diff --git a/assays/AbsorptionSpectraAndODMeasurements/README.md b/assays/AbsorptionSpectraAndODMeasurements/README.md index dbf4f5b5ecbe16b3c3a354c940e1ad14fc6fa370..ae5a12534092401bb68cb4ef38ee737f4cb2851f 100644 --- a/assays/AbsorptionSpectraAndODMeasurements/README.md +++ b/assays/AbsorptionSpectraAndODMeasurements/README.md @@ -1,3 +1,5 @@ +<img src=dataset/fpls-14-1024981-g004.jpg width=60%> + ### Figure 4 caption **Figure 4** Whole cell spectra of selected strains. Spectra were measured after three days incubation with 5 mM rhamnose in 1 cm cuvettes after equalizing the OD750 across all strains and subtracting the OD750 as a baseline correction. WT represents the *Synechocystis* sp. PCC 6803 wild type, while the control strain is *Synechocystis* sp. PCC 6803 Δshc pSHDY rhaS, from which the overexpression strains were constructed. The visually blue phenotype of the sqs overexpression strain in the cuvette is pictured in the bottom left. @@ -6,6 +8,8 @@ https://www.frontiersin.org/files/Articles/1024981/fpls-14-1024981-HTML/image_m/fpls-14-1024981-g004.jpg +<img src=dataset/SupplementaryFigure5.jpg width=60%> + ### Supplementary Figure 5 caption **Supplementary Figure 5.** Effect of overexpressions on growth of the different strains after 3 days of @@ -17,6 +21,8 @@ Average values from three biological replicates, error bars represent the standa https://www.frontiersin.org/articles/10.3389/fpls.2023.1024981/full#supplementary-material +<img src=dataset/SupplementaryFigure6.jpg width=60%> + ### Supplementary Figure 6 caption **Supplementary Figure 6:** Spectra of *Synechocystis* cells after 3 days incubation with 5 mM diff --git a/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/README.md b/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/README.md index ab04ed6df097d4f73e44f0bca1cfbbdcf41a604b..3d3db285b77ebcd525bee8fd20fb046102407887 100644 --- a/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/README.md +++ b/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/README.md @@ -1,3 +1,5 @@ +<img src=dataset\fpls-14-1024981-g002.jpg width=60%> + ### Figure 2 caption **Figure 2** Squalene concentrations [mg l-1 OD750-1] in response to gene overexpressions. Values are represented as the means of three biological replicates, standard deviations are shown. WT represents the *Synechocystis* sp. PCC 6803 wild type, while the control strain is *Synechocystis* sp. PCC 6803 Δshc pSHDY rhaS, from which the overexpression strains were constructed by inserting an additional copy of the specified gene under the control of the rhamnose-inducible promoter Prha into its genome. Asterisks ( * ) represent the p-value of the two-sided t-test between the respective strain and the control strain at the same rhamnose concentration (* denotes a value of p<0.05, ** denotes p<0.01 and *** denotes p<0.001). Samples were measured after three days of incubation with the specified concentration of rhamnose as an inducer. @@ -6,6 +8,8 @@ https://www.frontiersin.org/files/Articles/1024981/fpls-14-1024981-HTML/image_m/fpls-14-1024981-g002.jpg +<img src=dataset\fpls-14-1024981-g005.jpg width=60%> + ### Figure 5 caption **Figure 5** Timeseries of squalene production in sqs overexpression strain. Squalene production and OD750 of *Synechocystis* Δshc pEERM Prha sqs pSHDY rhaS in a 30 ml flask culture in mg l-1 over a period of two weeks after induction with 5 mM rhamnose to trigger overexpression of the squalene synthase (sqs). Means and standard deviations of three biological replicates are shown. @@ -14,6 +18,7 @@ https://www.frontiersin.org/files/Articles/1024981/fpls-14-1024981-HTML/image_m/ https://www.frontiersin.org/files/Articles/1024981/fpls-14-1024981-HTML/image_m/fpls-14-1024981-g005.jpg +<img src=dataset\SupplementaryFigure2.jpg width=60%> ### Supplementary Figure 2 caption **Supplementary Figure 2.** GC-MS calibration curve for squalene after extraction of 50, 25, 12.5, diff --git a/assays/MetabolicModeling/README.md b/assays/MetabolicModeling/README.md index cae435b2ed4b4860d8a2d4de90570c3901f677d8..1affc3487c920b6cc9ed923f2fa7f7447219140b 100644 --- a/assays/MetabolicModeling/README.md +++ b/assays/MetabolicModeling/README.md @@ -1,3 +1,4 @@ +<img src=dataset\fpls-14-1024981-g001.jpg width=60%> ### Figure 1 caption **Figure 1** Overview of fluxes predicted to change upon increased squalene production. Blue arrows indicate an increased flux and red arrows a decreased flux, respectively. Black arrows indicate no change. Reactions with no flux have a dotted line. The numbers indicate the maximum fold change of the corresponding flux. It is stated that this is not a minimal network but a part of the genome-scale model and not all active reactions are shown. 