD − t )/ τ )
Rest Stimuli
Parameters
YBL + A
A, Amplitude
τ, Time Constant A
TD, Delay Time
YBL
TD
t0 t, Time [min]

16. τ
Effect of time constant (τ)
on the physiological response
1.8
τ=30s
τ=
1.5
τ=30s
τ=
τ=90s
τ=
VO2 [L min ]
1.2
-1
0.9
0.6
0.3
0 100 200 300 400 500 600 700
[second]

17. VO2 Responses to Exercise in Human Subjects:
Type II Diabetes Mellitus (T2DM) & Health (Control)
T2DM
CONTROL
Time [s] PAD
Time [s]
Impaired cardiac responses to exercise
Alteration O2 diffusion and/or utilization in skeletal
muscle is also possible
Regensteiner et al. 1998, Journal of Applied Physiology

18. VO2 Responses to Exercise in Human Subjects:
Cystic Fibrosis (CF) & Health (Control)
Control CF
Time [s] Time [s]
Dynamic response of pulmonary O2 uptake (VO2) in
humans during exercise slower with CF than healthy
VO2 response can be affected by pulmonary
impairment but peripheral factors (O2 transport and
metabolism) may also play a role
Hebestreit et al., 2005

19. Effect of Exercise on VO2 response
to exercise in T2DM patients
Control
τ=40s
τ=
T2DM
τ=72s
τ=
Bradenburg et al., Diabetes Care 22, p1640–1646, 1999

20. Linking Cell, Tissue/Organ systems & Whole Body
Whole Body
Cell
Tissue/Organ Systems

21. Whole body & tissue-organ responses to exercise
Stimulus Response
LUNGS
LUNGS
Pulmonary
Pulmonary
Physiological O2 Uptake
O2 Uptake
Process
HEART
HEART
Cardiac Output
Cardiac Output
Arterio/venous
Arterio/venous
difference
difference SKELETAL MUSCLE
SKELETAL MUSCLE
-Blood O2 Saturation
-Blood O2 Saturation
-Tissue O2
-Tissue O2
Saturation
Saturation
-Muscle Blood Flow
-Muscle Blood Flow

22. Measurements of Muscle Blood Flow (Q),
Arterial and Venous O2 concentrations
Catheter
Radial Artery
Cart,O
2
Catheter
Femoral Vein
Cven,O
2 Muscle O2 Uptake
VO2m=Q (Cart,O2-Cven,O2)
MEASUREMENTS
Blood Samples: Arterial and venous O2 concentration (Cart,O2, Cven,O2) by Oximeter
Tissue Biopsies: Metabolite concentrations by GS, MS
Muscle Blood Flow (Q) by thermo-dilution technique

23. Cardio-respiratory & skeletal muscle responses
to exercise
VO2A , Alveolar
Oxygen Uptake
Qleg, Muscle Blood Flow,
Ca-Cv, Arterio-Venous diff.
VO2leg, Muscle Oxygen Uptake
Grassi et al., JAP (1996) 80, p988-998

24. Linking Cell, Tissue/Organ systems & Whole Body
Whole Body
Cell
Tissue/Organ Systems

25. Mitochondrial respiration responses
to different substrates
Stimulus Response
Substrates
Buffer
Polarographic Solution
System
Water Water
30°C 30°C Oxygen
∆V consumption Rate
Magnetic
Electrode System stir bar
Magnetic mixer

26. Oxidative phosphorylation rate
in healthy and disease states
Functional defects
in dehydrogenase activities
The mitochondria of patient ‘C’
Pyruvate oxidation is impaired
Defect in the pyruvate dehydrogenase
complex
The mitochondria of patient ‘D’
Glutamate and succinate oxidation are
impaired
Defect in fumarase activity
Puchowicz et al., 377–385 , 2004

27. Dynamic response of O2 utilization
at different whole body levels
Biological Systems Time constant
Cell 2.5 s
Skeletal Muscle 25÷30 s
Whole Body 30÷35 s

28. Factors affecting bioenergetics function
Central
Cardiovascular and respiratory systems
Ventilation;
O2 Diffusion from Alveoli to pulmonary capillary
Cardiac Output;
Peripheral
Skeletal Muscle systems
O2 Diffusion from muscle capillary to myocytes
Metabolic processes (Cytosol, mitochondria)

