Laurel and Hardy 1 mean data and simulations

Selected Cell

Cell:

Value:

Metadata Biomass Starch M+F plot_LH1_biomass_and_carbon_poo

Data	Laurel and Hardy 1 (Jan 2014)
Temperature	20.5
Light	145
Photoperiod	12
CO2 level	42

Model	FM 1.1.1.1 (FM v1 + toy starch + fixed starch synthesis + malate/fumarate); now "FMv2", DDS sims included in the last sheet

	Incorrect, old simulations		micromol CO2/g FW/h	micromol CO2/g FW/h	micromol CO2/cm2/h	micromol CO2/cm2/h
	cvRMSE	nRMSE	AperFW	RperFW	Aperarea	Rperarea
Col	0.1011	0.0367	45.0675	-8.1877	1.4177	-0.2547
lsf1	0.153	0.0562	53.7457	-11.296	1.418	-0.2944
prr7prr9 (starch only)	0.3179	0.1133	55.4703	-10.2331	1.4178	-0.2586
prr7prr9 (starch +m+f)	0.0805	0.0287	55.5061	-10.1297	1.4178	-0.2558

Sheets in this worksheet	Contents
Biomass	Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; simulation outputs from FMv2 default (for Col Wild Type plants), with the lsf1 starch defect, and two simulations for prr7prr9, where the mutation affects only starch degradation, or both starch degradation and malate/fumarate store mobilisation
Starch	Starch levels in carbon units (not C6) measured on multiple days, mean and SD, simulations as above
M + F	Malate and fumarate levels in carbon units (not C4) measured on multiple days, mean and SD, simulations as above
plot_LH1_biomass_and_carbon_poo[ls]	Simulation data from FMv2 runs in the conditions above, from the Matlab output file

Credits
Experimental setup, physiological data, sampling and model construction	Yin Hoon Chew, Millar group University of Edinburgh
Model refinement and final simulations	Daniel Seaton, Millar group University of Edinburgh
Starch, M+F and other metabolite analysis	Virginie Mengin et al, Stitt group, MPIMP

100

	Biomass (Data)						Biomass (simulation)	FW
Day	22	28	29	38			Day	Col	lsf-1	prr7/prr9 (starch defect)	prr7/prr9 (starch+store)
Col	0.033999999999999996	0.12620000000000003	0.2192	0.95014			0.041666666666666664	0	0	0	0
SD	0.004092676385936208	0.01788742575106885	0.03288251815174724	0.14407886035085077			0.08333333333333333	0	0	0	0
lsf-1	0.01866	0.08546000000000001	0.09680000000000004	0.48772000000000004			0.125	0	0	0	0
SD	0.0030369392486515184	0.007267255327838655	0.012679511031581592	0.04625761558921946			0.16666666666666666	0	0	0	0
prr7/prr9	0.021019999999999994	0.09237999999999995	0.10086000000000003	0.5743	0.6044372408276676	of WT mass	0.20833333333333331	0	0	0	0
SD	0.0014131525041551365	0.013399514916593077	0.00826032687004573	0.06114433743201409			0.24999999999999997	0	0	0	0
							0.29166666666666663	0	0	0	0
							0.3333333333333333	0	0	0	0
							0.375	0	0	0	0
							0.4166666666666667	0	0	0	0
							0.45833333333333337	0	0	0	0
							0.5	0	0	0	0
							0.5416666666666666	0	0	0	0
							0.5833333333333333	0	0	0	0
							0.6249999999999999	0	0	0	0
							0.6666666666666665	0	0	0	0
							0.7083333333333331	0	0	0	0
							0.7499999999999998	0	0	0	0
							0.7916666666666664	0	0	0	0
							0.833333333333333	0	0	0	0
							0.8749999999999997	0	0	0	0
							0.9166666666666663	0	0	0	0
							0.9583333333333329	0	0	0	0
							0.9999999999999996	0	0	0	0
							1.0416666666666663	0	0	0	0
							1.083333333333333	0	0	0	0
							1.1249999999999998	0	0	0	0
							1.1666666666666665	0	0	0	0
							1.2083333333333333	0	0	0	0
							1.25	0	0	0	0
							1.2916666666666667	0	0	0	0
							1.3333333333333335	0	0	0	0
							1.3750000000000002	0	0	0	0
							1.416666666666667	0	0	0	0
							1.4583333333333337	0	0	0	0
							1.5000000000000004	0	0	0	0
							1.5416666666666672	0	0	0	0
							1.583333333333334	0	0	0	0
							1.6250000000000007	0	0	0	0
							1.6666666666666674	0	0	0	0
							1.7083333333333341	0	0	0	0
							1.7500000000000009	0	0	0	0
							1.7916666666666676	0	0	0	0
							1.8333333333333344	0	0	0	0
							1.875000000000001	0	0	0	0
							1.9166666666666679	0	0	0	0
							1.9583333333333346	0	0	0	0
							2.0000000000000013	0	0	0	0
							2.041666666666668	0	0	0	0
							2.0833333333333344	0	0	0	0
							2.125000000000001	0	0	0	0
							2.1666666666666674	0	0	0	0
							2.208333333333334	0	0	0	0
							2.2500000000000004	0	0	0	0
							2.291666666666667	0	0	0	0
							2.3333333333333335	0	0	0	0
							2.375	0	0	0	0
							2.4166666666666665	0	0	0	0
							2.458333333333333	0	0	0	0
							2.4999999999999996	0	0	0	0
							2.541666666666666	0	0	0	0
							2.5833333333333326	0	0	0	0
							2.624999999999999	0	0	0	0
							2.6666666666666656	0	0	0	0
							2.708333333333332	0	0	0	0
							2.7499999999999987	0	0	0	0
							2.791666666666665	0	0	0	0
							2.8333333333333317	0	0	0	0
							2.8749999999999982	0	0	0	0
							2.9166666666666647	0	0	0	0
							2.9583333333333313	0	0	0	0
							2.999999999999998	0	0	0	0
							3.0416666666666643	0	0	0	0
							3.083333333333331	0	0	0	0
							3.1249999999999973	0	0	0	0
							3.166666666666664	0	0	0	0
							3.2083333333333304	0	0	0	0
							3.249999999999997	0	0	0	0
							3.2916666666666634	0	0	0	0
							3.33333333333333	0	0	0	0
							3.3749999999999964	0	0	0	0
							3.416666666666663	0	0	0	0
							3.4583333333333295	0	0	0	0
							3.499999999999996	0	0	0	0
							3.5416666666666625	0	0	0	0
							3.583333333333329	0	0	0	0
							3.6249999999999956	0	0	0	0
							3.666666666666662	0	0	0	0
							3.7083333333333286	0	0	0	0
							3.749999999999995	0	0	0	0
							3.7916666666666616	0	0	0	0
							3.833333333333328	0	0	0	0
							3.8749999999999947	0	0	0	0
							3.916666666666661	0	0	0	0
							3.9583333333333277	0	0	0	0
							3.9999999999999942	0	0	0	0
							4.041666666666661	0	0	0	0
							4.083333333333328	0	0	0	0

