ZucAt: FBA solution of the model under light growth conditions (III) Version 3
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.5 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is over-produced in plastid and a surplus is exported to cytoplasm. Flux through FQR represents cyclic electron flow through the light photosynthesis system. Flux through FRN represents non-cyclic electron flow through the light photosynthesis system.
SEEK ID: https://fairdomhub.org/data_files/1336?version=3
Filename:
2016-06-03 FBA light v4.0 (Photoresp=0.25, FQR=0.5).txt
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**** HEADER **** Method: FBA Mode: Precise Model: sugar transport Arabidopsis thaliana Version: 3.7.0 Date: 6/4/2016 - 18:28 Comment: Objective: 1.0*T.Biomass.ext 5000.0 Constraints: 1.0*SK = 0.0 0.5*FNR-1.0*FQR = 0.0 0.25*RPC_plastide-1.0*RPC2_plastide = 0.0 1.0*T.Biomass.ext <= 5000.0 1.0*T.starch.ext = 0.0 1.0*T.CO2.ext = 0.0 1.0*T.CO2.ext_rev >= 0.0 Equation: 3.26E7*CO2 + 1088000.0*h + 5.92E8*hv + 5040000.0*Nitrate + 1002000.0*Orthophosphate + 19940.0*Sulfate + 2.12E7*H2O = 3.98E7*O2 + 1.0*Biomass_plant **** EOF HEADER **** **** Flux **** ACL 3.323800642303585E8 ACL_root 5.492083576964151E7 ACOL 1.7217556268579718E8 ACOL_root 2.8449437314202804E7 ADG_plastid 2.5745878532455654E9 ADK 5.031602861192917E9 ADK_plastid 8.20649878222024E7 ADP_root 8.449571509848806E8 AGT 3.644725341484608E10 AICAR 2.789415754700131E9 AICAR_root 4.60909245299869E8 ALA 3.894064128033918E8 ALA_root 6.434358719660821E7 AL_plastid 1.818811658351766E11 AMP 1.4247425901480527E9 AMP_root 2.3541740985194728E8 APS 8.20649878222024E7 APS_reductase 8.20649878222024E7 ARG 9.01105748635948E7 ARG_root 1.4889425136405205E7 ASN 3.02514072756354E8 ASN_root 4.998592724364605E7 ASP 6.763686876322159E9 ASP_root 1.117598123677841E9 ATP/ADPtranslocator.mitochondrion -7.025679818296997E10 ATP/ADPtranslocator.mitochondrion.root -4.235809512500988E10 ATP/ADPtranslocator.plastid 0.0 ATP_synthase -8.698380635712927E11 Aldo -2.1569269542404446E10 Aldo_plastid 0.0 Aldo_root 1.5257777173363366E9 Ash 1287293.9266227828 Ash_root 212706.07337721722 BAM 0.0 Biomass_mesophyll 429097.9755409276 Biomass_plant 5000.0 Biomass_root 70902.0244590724 CAT 2.673913509427922E10 CIS_mitochondria 5.112750338194083E9 CIS_mitochondria_root 3.300648961130871E9 CMP 3.862267968046335E8 CMP_root 6.381820319536648E7 CPS 1.5921036735482807E9 CPS_root 2.6307132645171928E8 CTP 3.862267968046335E8 CTP_root 6.381820319536648E7 CYS 8.20649878222024E7 CYS_root 1.3560012177797597E7 Chor 2.2366731975070852E8 Chor_root 3.6957680249291494E7 ENO 9.921479710891043E9 ENO_root 4.095219588433912E9 ET 8.698380635712927E11 FBP 2.1569269542404446E10 FBP_plastid 0.0 FF_root 3.20835204813344E9 FK_root 3.20835204813344E9 FNR 5.115596859792769E11 FQR 2.5577984298963846E11 FUM 8.19962461912234E9 FUM_root 3.810708780202614E9 Formyl -5.630323266465174E9 Formyl_root -9.303267335348268E8 G6PDH 8.434978006668664E8 G6PDH_plastid 3.137032060208674E9 G6PDH_root 5.535227558110331E9 GAPDH 2.146279040256385E10 GAPDH_plastid 5.177516851118721E11 GAPDH_root 4.634830080883351E9 GAT 1.7031016773712364E10 GDC 2.530661295783461E10 GDH 0.0 GDH_root 0.0 GHMT -2.5282476196710434E10 GHMT_root 4.773939659866034E8 GLK 0.0 GLK_root 3.20835204813344E9 