29. Linking Cell, Tissue/Organ systems & Whole Body
Whole Body
Tissue/Organ Systems
Cell

30. Cellular Energy metabolism

31. Multi-compartmental System Model
Capillary Blood
Q Ca,j Q Cv,j
Cb,j
Interstitial
Fluid Jb↔c,j Cisf,j
↔
Specie j Specie j transport rate
Ca,j: Arterial concentration Cc,j | Rc,j from blood to cytosol, Jb↔c,j
Cv,j: Venous concentration from cytosol to mitochondria, Jc↔m,j
Pc,j Uc,j
Cb,j: Capillary blood concentration Cytosol Jc↔m,j
↔
Species j reaction rate
Cisf,j: Interstitial fluid concentration
Rc,j=Pc,j – Uc,j cytosol
Cc,j: Cytosolic concentration Cm,j | Rm,j
Rm,j=Pm,j – Um,j mitochondria
Cm,j: Mitochondrial concentration
Pm,j Um,j
Mitochondria
Px,j =∑p βx,j,p φx,p φ Reaction flux
Ux,j = ∑u βx,j,u φx,u β Stoichiometric coefficient

32. Dynamic Mass Balance Equations
( )
dCb, j
Blood (b): Vb = Q Ca, j − Cb, j − J b↔ c, j
dt
dCc, j
Cytosol (c): Vc = ∑ β c, j, pφ c, p − ∑ β c, j,uφ c,u + J b↔ c, j − J c ↔ m, j
dt p u
dCm, j
Mitochondria (m): Vm = ∑ β m, j, pφ m, p − ∑ β m, j,uφ m,u + J c ↔ m, j
dt p u
Q: Muscle blood flow
Cx,j: Species concentration in each domain (blood, cytosol or mitochondria)
Jb↔c,j : Transport fluxes between blood and cytosolic domain
↔
Jc↔m,j : Transport fluxes between cytosolic and mitochondrial domain
↔
φp, φu: Metabolic reaction fluxes: production or utilization
βp, βu: Stoichiometric coefficients.

33. Metabolic Reaction Fluxes
Reaction
A+ B C+D
Ordered bi-bi Michaelis-Menten kinetics
Vmax,f [ A][ B ] Vmax,r [ P ][Q]
−
K a Kb K p Kq
φ=
[ A] [ B ] [ A][ B ] [ P] [Q] [ P][Q]
1+ + + + + +
K a Kb K a Kb K p K q K p K q
Haldane Relation Metabolic Parameters
Vmax, f K p K q
Vmax,r = K eq , K a , Kb , K p , K q
K a K b K eq

34. Inter-domain Transport Fluxes
Transport Processes
Blood-Cytosol (b↔c ) Cytosol-Mitochondria (c↔m )
b↔c,p: Ala, Glr, CO2, O2, H+ c↔m,p: CO2 and O2
b↔c,f: Glc, Pyr, Lac, FFA c↔m,f: Pyr, FAC, Pi, CoA, H+, Cit, Mal
PASSIVE
Jxp↔y, j = λx↔y, j (Cx, j −Cy, j ) 
  


Jx↔y, j =  FACILITATED

J f = T  Cx, j Cy, j 
−
 x↔y, j x↔y, j  Mx↔y, j + Cx, j Mx↔y,, j + Cy, j 
 
  

35. Whole body model O2 Transport between
Lungs & Skeletal muscle
Dynamic balance of O2 in Lungs
Alveoli
LUNGS V
dCAO2 Lb
VA(t), C IO2
Alveolar Space VO2p
CAO2
VA = VA( t )( CI O2 − CAO2 ) − ∫ JA ↔ LO2 ,b dv
&
dt 0
Capillary VO2A
Cven Cart Lung Capillary Blood
Q(t) ∂CLO2 ,b ∂CLO2 ,b ∂ 2 CLO2 ,b
OTHER ORGANS organs = −Q +D + JA ↔ LO2 ,b 0 < v < VLb
∂t ∂v ∂v 2
Tissue
Qo
Capillary Other Organs
Tissue
VRb
dCRO2 ,c
=− ∫J R ↔ RO2 ,b dv + MRO2
MUSCLE Qm(t) VR
Tissue UO2m dt
0
Cven,m Cart,m Blood 0 < v < VR ,b
Capillary VO2m
∂CRO2 ,b ∂CRO2 ,b ∂ CRO2 ,b
2
= −Q0 + DR + JR ↔ RO2 ,b
∂t ∂v ∂v 2
Arterial & Venous Systems O2 Diffusion
∂CrO2 ∂CrO2 ∂ 2 CrO2 JR ↔ RO ,b = PS R ( PRO2 ,b − PRO2 ,c )
= −Q + Dr ; 0 < v < Vr 2
∂t ∂v ∂v 2
JA ↔ LO2 ,b = PS L ( PAO2 − PLO2 ,b )