In C6					in C6	from plot_LH1 "starchC6"	Rows 674-698			In C					in C
	Starch (data)				Starch (simulation)						Starch (data)				Starch (simulation)
Hour	0	12	24		Hour	Col	lsf-1	prr7/prr9 (starch defect)	prr7/prr9 (starch+store)	Hour	0	12	24	ave 0,24	Hour	Col	lsf-1	prr7/prr9 (starch defect)	prr7/prr9 (starch+store)
Col	2.41	42.7	4.55	day 28	0	2.8870309143924	44.6972045680592	14.5800949253619	14.6446048931179	Col	14.46	256.20000000000005	27.299999999999997	20.88	0	17.3221854863544	268.1832274083552	87.4805695521714	87.8676293587074
SD	0.35	2.37	0.31		1	6.68110801007285	48.7061814000054	19.0481330028861	19.1184382076686	SD	2.0999999999999996	14.22	1.8599999999999999		1	40.0866480604371	292.2370884000324	114.2887980173166	114.71062924601159
lsf-1	45.28	90.19	44.25		2	10.4021745706164	52.6385070581877	23.4309715788264	23.5061725690627	lsf-1	271.68	541.14	265.5	268.59000000000003	2	62.4130474236984	315.83104234912616	140.5858294729584	141.0370354143762
SD	1.05	4.61	2.08		3	14.0544172846135	56.4973203668908	27.7326378511361	27.8118268767474	SD	6.300000000000001	27.660000000000004	12.48		3	84.326503707681	338.9839222013448	166.3958271068166	166.8709612604844
prr7/prr9	9.93	67.31	23.77		4	17.6393660022287	60.2855965713722	31.9551725179706	32.0381477772893	prr7/prr9	59.58	403.86	142.62	101.1	4	105.83619601337222	361.71357942823323	191.7310351078236	192.2288866637358
SD	0.08	0.01	0.14		5	21.158514009272	64.0047976561692	36.1003216658608	36.1868707110767	SD	0.48	0.06	0.8400000000000001		5	126.95108405563201	384.0287859370152	216.60192999516477	217.12122426646022
					6	24.6133096072843	67.6564361238556	40.1697865406116	40.2597064260162						6	147.67985764370582	405.9386167431336	241.01871924366958	241.5582385560972
					7	28.0674734555104	71.2419789866158	44.1652176817982	44.2583144420467						7	168.4048407330624	427.45187391969483	264.9913060907892	265.5498866522802
					8	31.4563803050801	74.7628502894492	48.1621671697776	48.2576726169447						8	188.7382818304806	448.5771017366952	288.97300301866557	289.5460357016682
P.ksX = 10*P.ksX;					9	34.7840541511642	78.2884279494454	52.082755891678	52.1803953395137						9	208.7043249069852	469.73056769667244	312.496535350068	313.0823720370822
P.kdS = 0.045*P.kdS;					10	38.0517383789399	81.7440917526615	55.9328173563441	56.0323045926233						10	228.3104302736394	490.464550515969	335.5969041380646	336.1938275557398
					11	41.2606693675323	85.1380538377186	59.713769819949	59.8149852117126						11	247.5640162051938	510.82832302631164	358.282618919694	358.8899112702756
					12	44.4120515737664	88.4715962812877	63.4270278945593	63.5298474881387						12	266.4723094425984	530.8295776877262	380.5621673673558	381.1790849288322
					13	40.066528681058	84.045652444464	58.6157337892267	58.7264686966289						13	240.39917208634802	504.273914666784	351.6944027353602	352.3588121797734
					14	35.8549554426391	79.7551284799338	53.9204385676463	54.036498722315						14	215.12973265583463	478.5307708796028	323.5226314058778	324.21899233389
					15	31.7872676080172	75.6038431339438	49.3490546770408	49.4681229188195						15	190.7236056481032	453.6230588036628	296.0943280622448	296.808737512917
					16	27.8670660498943	71.589345584681	44.90387546285	45.0236185342239						16	167.2023962993658	429.536073508086	269.4232527771	270.1417112053434
					17	24.100709176481	67.7093072019956	40.5860222717602	40.7042479483274						17	144.604255058886	406.25584321197357	243.5161336305612	244.22548768996438
					18	20.4961936262059	63.964224745784	36.4019478511828	36.5166559122563						18	122.97716175723541	383.785348474704	218.41168710709678	219.09993547353778
					19	17.0602513626595	60.3472637358407	32.3528525543184	32.4618584185956						19	102.361508175957	362.0835824150442	194.11711532591042	194.77115051157358
					20	13.8050657478156	56.8582255430244	28.4444013482235	28.5464045935063						20	82.8303944868936	341.14935325814645	170.66640808934102	171.2784275610378
					21	10.7441241902008	53.4951294307891	24.6829175239283	24.7763908077005						21	64.4647451412048	320.9707765847346	148.0975051435698	148.65834484620302
					22	7.8930993141054	50.2560769601912	21.0755450085064	21.1591455639077						22	47.3585958846324	301.5364617611472	126.4532700510384	126.9548733834462
					23	5.26388802051619	47.1390405532428	17.6308446521628	17.7034443627892						23	31.58332812309714	282.8342433194568	105.7850679129768	106.2206661767352
				day 29	24	2.85803055010407	44.1411255085192	14.3589503938466	14.4196877143632						24	17.14818330062442	264.84675305111523	86.1537023630796	86.5181262861792