GLO 5.347827018855844E10 GLU_plastid 3.739246638948723E10 GLYK 3.644725341484608E10 GMP 1.4161649216169896E9 GMP_root 2.3400007838301042E8 GOGAT_root 1.9970065683473847E9 GPDH 3763017.606303719 GPDH_root 621782.3936962814 GS_plastid 4.550905627289238E10 GS_root 3.338151684942235E9 Glyc 3763017.606303719 Glyc_root 621782.3936962814 H-ATPase2_root 2.493201379295511E10 H-ATPase_mesophyll 2.6907436301110283E10 H-ATPase_phloem1 2.7260063043579817E9 H-ATPase_phloem2 2.6907436301110283E10 H-ATPase_root 2.367537240582156E9 HPR 3.644725341484608E10 Hexa 7822627.733301327 Hexa_root 1292572.2666986736 His 5.149175706491131E7 His_root 8508242.935088689 HomoSer 3.523967124129868E8 HomoSer_root 5.8228287587013215E7 IDH 0.0 IDH_mitochondria 4.780370273963725E9 IDH_mitochondria_root 3.2457281253612294E9 ILE 1.0941998376293653E8 ILE_root 1.8080016237063464E7 IMP 2.8409075117650423E9 IMP_root 4.694174882349577E8 Leu 2.1883996752587306E8 Leu_root 3.616003247412693E7 Lino 6951.387203763027 Lino_root 1148.612796236973 Lipidpoly 3861881.7798683485 Lipidpoly_root 638118.2201316516 Lys 4.827352224835435E7 Lys_root 7976477.751645645 MDH -3.120073246847181E9 MDH_mitochondria 1.131969786596952E10 MDH_mitochondria_root 4.837889729787592E9 MDH_root -1.027180949584978E9 MET 2.4136761124177177E7 MET_root 3988238.8758228226 MH 0.0 MS3 0.0 MS3_root 4.7340572711078054E8 MTHFR 2.4136761124177177E7 MTHFR_root 4.773939659866034E8 NADP_MDH 0.0 NIA 2.1660990243718933E10 NIA_root 3.5791547562810683E9 NiR 2.1660990243718933E10 NiR_root 3.5791547562810683E9 Octa 2685552.5897204494 Octa_root 443747.41027955053 Orni 9.01105748635948E7 Orni_root 1.4889425136405205E7 OxPhos1.mitochondrion_mesophyll 2.510817417753789E10 OxPhos1.mitochondrion_root 1.4483759516194084E10 OxPhos1_phloem 7.169381275516516E9 OxPhos2.mitochondrion_mesophyll 3.8953556994105616E9 OxPhos2.mitochondrion_root 3.0994926999143925E9 OxPhos2_phloem 1.4338762551033032E9 OxPhos3.mitochondrion_mesophyll 2.9003529876948452E10 OxPhos3.mitochondrion_root 1.758325221610848E10 OxPhos3_phloem 8.60325753061982E9 OxPhos4.mitochondrion_mesophyll 1.4501764938474226E10 OxPhos4.mitochondrion_root 8.79162610805424E9 OxPhos4_phloem 4.30162876530991E9 OxPhos5.mitochondrion_mesophyll 6.636144248355941E10 OxPhos5.mitochonrion_root -3.925860242509548E10 OxPhos5_phloem 2.6765690095261658E10 PDC_TCA 1.4338762551033032E9 PDH 5.112750338194083E9 PDH_root 3.300648961130871E9 PFK 0.0 PFK_root 1.5257777173363366E9 PGDH 8.434978006668664E8 PGDH_plastid 3.137032060208674E9 PGDH_root 5.535227558110331E9 PGI -1.557286627664025E10 PGI_plastid 5.71161991345424E9 PGI_root -4.879348390503497E9 PGK 2.146279040256385E10 PGK_plastid 5.177516851118721E11 PGK_root 4.634830080883351E9 PGL 8.434978006668664E8 PGL_plastid 3.137032060208674E9 PGL_root 5.535227558110331E9 PGM 9.921479710891043E9 PGM3 -1.4729368475973383E10 PGM3_plastid 2.5745878532455654E9 PGM3_root -2.5524728805266066E9 PGM_root 4.095219588433912E9 PGP 5.347827018855844E10 PK 6.129712540226082E9 PK_root 3.468686759098872E9 PMet 2.1883996752587306E8 PMet_root 3.616003247412693E7 PPC 3.3444325311635437E9 PPC_root 5.526174688364562E8 PRK_plastid 2.673913509427922E11 PRO 3.218234816556957E7 PRO_root 5317651.83443043 PSI 1.7396761271425854E12 PSII 3.0702911029082715E11 Phe 1.0298351412982263E8 