36. Model Prediction of metabolic processes
at cellular level: Cytosol and Mitochondria
Response to Exercise
Variations in Glycogen
concentration
Under pathological conditions
or with special diet, glycogen
stores in skeletal muscle at
rest can differ significantly
Li et al., AJPEM 298, p1198-1209, 2010

37. Model Prediction of metabolic processes
at whole skeletal muscle
120
Muscle
Q [mL 100g min ]
Effect of blood flow
-1
100
Blood Flow 80 Model Simulation
on VO2m response
-1
Exp.Data - Normoxia
60
40
Self Perfused (SP)
Model Simulation
to contraction
Exp.Data - Normoxia
20 Pump Perfused (PP) Catheter
0 Radial Artery
18
Arterio-Venous 16 Cart,O2
14
Difference
VO 2 [mLO 2 100g min ] CA-V [vol %]
12 Model Prediction
10 Exp.Data - Normoxia
8 Self Perfused (SP)
6 Model Prediction
Catheter
4 Exp.Data - Normoxia Femoral Vein
T
2 Pump Perfused (PP)
0 Cven,O2
-1
18
Muscle O2 16
14
Uptake
-1
12 Model Prediction
10 Exp.Data - Normoxia
8 Self Perfused (SP)
6 Model Prediction
4 Exp.Data - Normoxia *Grassi et al., 2000
2 Pump Perfused (PP) JAP. 89: 1293-1301
0
0 30 60 90 120 150 180 210 240 270 300
Spires et al., 2011
Time [s] JAP. Submitted

38. Model Prediction of metabolic processes
at whole body level
0.2 Dynamic responses of Muscle
0.1
O2 saturation & Pulmonary O2
uptake to exercise
0.0
LUNGS
LUNGS
∆StO2m/StO2m
w
-0.1
Pulmonary
Pulmonary
-0.2
O2 Uptake
O2 Uptake
-0.3 Model Simulation
Experimental Data
-0.4 HEART
HEART
2.5
Cardiac
Cardiac
2.0
Output
Output
VO2p [L O2/min]
1.5
1.0
MUSCLE
MUSCLE
0.5 Model Simulation
Experimental data
Oxygen
Oxygen
0.0 Saturation
Saturation
-1 0 1 2 3 4
Time [min]

39. Factors affecting bioenergetics function
Central
Cardiovascular and respiratory systems
Ventilation;
O2 Diffusion from Alveoli to pulmonary capillary
Cardiac Output;
Peripheral
Skeletal Muscle systems
O2 Diffusion from muscle capillary to myocytes
Metabolic processes (Cytosol, mitochondria)

40. Mathematical Modeling and Analysis:
Hypotheses of cellular and physiological regulation
Inputs: Outputs:
Mathematical
Experimental Metabolic
Model
Conditions Responses
Hyp.1
Hypotheses
Hyp.2
Hyp.1: Impairment of cellular transport
(e.g. facilitate diffusion)
Hyp.2: Activation/Inhibition of enzymatic Hyp.3
reactions and/or metabolic pathway
Hyp.3: Impairment of substrate delivery
(e.g., reduced blood flow)

41. Cystic Fibrosis: Genetic Complex Disorder
Cystic Fibrosis is a complex, systemic,
and multi-organ disorder
Although CFTR gene is identified, many
aspects of CF cannot be related directly
to chloride channel defect
Are pulmonary infection, inflammation,
and growth retardation primary effects or
secondary consequences?
A Systems Approach is Needed !