In C4				in C4					In C						in C
	M+F (data)			M+F (simulation)						M+F (data)					M+F (simulation)
Hour	0	12	24	Hour	Col	lsf-1	prr7/prr9 (starch defect)	prr7/prr9 (starch+store)	Hour	0	12	24	ave 0,24		Hour	Col	lsf-1	prr7/prr9 (starch defect)	prr7/prr9 (starch+store)
Col	4.85	17.87	5.38	0	4.92162320916166	6.09914549511857	6.03812050934966	28.7753195639645	Col	19.4	71.48	21.52	20.46		0	19.68649283664664	24.39658198047428	24.15248203739864	115.101278255858
SD	0.51	1.24	0.71	1	5.99649249916805	7.41655168107333	7.35251306431219	29.7355394379101	SD	2.04	4.96	2.84			1	23.9859699966722	29.66620672429332	29.41005225724876	118.9421577516404
lsf-1	6.62	24.18	7.85	2	7.05084205809709	8.70842103901682	8.64191141684524	30.6783164961017	lsf-1	26.48	96.72	31.4	28.939999999999998		2	28.20336823238836	34.83368415606728	34.56764566738096	122.7132659844068
SD	1.18	1.07	0.27	3	8.08578669087373	9.9759430232152	9.90746917572675	31.6040398912251	SD	4.72	4.28	1.08			3	32.34314676349492	39.9037720928608	39.629876702907	126.4161595649004
prr7/prr9	18.65	41.8	25.31	4	9.10174232191218	11.2201110378878	11.1497810717199	32.5132374462616	prr7/prr9	74.6	167.2	101.24	87.91999999999999		4	36.40696928764872	44.8804441515512	44.5991242868796	130.0529497850464
SD	2.14	2.69	4.04	5	10.0991283264527	12.441428106149	12.369358687508	33.4062318853059	SD	8.56	10.76	16.16			5	40.3965133058108	49.765712424596	49.477434750032	133.6249275412236
				6	11.0783515316174	13.6403985770558	13.5667010032222	34.2833685758239							6	44.3134061264696	54.5615943082232	54.2668040128888	137.1334743032956
				7	12.0578230177691	14.8175116305174	14.742292137183	35.1449826168786							7	48.2312920710764	59.2700465220696	58.969168548732	140.5799304675144
				8	13.0185200281191	15.9732420487196	15.9185118692287	36.0094087826016							8	52.0740801124764	63.8929681948784	63.6740474769148	144.0376351304064
				9	13.9619329529969	17.1296326952275	17.0721441050678	36.8555836545431							9	55.8477318119876	68.51853078091	68.2885764202712	147.4223346181724
				10	14.8884075974977	18.2636604776275	18.20505434521	37.6869336175445							10	59.5536303899908	73.05464191051	72.82021738084	150.747734470178
				11	15.7982913537446	19.3772922499184	19.3176574361417	38.5037691832618							11	63.1931654149784	77.5091689996736	77.2706297445668	154.0150767330472
				12	16.6919226724099	20.4709601700179	20.4103683419115	39.3063709330236							12	66.7676906896396	81.8838406800716	81.641473367646	157.2254837320944
				13	15.6582328369508	19.2234783852199	19.1573346010194	38.3729232435251							13	62.6329313478032	76.8939135408796	76.6293384040776	153.4916929741004
				14	14.6338294535794	17.98420399891	17.9133279364587	37.4468527931703							14	58.5353178143176	71.93681599564	71.6533117458348	149.7874111726812
				15	13.6191537516024	16.7537014187681	16.679034816158	36.5301157981148							15	54.4766150064096	67.0148056750724	66.716139264632	146.1204631924592
				16	12.6137276876801	15.5314272173803	15.4540363383957	35.6224978983033							16	50.4549107507204	62.1257088695212	61.8161453535828	142.4899915932132
				17	11.6171005362401	14.3168546273621	14.2378881393555	34.7237452828872							17	46.4684021449604	57.2674185094484	56.951552557422	138.8949811315488
				18	10.6292647799317	13.110028600182	13.0307589763276	33.8351976815001							18	42.5170591197268	52.440114400728	52.1230359053104	135.3407907260004
				19	9.64890681773475	11.909458816515	11.8312156933611	32.9542348384016							19	38.595627270939	47.63783526606	47.3248627734444	131.8169393536064
				20	8.67585088393906	10.7150439901414	10.6392037461097	32.0816738563747							20	34.70340353575624	42.8601759605656	42.5568149844388	128.3266954254988
				21	7.70955640055941	9.52630067757854	9.45426751208936	31.2173790367213							21	30.83822560223764	38.10520271031416	37.81707004835744	124.8695161468852
				22	6.7494334934794	8.34275602580856	8.27592708002213	30.36123960053							22	26.9977339739176	33.37102410323424	33.10370832008852	121.44495840212
				23	5.79478119031715	7.16394449004059	7.10367712346882	29.5131649484002							23	23.1791247612686	28.65577796016236	28.41470849387528	118.0526597936008
				24	4.8447649665728	5.98940443473167	5.93697676095253	28.6730856302845							24	19.3790598662912	23.95761773892668	23.74790704381012	114.692342521138