Phe_root 1.7016485870177377E7 Proteinpoly 1.072744938852319E7 Proteinpoly_root 1772550.6114768102 R5PI 3.2670799545217953E9 R5PI_plastid 8.808477296086118E10 R5PI_root 2.3384534984039373E9 RDPK 4.367037371573905E9 RDPK_root 7.215876284260947E8 RNApoly 429097.9755409276 RNApoly_root 70902.0244590724 RPC2_plastide 5.347827018855844E10 RPC_plastide 2.1391308075423376E11 RPE -2.423582153854929E9 RPE_plastid 1.7616954592172235E11 RPE_root 3.1967740597063937E9 SBP_plastid 1.818811658351766E11 SCL 3.8953556994105616E9 SCL_root 3.0994926999143925E9 SER 1.1541310691672808E10 SER_root 5.396104924494394E8 SK 0.0 SPP 3.572821111909266E9 SPS 3.572821111909266E9 SUL_root 1.3560012177797597E7 Suc-CoA 3.8953556994105616E9 Suc-CoA_root 3.0994926999143925E9 Sulfite_reductase 8.20649878222024E7 T.ADP.mesophyll (mitochondria <=> mesophyll) 7.025679818296997E10 T.ADP.plastid 0.0 T.ADP.root (mitochondria <=> root) 4.235809512500988E10 T.ATP.mesophyll (mitochondria <=> mesophyll) -7.025679818296997E10 T.ATP.plastid 0.0 T.ATP.root (mitochondria <=> root) -4.235809512500988E10 T.Biomass.ext 5000.0 T.Biomass.mesophyll 429097.9755409276 T.Biomass.root 70902.0244590724 T.CO2.ext -1.6377850025772134E11 T.CO2.mesophyll -1.8190576110232556E11 T.CO2.mesophyll (mitochondria <=> mesophyll) -1.3788476311568369E10 T.CO2.mesophyll(plastid<=>mesophyll) -2.107760486940251E11 T.CO2.mitochondria (mitochondria <=> mesophyll) -1.3788476311568369E10 T.CO2.mitochondria (mitochondria <=> root) -9.645869786406492E9 T.CO2.phloem 4.30162876530991E9 T.CO2.plastid(plastid<=>mesophyll) -2.107760486940251E11 T.CO2.root 1.3825632079294298E10 T.CO2.root (mitochondria <=> root) -9.645869786406492E9 T.Fumarate.mesophyll (mitochondria <=> mesophyll) 4.304268919711779E9 T.Fumarate.mitochondria (mitochondria <=> mesophyll) 4.304268919711779E9 T.Fumarate.mitochondria (mitochondria <=> root) 7.112160802882215E8 T.Fumarate.root (mitochondria <=> root) 7.112160802882215E8 T.GAP.plastid 6.5904580480657684E10 T.GAP.plastid2 6.5904580480657684E10 T.Glu.plastid1 2.9275876506082077E10 T.Glu.plastid2 2.9275876506082077E10 T.Glutamine.plastid1 8.116589883405149E9 T.Glutamine.plastid2 -8.116589883405149E9 T.Glyceraate.mesophyll 3.644725341484608E10 T.Glycerate.plastid 3.644725341484608E10 T.Glycolate.mesophyll 5.347827018855844E10 T.Glycolate.plastid 5.347827018855844E10 T.H2O.ext 1.0606335187815175E11 T.H2O.ext2 0.0 T.H2O.mesophyll (mitochondria <=> mesophyll) -8.205259740319144E10 T.H2O.mesophyll(plastid<=>mesophyll) -1.5571818323870233E11 T.H2O.mesophyll.load 1.2903311811062337E11 T.H2O.mesophyll.unload 0.0 T.H2O.mitochondria (mitochondria <=> mesophyll) -8.205259740319144E10 T.H2O.mitochondria (mitochondria <=> root) -4.9730496899870476E10 T.H2O.phloem.load 1.250899584090893E11 T.H2O.phloem.unload 1.2903311811062337E11 T.H2O.plastid(plastid<=>mesophyll) -1.5571818323870233E11 T.H2O.root (mitochondria <=>root) -4.9730496899870476E10 T.H2O.root.load 1.0606335187815175E11 T.H2O.root.unload 1.250899584090893E11 T.H2S.plastid1 8.20649878222024E7 T.H2S.plastid2 8.20649878222024E7 T.Isocitrate.mesophyll (mitochondria <=> mesophyll) -3.323800642303585E8 T.Isocitrate.mitochondria (mitochondria <=> mesophyll) -3.323800642303585E8 T.Isocitrate.mitochondria (mitochondria <=> root) -5.492083576964151E7 T.Isocitrate.root (mitochondria <=> root) -5.492083576964151E7 T.KG.plastid1 -3.739246638948723E10 T.KG.plastid2 3.739246638948723E10 T.Malate.mesophyll(plastid<=>mesophyll) 0.0 T.Malate.mit 3.120073246847181E9 T.Malate.mit2 3.120073246847181E9 T.Malate.mitochondria(mitochondria<=>root) 1.027180949584978E9 T.Malate.plastid 0.0 T.Malate.root(mitochondria<=>root) 1.027180949584978E9 T.N.ext -2.5256104794067173E10 T.N.mesophyll.load 2.167468687436748E10 T.N.phloem.load 2.167468687436748E10 T.N.phloem.unload 2.167468687436748E10 T.N.root.load 2.5256104794067173E10 T.N.root.unload 2.167468687436748E10 T.NH4.mesophyll -2.3848066029173447E10 T.NH4.plastid -2.3848066029173447E10 T.NO2.plastid1 2.1660990243718933E10 T.NO2.plastid2 2.1660990243718933E10 T.O2.ext 1.992115403461511E11 T.O2.mesophyll 2.1230552478007632E11 T.O2.mesophyll (mitochondria <=> mesophyll) 1.4501764938474226E10 T.O2.mesophyll (palstid <=> mesophyll) 2.5355084010226868E11 T.O2.mitochondria (mitochondria <=> mesophyll) 1.4501764938474226E10 T.O2.mitochondria (mitochondria <=> root) 8.79162610805424E9 T.O2.phloem -4.30162876530991E9 T.O2.plastid (palstid <=> mesophyll) 2.5355084010226868E11 T.O2.root -8.792355668615314E9 T.O2.root (mitochondria <=> root) 8.79162610805424E9 T.OAA.mesophyll (mitochondrion <=> mesophyll) 6.206947527775437E9 T.OAA.mesophyll (palstid <=> mesophyll) 0.0 T.OAA.mitochondrion -6.206947527775437E9 T.OAA.mitochondrion (mitochondrion <=> root) 1.537240768656721E9 T.OAA.plastid 0.0 T.OAA.root (mitochondrion <=> root) 1.537240768656721E9 T.Orthophosphate.mesophyll (mesophyll<=>mitochondria) 7.025679818296997E10 T.Orthophosphate.root (root<=>mitochondria) 4.235809512500988E10 T.Oxoglutarate.mesophyll(mitochondria<=>mesophyll) -8.850145745531632E8 T.Oxoglutarate.mitochondria(mitochondria<=>mesophyll) -8.850145745531632E8 T.Oxoglutarate.mitochondria(mitochondria<=>root) -1.4623542544683683E8 T.Oxoglutarate.root(mitochondria<=>root) -1.4623542544683683E8 T.P.ext -5.016915788183378E9 T.P.mesophyll.load 4.305496816337609E9 T.P.mit_mesophyll 7.025679818296997E10 T.P.mitochondria_root2 4.235809512500988E10 T.P.phloem.load 4.305496816337609E9 T.P.phloem.unload 4.305496816337609E9 T.P.plastid 6.5904580480657684E10 T.P.plastid2 0.0 T.P.root.load 5.016915788183378E9 T.P.root.unload 4.305496816337609E9 T.Pyruvate.mesophyll (mesophyll<=>mitochondria) 5.112750338194083E9 T.Pyruvate.mit_mesophyll2 5.112750338194083E9 T.Pyruvate.mitochondria_root 3.300648961130871E9 T.Pyruvate.root (root<=>mitochondria) 3.300648961130871E9 T.S.ext -9.972894704584457E7 T.S.mesophyll.load 8.558697856040056E7 T.S.phloem.load 8.558697856040056E7 T.S.phloem.unload 8.558697856040056E7 T.S.root.load 9.972894704584457E7 T.S.root.unload 8.558697856040056E7 T.Starch.Plastid (Plastid <=> Plant) 0.0 T.Starch.plant(plant<=>mesophyll) 4290979.755409276 T.Starch.plastid(plastid<=>mesophyll) 4290979.755409276 T.Sucrose.mesophyll 3.567671936202775E9 T.Sucrose.phloem.load 3.567671936202775E9 T.Sucrose.phloem.unload 3.209202872426949E9 T.Sucrose.root -3.209202872426949E9 T.Sulfate.plastid 8.20649878222024E7 T.Sulfate.plastid2 -8.20649878222024E7 T.alpha-Maltose.mesophyll(plastid<=>mesophyll) 0.0 T.alpha-Maltose.plastid(plastid<=>mesophyll) 0.0 T.h.ext 2.493201379295511E10 T.h.mit_mesphyll1 7.50371684569337E10 T.h.mit_mesphyll2 