42. Energy Homeostasis in CF
Energy Supply
Intake of FAT, CHO, and protein
Digestion and absorption of nutrients
Energy Utilization
Oxidation of FAT, CHO and Protein
Leaks: lower efficiency, cachexia
Total energy expenditure
Energy Balance
Body composition Insulin

43. Hormonal and Metabolic
Characteristics of Tissues in CF
Skeletal Muscle
Lower work efficiency and inorganic phosphorus-to-
phosphocreatine ratio during exercise
Dysfunction of aerobic and anaerobic metabolism
Liver
Impaired suppression of hepatic glucose production and
non-oxidative glucose metabolism stimulated by insulin
De novo lipogenesis related to carbohydrate utilization
Adipose Tissue
Plasma palmitate 50% higher in human CF than control
during insulin infusion
Impaired suppression of adipose tissue lipolysis by insulin

44. System Model: Whole-Body & Organ-Tissues
Gas Exchange
O2 CO2
Brain
Heart
Exercise
Skeletal
Muscle
Liver Insulin
Glucagon
Organ system is connected via GI
blood carrying substrates
Adipose
Carbohydrates and fat utilization
during exercise Others
Hormonal activation/inhibition of
metabolic pathways

45. Multi-compartmental System Model
Capillary Blood
Q Ca,j Q Cv,j
Cb,j
Interstitial
Fluid Jb↔c,j Cisf,j
↔
Specie j Specie j transport rate
Ca,j: Arterial concentration Cc,j | Rc,j from blood to cytosol, Jb↔c,j
Cv,j: Venous concentration from cytosol to mitochondria, Jc↔m,j
Pc,j Uc,j
Cb,j: Capillary blood concentration Cytosol Jc↔m,j
↔
Species j reaction rate
Cisf,j: Interstitial fluid concentration
Rc,j=Pc,j – Uc,j cytosol
Cc,j: Cytosolic concentration Cm,j | Rm,j
Rm,j=Pm,j – Um,j mitochondria
Cm,j: Mitochondrial concentration
Pm,j Um,j
Mitochondria
Px,j =∑p βx,j,p φx,p φ Reaction flux
Ux,j = ∑u βx,j,u φx,u β Stoichiometric coefficient

46. Dynamic Mass Balance Equations
( )
dCb, j
Blood (b): Vb = Q Ca, j − Cb, j − J b↔ c, j
dt
dCc, j
Cytosol (c): Vc = ∑ β c, j, pφ c, p − ∑ β c, j,uφ c,u + J b↔ c, j − J c ↔ m, j
dt p u
dCm, j
Mitochondria (m): Vm = ∑ β m, j, pφ m, p − ∑ β m, j,uφ m,u + J c ↔ m, j
dt p u
Q: Muscle blood flow
Cx,j: Species concentration in each domain (blood, cytosol or mitochondria)
Jb↔c,j : Transport fluxes between blood and cytosolic domain
↔
Jc↔m,j : Transport fluxes between cytosolic and mitochondrial domain
↔
φp, φu: Metabolic reaction fluxes: production or utilization
βp, βu: Stoichiometric coefficients.

47. Metabolic Pathways in Adipose Tissue
Lactate Pyruvate Alanine CO2
CO2 CoA
LAC PYR ALA NADH CoA CO2 PYR
ATP NADH
NAD+ NADH NAD+ ATP
CoA NADP+ NADPH ADP+Pi ADP+Pi NAD+
NADH ATP
Proteins FA ACoA NADH NAD+ GAP2
NAD+ ADP+Pi ATP NADH NADH
ADP+Pi
CoA NAD+
CoA NAD+
GAP1 G3P1 FAC ATP GLR G3P2
ADP
NADH NAD+ ADP+Pi FAC ATP ADP FAC
CoA Pi CoA
ATP Pi CoA
DG TG DG
F6P R5P GLR
CO2
DG MG FAC
NADPH
ADP+2Pi ATP FAATGL MG
NADP+ HSL DG
GLY G6P ADP+Pi ATP GLR
Pi ADP O2 H2O HSL
NADH NAD+ FA MG
ATP
MG GLR
GLC ATP ADP MGL
HSL
Tissue FA
Glucose O2 FFA
Blood VLDL-TG
Glycerol
+ Epinephrine Insulin Work Rate

