metabolic network model Search Results


metabolic network model for corynebacterium glutamicum  (Hirasawa Works)
90
Hirasawa Works metabolic network model for corynebacterium glutamicum
Metabolic Network Model For Corynebacterium Glutamicum, supplied by Hirasawa Works, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
metabolic network model for corynebacterium glutamicum - by Bioz Stars, 2026-03
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metabolic network model ijp815  (Biomodels LLC)
90
Biomodels LLC metabolic network model ijp815
Metabolic Network Model Ijp815, supplied by Biomodels LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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metabolic network model ijp815 - by Bioz Stars, 2026-03
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constraints-based genome-scale metabolic network model of s. clavuligerus  (Medema labs)
90
Medema labs constraints-based genome-scale metabolic network model of s. clavuligerus
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Constraints Based Genome Scale Metabolic Network Model Of S. Clavuligerus, supplied by Medema labs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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constraints-based genome-scale metabolic network model of s. clavuligerus - by Bioz Stars, 2026-03
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urban carbon metabolism network model  (Dongguan City Kexiang Test)
90
Dongguan City Kexiang Test urban carbon metabolism network model
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Urban Carbon Metabolism Network Model, supplied by Dongguan City Kexiang Test, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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urban carbon metabolism network model - by Bioz Stars, 2026-03
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metabolic network model  (Verlag GmbH)
90
Verlag GmbH metabolic network model
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Metabolic Network Model, supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/metabolic network model/product/Verlag GmbH
Average 90 stars, based on 1 article reviews
metabolic network model - by Bioz Stars, 2026-03
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metabolic network reconstruction and constraint-based modeling  (WholeGenome LLC)
90
WholeGenome LLC metabolic network reconstruction and constraint-based modeling
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Metabolic Network Reconstruction And Constraint Based Modeling, supplied by WholeGenome LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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metabolic network reconstruction and constraint-based modeling - by Bioz Stars, 2026-03
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metabolic network model  (Portland Press Ltd)
90
Portland Press Ltd metabolic network model
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Metabolic Network Model, supplied by Portland Press Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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metabolic network model - by Bioz Stars, 2026-03
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extended e. coli genome-scale metabolic network model including the nonoxidative glycolysis (nog) pathway  (Verlag GmbH)
90
Verlag GmbH extended e. coli genome-scale metabolic network model including the nonoxidative glycolysis (nog) pathway
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Extended E. Coli Genome Scale Metabolic Network Model Including The Nonoxidative Glycolysis (Nog) Pathway, supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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extended e. coli genome-scale metabolic network model including the nonoxidative glycolysis (nog) pathway - by Bioz Stars, 2026-03
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metabolic network model  (Nissen)
90
Nissen metabolic network model
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Metabolic Network Model, supplied by Nissen, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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metabolic network model - by Bioz Stars, 2026-03
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knowledge-based modeling of the e. coli metabolic network  (SRI International)
90
SRI International knowledge-based modeling of the e. coli metabolic network
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
Knowledge Based Modeling Of The E. Coli Metabolic Network, supplied by SRI International, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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knowledge-based modeling of the e. coli metabolic network - by Bioz Stars, 2026-03
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metabolic network modeling  (Ricerche Srl)
90
Ricerche Srl metabolic network modeling
Differential gene expression in S. <t>clavuligerus</t> DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .
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Differential gene expression in S. clavuligerus DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .

Journal: Microbial Biotechnology

Article Title: Genome‐wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus

doi: 10.1111/j.1751-7915.2010.00226.x

Figure Lengend Snippet: Differential gene expression in S. clavuligerus DS48802 and ATCC 27064. Sliding window plot (size = 50) of the difference in gene expression between S. clavuligerus DS48802 and wild‐type ATCC 27064. Key upregulated operons or genes at the peaks are noted in the figure. See Table S2 for description of the ten gene clusters shown. For gene expression analysis, cultivations were performed in shake flasks directly inoculated with spore suspensions at 28°C and 280 r.p.m. The semi‐synthetic growth medium used consisted of 30 g l −1 glycerol, 5 g l −1 wheat gluten, 3.5 g l −1 asparagine monohydrate, 1.5 g l −1 l ‐lysine, 0.7 g l −1 KH 2 PO 4 , 0.3 g l −1 MgSO 4 ·7H 2 O, 0.2 g l −1 CaCl 2 ·2H 2 O, 0.2 g l −1 FeSO 4 ·7H 2 O, 10 g l −1 MOPS, 0.1 ml l −1 Basilodon and 1 ml l −1 trace elements solution at pH 7.0. The trace element solution consisted of 20.4 g l −1 H 2 SO 4 , 50 g l −1 citric acid H 2 O, 16.75 g l −1 ZnSO 4 ·7H 2 O, 1.6 g l −1 CuSO 4 . 5 H 2 O, 1.5 g l −1 MnCl 2 ·4H 2 O, 2 g l −1 H 3 BO 3 and 2 g l −1 Na 2 MoO 4 ·2H 2 O. After 70 h of cultivation, the cells were harvested by centrifugation, treated with RNAprotect (Qiagen) and directly frozen with liquid nitrogen and stored at −80°C. To isolate total RNA, the frozen mycelium was ground in a mortar, resuspended in TE buffer with 5 mg l −1 lysozyme and incubated for 5 min at room temperature. RNA isolation and purification were performed using phenol extraction (TRIzol reagent, Invitrogen) and RNeasy Kit (Qiagen). The RNA was quantified by measuring the absorbance at 260 nm. Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol using GC rich (average 72%) primers from 10 µg total RNA. For hybridization, 5 µg and 7 µg biotinylated cDNA were used per Affymetrix gene Chip. Microarray data have been deposited at Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE24033. Flux‐balance analysis was performed using a recently published genome‐scale metabolic model of S. clavuligerus ( Medema et al ., 2010 ). In this study, we slightly changed our objective function and included both clavulanic acid and cephamycin C biosynthesis pathways. We dynamically changed the antibiotic concentration in the biomass composition based on experimental observations of ) and optimized the objective function for different concentrations of each antibiotic. Among the 785 genes that the model contains, 497 genes showed non‐zero flux for at least one antibiotic concentration. We calculated Spearman correlation of fluxes of each reaction with increasing antibiotic concentrations. If an enzyme was involved in multiple reactions, we assigned the flux which had the highest r 2 .

Article Snippet: In order to assess which changes could be causatively linked to antibiotic overproduction, we computationally predicted the metabolic fluxes during antibiotic overproduction, using a constraints‐based genome‐scale metabolic network model of S. clavuligerus ( Medema et al ., 2010 ).

Techniques: Gene Expression, Centrifugation, Incubation, Isolation, Purification, Extraction, Hybridization, Microarray, Concentration Assay

Changes in S. clavuligerus primary and secondary metabolism affecting clavulanic acid production. Changes in gene expression in S. clavuligerus DS48802 compared to the wild‐type ATCC 27064 projected onto a metabolic map. Green arrows represent reactions catalyzed by genes expressed over twofold higher in DS48802 than in the wild‐type. Red arrows represent reactions catalyzed by genes expressed over twofold lower in DS48802. The orange arrow represents the reaction catalyzed by pyruvate kinase, for which two isoenzymes exist which have changed in expression differently, one being downregulated (SCLAV_4329) and the other being upregulated (SCLAV_1203). Black arrows represent unchanged steps; solid arrows represent single biosynthetic steps; and dashed arrows represent multiple steps.

Journal: Microbial Biotechnology

Article Title: Genome‐wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus

doi: 10.1111/j.1751-7915.2010.00226.x

Figure Lengend Snippet: Changes in S. clavuligerus primary and secondary metabolism affecting clavulanic acid production. Changes in gene expression in S. clavuligerus DS48802 compared to the wild‐type ATCC 27064 projected onto a metabolic map. Green arrows represent reactions catalyzed by genes expressed over twofold higher in DS48802 than in the wild‐type. Red arrows represent reactions catalyzed by genes expressed over twofold lower in DS48802. The orange arrow represents the reaction catalyzed by pyruvate kinase, for which two isoenzymes exist which have changed in expression differently, one being downregulated (SCLAV_4329) and the other being upregulated (SCLAV_1203). Black arrows represent unchanged steps; solid arrows represent single biosynthetic steps; and dashed arrows represent multiple steps.

Article Snippet: In order to assess which changes could be causatively linked to antibiotic overproduction, we computationally predicted the metabolic fluxes during antibiotic overproduction, using a constraints‐based genome‐scale metabolic network model of S. clavuligerus ( Medema et al ., 2010 ).

Techniques: Gene Expression, Expressing