										M+F + starch (data)
									Hour	0	12	24		Turnover
									Col	33.86	327.68000000000006	48.81999999999999		0.85101318359375

									lsf-1	298.16	637.86	296.9		0.5345373592951432

									prr7/prr9	134.18	571.06	243.86		0.5729695653696634

100

simulation	WT	WT	WT	WT	WT	WT	WT	WT	WT	WT	WT	WT	WT	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	lsf1	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9_noMF	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9	prr7prr9
variable	Total_shoot	Starch_carbon	MF_carbon	starch	sucrose	NPP	Gas_exchange_perFW	starch_perFW	sucrose_perFW	FW	starchC6	malatefumarateC4	sugar	Total_shoot	Starch_carbon	MF_carbon	starch	sucrose	NPP	Gas_exchange_perFW	starch_perFW	sucrose_perFW	FW	starchC6	malatefumarateC4	sugar	Total_shoot	Starch_carbon	MF_carbon	starch	sucrose	NPP	Gas_exchange_perFW	starch_perFW	sucrose_perFW	FW	starchC6	malatefumarateC4	sugar	Total_shoot	Starch_carbon	MF_carbon	starch	sucrose	NPP	Gas_exchange_perFW	starch_perFW	sucrose_perFW	FW	starchC6	malatefumarateC4	sugar
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