48. Tissue Specific Metabolic Pathways
Pathways Brain Heart Muscle GI Liver
1. Glucose Utilization: GLC + ATP ⇒ G6P + ADP
2. G6P Breakdown: G6P + ATP ⇒ 2GA3P + ADP
3. GA3P Breakdown:GA3P + Pi + 2ADP + NAD+⇒ PYR + 2ATP + NADH
4. Gluconeogenesis-1: PYR + 3ATP + NADH ⇒ GAP + 3ADP + Pi + NAD+
5. Gluconeogenesis-2: 2GA3P ⇒ G6P + Pi
6. Gluconeogenesis-3: G6P ⇒ GLC + Pi
7. Glycogenesis: G6P + ATP ⇒ GLY + ADP + 2Pi
8. Glycogenolysis: GLY + Pi ⇒ G6P
9. Pyruvate Reduction: PYR + NADH ⇒ LAC + NAD
10. Lactate Oxidation: LAC + NAD ⇒ PYR + NADH
11. Glycerol Phosphorylation: GLR + ATP ⇒ G3P + ADP
12. GA3P Reduction: GA3P + NADH ⇒ G3P + NAD
13. Glycerol-3-P Oxidation: G3P + NAD ⇒ GA3P + NADH
14. Alanine Formation: PYR ⇒ ALA
15. Alanine Conversion: ALA ⇒ PYR
16. Pyruvate Oxidation: PYR + CoA + NAD ⇒ ACoA + NADH + CO2
17. Palmitate Oxidation: FA+8CoA+14NAD+2ATP ⇒ 8ACoA+14NADH+2ADP+2Pi
18. Palmitate Synthesis: 8ACoA + 7ATP + 14NADH ⇒ FA + 8CoA + 7ADP + 7Pi + 14NAD
19. Lypolysis: TG ⇒ 3FA + GLR
20. Triglyceride Production: 3FA + G3P + 6ATP ⇒ TG + 6ADP + 6Pi
21. TCA Cycle: ACoA + 4NAD + ADP + Pi ⇒ 4NADH + CoA + ATP +2CO2
22. Oxygen Consumption: 2NADH + 6ADP + 6Pi + O2 ⇒ 2NAD + 6ATP
23. Phosphocreatine Breakdown: PCR + ADP ⇒ CR + ATP
24. Phosphocreatine Synthesis: CR + ATP ⇒ PCR + ADP
25. ATP Hydrolysis: ATP ⇒ ADP + Pi + Energy

49. Skeletal Muscle/Adipose Tissue Interactions
CO2 LPL
LAC PYR ALA GLR
VLDL-TG
FFA
NAD+ NADH
+ Proteins
CO2
LAC PYR ALA NADH CoA
CoA
– ATP
ATP CO2 ATP
NADH NAD+
ADP+Pi ADP+Pi –
NAD+ ADP+Pi
NAD+ CoA
NADH
– ADP
GAP1 NADH GAP2 NADH NAD+
NADH ACoA NADH NAD+
CoA
NAD+ NAD+
ATP ATP
ADP+Pi
F6P R5P G3P1 G3P2 FAC FA
CO2 CoA
NADH ADP+Pi ATP
+ GLR
NADP+
CoA MGL
+ Pi ATGL HSL
CoA
Pi
G6P GLY HSL HSL
ADP+Pi DG TG DG MG
ADP ATP ADP+2Pi
– – ATP MG DG
GLR MG GLR MG
ATP
GLC
ADP+Pi ATP Pi
O2 H2 O ATP ADP
NADH NAD+
Tissue
Blood
GLC O2
LAC PYR ALA GLR FFA CO2
NAD+ NADH
CO2
LAC PYR ALA NADH CoA
NAD+ NADH CO2 PYR
NAD+ ATP
NADH ATP ATP ADP
NAD NADH CoA
ATP ADP+Pi
ADP
NAD+ ADP+Pi GLR FA ACoA NAD+
NADH
CoA
GAP G3P ATP ADP ATP
ADP
ADP PCR CR
Pi ATP ADP
ADP+2Pi ATP ATP
GLY G6P
TG ATP ADP
Pi ADP
ATP ADP+Pi ATP
GLC O2 H2 O
Tissue NADH NAD+
Blood
GLC TG O2

50. Experimental protocol and measurements
WR PROTOCOL MEASUREMENTS
[watt] Blood
100 Hormones:
Insulin;
Norepinephrine
60 minute
50 Epinephrine
Growth Hormon (GH)
Substrates:
Lactate
T Glycerol
T UP
ES M T AN TE Time Glucose
R NS RA
AR
W CO RK [min] Nonesterified Fatty Acid
WO
Tissue
Exercise maximal test; Substrates:
Exercise at moderate work rate (WR) Dialysate Glycerol
equivalent to 50% of VO2peak
Koppo et al., 2010

