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assays/AbsorptionSpectraAndODMeasurements/README.md
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<img src=dataset/fpls-14-1024981-g004.jpg width=60%>
### Figure 4 caption ### 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. **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.
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https://www.frontiersin.org/files/Articles/1024981/fpls-14-1024981-HTML/image_m/fpls-14-1024981-g004.jpg 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 caption
**Supplementary Figure 5.** Effect of overexpressions on growth of the different strains after 3 days of **Supplementary Figure 5.** Effect of overexpressions on growth of the different strains after 3 days of
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https://www.frontiersin.org/articles/10.3389/fpls.2023.1024981/full#supplementary-material 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 caption
**Supplementary Figure 6:** Spectra of *Synechocystis* cells after 3 days incubation with 5 mM **Supplementary Figure 6:** Spectra of *Synechocystis* cells after 3 days incubation with 5 mM
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assays/GC-MSMeasurementsForTheQuantificationOfSqualene/README.md
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<img src=dataset\fpls-14-1024981-g002.jpg width=60%>
### Figure 2 caption ### 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. **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.
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https://www.frontiersin.org/files/Articles/1024981/fpls-14-1024981-HTML/image_m/fpls-14-1024981-g002.jpg 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 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. **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.
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https://www.frontiersin.org/files/Articles/1024981/fpls-14-1024981-HTML/image_m/fpls-14-1024981-g005.jpg 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 caption
**Supplementary Figure 2.** GC-MS calibration curve for squalene after extraction of 50, 25, 12.5, **Supplementary Figure 2.** GC-MS calibration curve for squalene after extraction of 50, 25, 12.5,
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assays/MetabolicModeling/README.md
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<img src=dataset\fpls-14-1024981-g001.jpg width=60%>
### Figure 1 caption ### 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. **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.
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assays/PigmentQuantification/README.md
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<img src=dataset\fpls-14-1024981-g003.jpg width=60%>
### Figure 3 caption ### 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. **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.
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assays/qPCR/README.md
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<img src=dataset\SupplementaryFigure3.jpg width=60%>
### Supplementary Figure 3 caption ### Supplementary Figure 3 caption
**Supplementary Figure 3:** Cq values of qRT-PCR primer pairs used with dilution series of cDNA. **Supplementary Figure 3:** Cq values of qRT-PCR primer pairs used with dilution series of cDNA.
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https://www.frontiersin.org/articles/10.3389/fpls.2023.1024981/full#supplementary-material 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 caption
**Supplementary Figure 4:** Results of qRT-PCR for genes sqs and dxs as log10-fold changes **Supplementary Figure 4:** Results of qRT-PCR for genes sqs and dxs as log10-fold changes
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studies/PlasmidAndStrainConstruction/README.md
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<img src=protocols\SupplementaryFigure1.jpg width=60%>
### Supplementary Figure 1 caption ### Supplementary Figure 1 caption
**Supplementary Figure 1.** Agarose gel electrophoresis of colony PCR products to prove the **Supplementary Figure 1.** Agarose gel electrophoresis of colony PCR products to prove the
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