13DPG, 1;3-bisphosphoglycerate; 2OG, 2-oxoglutarate; 2PGL, 2-phosphoglycolate; AcCoA, acetyl-CoA; ATP synth., ATP synthase; CDP-ME, 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol; CDP-MEP, 2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol; Cit, citrate; Cytb6f, cytochrome b6f complex; DHAP, dihydroxyacetone phosphate; DMAPP, dimethylallyl diphosphate; DXP, 1-deoxy-D-xylulose 5-phosphate; E4P, erythrose 4-phosphate; F6P, fructose 6-phosphate; Fdox, ferredoxin (oxidized); Fdred, ferredoxin (reduced); FDP, fructose 1;6-biphosphate; FNR, ferredoxin-NADP+ reductase; FPP, farnesyl pyrophosphate; Fum, fumarate; G3P, glyceraldehyde 3-phosphate; Glc, D-glycerate; Glx, glyoxylate; Gly, glycolate; GPP, geranyl pyrophosphate; HMBPP, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate; IsoCit, isocitrate; IPP, isopentenyl diphosphate; Mal, malonate; MEcPP, 2-C-methyl-D-erythritol 2;4-cyclodiphosphate; MEP, 2-C-methyl-D-erythritol 4-phosphate; NDH, NADPH dehydrogenase; OAA, oxaloacetate; PC, plastocyanin; PEP, phosphoenolpyruvate; PG2, 2-phosphoglycerate; PG3, 3-phosphoglycerate; Pi, orthophosphate; PPi, diphosphate; PQ, plastoquinone; PQH2, plastohydroquinone; PSI, photosystem I; PSII, photosystem II; Pyr, pyruvate; R5P, ribose 5-phosphate; Ru5P, ribulose 5-phosphate; RuBP, ribulose 1;5-biphosphate; S17DP, sedoheptulose 1;7-bisphosphate; S7P, sedoheptulose 7-phosphate; Succ, succinate; X5P, xylulose 5-phosphate. diff --git a/assays/PigmentQuantification/README.md b/assays/PigmentQuantification/README.md index 2dc623daf41ac8aaca4ac1daaff9777090cf20a1..f9367aac0338d2e9aa60da8c64c89c864ff0c766 100644 --- a/assays/PigmentQuantification/README.md +++ b/assays/PigmentQuantification/README.md @@ -1,4 +1,6 @@ +<img src=dataset\fpls-14-1024981-g003.jpg width=60%> + ### Figure 3 caption **Figure 3** Relative change in chlorophyll (left) and carotenoid (right) concentrations [mg l-1 OD750-1] of the overexpression strains compared to the Δshc control strain. Values are represented as the means of three biological replicates. WT represents the Synechocystis sp. PCC 6803 wild type, while the control strain is Synechocystis sp. PCC 6803 Δshc pSHDY rhaS, from which the overexpression strains were constructed by inserting an additional copy of the specified gene under the control of the rhamnose-inducible promoter Prha into its genome. Asterisks (*) represent the p-value of the two-sided t-test between the respective strain and the control strain at the same rhamnose concentration (* denotes a value of p<0.05, ** denotes p<0.01 and *** denotes p<0.001). Samples were measured after three days of incubation with the specified concentration of rhamnose as an inducer. diff --git a/assays/qPCR/README.md b/assays/qPCR/README.md index 118cad37577532c861cc466d79dcfb7b45f375e7..829352cba6f792e19a38fc2e1bc762c321e4aee7 100644 --- a/assays/qPCR/README.md +++ b/assays/qPCR/README.md @@ -1,3 +1,5 @@ +<img src=dataset\SupplementaryFigure3.jpg width=60%> + ### Supplementary Figure 3 caption **Supplementary Figure 3:** Cq values of qRT-PCR primer pairs used with dilution series of cDNA. @@ -10,6 +12,8 @@ Suppl. Table 2. https://www.frontiersin.org/articles/10.3389/fpls.2023.1024981/full#supplementary-material +<img src=dataset\SupplementaryFigure4.jpg width=60%> + ### Supplementary Figure 4 caption **Supplementary Figure 4:** Results of qRT-PCR for genes sqs and dxs as log10-fold changes diff --git a/studies/PlasmidAndStrainConstruction/README.md b/studies/PlasmidAndStrainConstruction/README.md index 8fc7e154761da00498985e4bb5d28d7ac386189a..8847e03d3d44ab95fdb5ff74045ec65cdfcd572b 100644 --- a/studies/PlasmidAndStrainConstruction/README.md +++ b/studies/PlasmidAndStrainConstruction/README.md @@ -1,3 +1,5 @@ +<img src=protocols\SupplementaryFigure1.jpg width=60%> + ### Supplementary Figure 1 caption **Supplementary Figure 1.** Agarose gel electrophoresis of colony PCR products to prove the