7.50371684569337E10 T.h.mitochondria_root1 4.560382325037111E10 T.h.mitochondria_root2 4.560382325037111E10 T.h.plastid_mesophyll1 0.0 T.h.plastid_mesophyll2 0.0 T.hv.ext -2.967792568305894E12 T.starch.ext 0.0 TA -1.0999574170521102E9 TA_plastid 9.379639287431541E10 TA_root 1.6168658699778426E9 TKa -1.0999574170521102E9 TKa_plastid 8.808477296086118E10 TKa_root 1.6168658699778426E9 TKb -1.3236247368028185E9 TKb_plastid 8.808477296086118E10 TKb_root 1.5799081897285511E9 TPI 2.157303256001075E10 TPI_plastid 1.818811658351766E11 TPI_root -1.5251559349426403E9 TRP 2.4136761124177177E7 TRP_root 3988238.8758228226 Thr 3.282599512888096E8 Thr_root 5.424004871119039E7 Tyr 9.65470444967087E7 Tyr_root 1.595295550329129E7 UDP 3.862267968046335E8 UDP_root 6.381820319536648E7 UGD 2.5745878532455654E9 UGD_root 4.254121467544344E8 UGP -1.4729368475973383E10 UGP_root -2.5524728805266066E9 UMP 1.501993098684686E9 UMP_root 2.4818190131531408E8 UTP 1.5115595272778017E10 UTP_root 2.616291083721973E9 VAL 6.436469633113914E7 VAL_root 1.063530366886086E7 cellulose_mesophyll 8581959.510818552 cellulose_root 2127060.733772172 cis-Hexa 4020218.932842951 cis-Hexa_root 664281.0671570493 cis-Octa 2398228.5852982444 cis-Octa_root 396271.4147017557 pH_mesophyll 2.6907436301110283E10 pH_mit_root -3.925860242509548E10 pH_phloem 2.9633442605468266E10 pH_root 2.7299551033537262E10 pectin_mesophyll 8581959.510818552 pectin_root 1418040.489181448 starch synthase 4290979.755409276 suc_hydrolysis_glycolysis 3.584690637758258E8 vac_C 9.742280832273917E7 vac_C_root 1.6097662380864661E7 vac_N 1.3696630648548363E7 vac_N_root 2263163.4186249636 vac_P 1.4087962952792602E7 vac_P_root 2327825.230585677 vac_S 3521990.7381981504 vac_S_root 581956.3076464193 vac_suc 5149175.706491131 vac_suc_root 850824.2935088689 **** EOF Flux ****
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Created: 16th Apr 2016 at 21:19
Last updated: 4th Jun 2016 at 21:51
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Version 3 (latest) Created 4th Jun 2016 at 21:51 by Maksim Zakhartsev
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Projects: MOSES, ExtremoPharm, ZucAt, GenoSysFat, DigiSal, EraCoBiotech 2 nd call proposal preparation, FAIRDOM & LiSyM & de.NBI Data Structuring Training
Institutions: University of Stuttgart, University of Hohenheim, Norwegian University of Life Sciences, Norwegian University of Science and Technology
https://orcid.org/0000-0002-7973-9902
I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to ...
The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...
Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, SABIO-VIS
Web page: http://www.denbi.de
ZucAt - Sucrose (from german Zucker) translocation in Arabidopsis thaliana. Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the ...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped ...
we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll ...
Submitter: Maksim Zakhartsev
Investigation: Metabolic analysis of effects of sucrose transl...
Assays: Flux Balance Analysis of multi-compartment metabolic model of growing Ar...
The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both ...
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Investigation: Metabolic analysis of effects of sucrose transl...