51. Hormone responses to exercise
450 35
400
Model simulation 30
350 Experimental Data
300 25
Epinephrine [pm]
Hormone [pm]
250
20
200
15 Glucagon
150
Model Simulation
100 10 Experimental Data
Insulin
50
Model Simulation
5
0 Experimental Data
-50 0
-10 0 10 20 30 40 50 60 70 80 -10 0 10 20 30 40 50 60 70 80
Time [min] Time [min]
Koppo et al., 2010

52. Glucose Homeostasis During Exercise
6000 2000
1800
5000 Glucose
1600 Utilization
Rate [µmol/min]
Production
Glucose [µmmol/min]
1400
4000
1200
3000 1000
800
2000
Model Simulation 600
Experimental Data 400
1000
200
0 0
-10 0 10 20 30 40 50 60 70 80 -10 0 10 20 30 40 50 60 70 80
Time [min] Time [min]
Koppo et al., 2010

53. Plasma Metabolite Responses to Exercise
1.4 3.0
Model Simulation
Experimental Data 2.5
1.2
Lactate, LAC/LAC0 [-]
Fatty Acid, FA/FA0 [-]
2.0
1.0 1.5
1.0
0.8
0.5 Model Simulation
Experimental Data
0.6 0.0
-10 0 10 20 30 40 50 60 70 80 -10 0 10 20 30 40 50 60 70 80
Time [min] Time [min]
Koppo et al., 2010

54. Glycerol Responses to Exercise
Plasma Adipose Tissue
3.5 3.5
3.0 3.0
Model Simulation
Glycerol, GLC/GLC0 [-]
Glycerol, GLC/GLC0 [-]
2.5 2.5 Experimental Data
2.0 2.0
1.5 1.5
1.0 1.0
Model Simulation
0.5 Experimental Data 0.5
0.0 0.0
-10 0 10 20 30 40 50 60 70 80 -10 0 10 20 30 40 50 60 70 80
Time [min] Time [min]
Koppo et al., 2010

55. Hypothesis: Fatty Acid Oxidation Impaired in
Skeletal Muscle at High-intensity Exercise
Transport of long-chain fatty acid into
mitochondria impaired via CPT-I
inhibition
Perfusion of adipose tissue inadequate
to deliver fatty acid to skeletal muscle
Lipolysis inhibited via lactate or high
catecholamine concentration

56. Effect of Adipose Tissue Blood Flow
on Fatty Acid oxidation in skeletal muscle
1.0
Fatty Acid (FA) Release of Adipose Tissue (AT)
0.9 FA Oxidation of Skeletal Muscle (SM)
Lipolysis
0.8
FA Uptake
0.7 SM SM SM SM SM
Rate [mmol/min]
AT AT AT AT
0.6
0.5
0.4
AT
0.3
0.2 AT
SM
0.1
0.0
Rest 10% 30% 50% 100% 150%
Exercise*
*Horizontal axis: ATBF/ATBF0 adipose tissue blood flow at steady-state
moderate exercise relative to basal physiological value

57. Relation between experimental and computational models to
optimal design experiments and generate hypotheses

58. Integrative Systems Biology Approach
Aim
Support the iterative process in defining
alternative hypotheses, and designing
optimum experiments
Impact
Design of experimental protocols for specific
evaluation of disease and improved
treatments based on simulations with
experimentally validated mechanistic
models

59. Conclusion
Physiological-based models of a complex system can
Integrate knowledge about components
Incorporate interactions of system elements
Facilitate quantitative understanding of function
Hierarchical multilevel models provide means
For testing hypotheses
For predicting critical experiments

60. Projects & Sponsors
Agency: NASA, National Aeronautics and Space Administration
Project: Time Course of Metabolic Adaptation during Loading & Unloading
Agency: NSF, National Science Foundation
Project: Database-enabled tools for Regulatory Metabolic Networks
Agency: NIDDK, National Institute of Diabetes and Digestive & Kidney Diseases
Project: Systems Biology Approach to Growth Regulation in Cystic Fibrosis
Agency: Ministero degli Affari Esteri - International Environmental &
Scientific Affairs Department of State.
Project: Central and peripheral factors contributing to the impaired oxidative
metabolism in microgravity: experimental and theoretical approach
Agency: NIGMS - National Institute of General Medical Sciences
Project: Center for Modeling Integrated Metabolic Systems