Laure Pecquerie Laboratoire des Sciences de l’Environnement Marin UMR LEMAR, IRD...
-
Upload
sophia-ryan -
Category
Documents
-
view
215 -
download
1
Transcript of Laure Pecquerie Laboratoire des Sciences de l’Environnement Marin UMR LEMAR, IRD...
Laure PecquerieLaboratoire des Sciences de l’Environnement Marin
UMR LEMAR, [email protected]
21st -22nd April 2015,DEB Course 2015, Marseille
Metabolic products within a DEB context
Respiration in bioenergetic models
• The conceptual relationship between respiration and use of energy has changed with time. – Von Bertalanffy identified it with anabolic processes, – while e.g. a Scope For model relates it to catabolic processes
• DEB theory relates it to the three transformations : assimilation, dissipation and growth (which all have an anabolic and a catabolic components)
• DEB theory defines O2 consumption and CO2 production as product “formations” and not as mechanistic processes (ie fluxes driving the dynamics of the state variables)
Outlinelecture 1 (Tue. 21. ) and 2 (Wed. 22.)
• [A bit of networking]
• Definition of products in a DEB context
• Example : Torpedo marmorata – Univariate data t-L, L-W– Respiration data L-JO
• Steps to calculate the respiration rate from the standard DEB expressed in an energy-length-time framework
• Hard to believe at first (for me!) but true (and we gained a lot of insights from it) : otoliths and other biocarbonates are also DEB products
2005 2015 and next!
• Participant of the Brest group of the 2005 DEB telecourse : 10th DEB anniversary for Jonathan, Fred, me and a few others you’ll meet Changed the direction of my anchovy PhD project Helped me getting an interview for a post-doc position in Santa Barbara with Roger
Nisbet Got me a job in Brest !
• Brest group: DEB applications inmarine ecology, aquaculture and fisheries sciences:
16 people! 3 assistant professors, 6 researchers, 2 associated researchers, 1 post-doc, 4 PhD students + 5 Master and PhD students in the US, Peru and Mexico
Call for Post-docs and PhD’s contact us!
Grand merci : Bas, Roger, Brest group – Jonathan, Fred, Marianne, Cédric and Véro - , and Starrlight, Dina and Gonçalo for taking me on board
Daphnia pulex (Kooijman, 2010)
Respiration rate as a function of length
R = aLb = 0.0516 L2.437
Allometric model = 2 parameters
Respiration rate as a function of length
R = aLb = 0.0516 L2.437
R = aL2 + bL3
= 0.0336 L2 + 0.01845 L3
Daphnia pulex (Kooijman, 2010)
Allometric model = 2 parameters
DEB model = same number of parameters but parameters with measureable dimensions
Respiration rate as a function of length
R = aLb = 0.0516 L2.437
R = aL2 + bL3
= 0.0336 L2 + 0.01845 L3
Daphnia pulex (Kooijman, 2010)
Assimilation proportional to L2
Dissipation prop to L3
Growth prop. to L2 and L3
Respiration in DEB theory
• Weighted sum of L2 and L3 processes as product formation is a weighted sum of :– Assimilation (L2), – Dissipation(L3 - and L2) and – Growth (L3 and L2)
• Definition of Dissipation : sum of somatic maintenance, maturity maintenance, development and reproduction overheads
For embryos and juveniles
For adults
Definition of products in a DEB context
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Product formation can occur during one, two or all the three DEB transformations : assimilation, dissipation and growth
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Reserve
Structure
1
Assimilation pA
Growth pG
Somaticmaintenance pM
Maturitymaintenance pJ
Reproduction pR
Food
pC
Reproductionbuffer
Assimilation Products
Dissipation Products
Growth Products
pDpA
pA
Faeces
CO2
pD pG
pG
(b)
(c)
(d)
(a)
Torpedo marmorata example
• Constant food and temperature = 15°C• Weight, length and respiration data from birth to max age
• Time (d), Wet weight (g) , Total length (cm), Respiration rate (mg O2 /h)
• Let’s start with the first 2 univariate datasets: t-L and L-W
t-L and L-W predictions
• Defined in predict_Torpedo_marmorata.m• Lw as a function of t?
– Constant food von Bertalanffy growth
L_w = L_wi – (L_wi – L_wb) * exp( -r_BT * t)– L_wi? L_wb? r_BT? t?
• Ww as a function of Lw ?– Constant food constant reserve density– Ww = Ww_V + Ww_E (+ Ww_ER)
• t = time from birth to max age : defined in mydata_Torpedo_marmorata.m
• Parameters– v: primary parameter defined in pars_init_Torpedo_marmorata.m– T_A : environmental parameter– k_M, L_m, g, k, v_Hb: computed in parscomp_st.m – del_M : auxiliary param defined in pars_init_Torpedo_marmorata.m
• Environment– X f: treated as param defined in pars_init_Torpedo_marmorata.m– T TC_tL : calculated by tempcorr.m
TC_tL = tempcorr(temp.tL, T_ref, T_A);
• Initial conditions : at E_Hb defined in pars_init_Torpedo_marmorata.m– L_b (NOTA : E_b = f [E_m]L_b, E_Rb = 0) calculated by get_lb.m
pars_lb = [g; k; v_Hb]– Lw_b = get_lb(pars_lb, f) * L_m/ del_M;
• Von Bertalanffy parameters– rB = 1 / (3 kM + 3 f L_m / v) – Lw_i = f * L_m / del_M
predict_Torpedo_marmorata.m
• Calculation
– EL = Lw_i - (Lw_i - Lw_b) * exp( - TC_tL * r_B * tL(:,1));
– Ww_V = (EL * del_M)^3 assumption that d_V = 1 g/cm^3 for wet weight
– Ww_E = (EL * del_M)^3 * f * wwith w = m_Em * w_E * d_E/ d_V/ w_V;
predict_Torpedo_marmorata.m
L-JO predictions
• Hold your breath, we’ll dive deeper into DEB notations!