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Perturbation Experiments: Approaches for Metabolic Pathway Analysis in Bioreactors

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Bioreactor Engineering Research and Industrial Applications II

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 152))

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Abbreviations

µLC:

Microcapillary liquid chromatography

13C-MFA:

Labeling experiments for metabolic flux analysis

13DPG:

1,3-bisphospho-D-glycerate

2PG:

2-phospho-D-glycerate

3DHS:

3-dehydroshikimate

3PG:

3-phospho-D-glycerate

AcCoA:

Acetyl coenzyme A

AKG:

α-ketoglutarate

CDW:

Cell dry weight

CE:

Capillary electrophoresis

CIT:

Citrate

CER:

Carbon dioxide evolution rate

COBRA:

Constraint-based reconstruction and analysis

DAHP:

3-deoxy-D-arabino-heptulosonate-7-phosphate

DHAP:

Dihydroxyacetone phosphate

E. coli :

Escherichia coli

E4P:

Erythrose-4-phosphate

ESI:

Electrospray ionization

F6P:

Fructose-6-phosphate

FBA:

Flux balance analysis

FBP:

Fructose-1,6-bisphosphate

FUM:

Fumarate

FVA:

Flux variability analysis

G6P:

Glucose-6-phosphate

GAP:

Glyceraldehyde-3-phosphate

GC:

Gas chromatography

gFBA:

Geometric flux balance analysis

GLYC:

Glycerol

ICIT:

Isocitrate

IDMS:

Isotope dilution mass spectrometry

IPTG:

Isopropyl β-D-1-thiogalactopyranoside

LC:

Liquid chromatography

llFVA:

Loopless FVA

LP:

Linear programming

L-phe:

L-phenylalanine

L-trp:

L-tryptophan

L-tyr:

L-tyrosine

m/z:

Mass to charge ratio

MAL:

Malate

MALDI:

Matrix-assisted laser desorption ionization

MCA:

Metabolic control analysis

MFA:

Metabolic flux analysis

MS:

Mass spectrometry

NMR:

Nuclear magnetic resonance

OAA:

Oxaloacetate

OUR:

Oxygen uptake rate

PEP:

Phosphoenolpyruvate

PPHN:

Prephenate

PYR:

Pyruvate

R5P:

Ribose-5-phosphate

Ru5P:

Ribulose-5-phosphate

S7P:

Sedoheptulose-7-phosphate

SHIK:

Shikimate

S3P:

Shikimate-3-phosphate

SUC:

Succinate

SuccCoA:

Succinyl coenzyme A

tFVA:

Thermodynamically constrained FVA

TOF:

Time of flight

UHPLC:

Ultrahigh-performance liquid chromatography

U-13C:

Uniform 13C labeled

X5P:

Xylulose-5-phosphate

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Acknowledgments

Support of the German Research Foundation DFG (Grant numbers WE 2715/11-1, SP 503/7-1) is gratefully acknowledged.

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Authors and Affiliations

  1. Lehrstuhl für Bioverfahrenstechnik, Technische Universität München, Garching, Germany

    Michael Weiner, Julia Tröndle & Dirk Weuster-Botz

  2. Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany

    Christoph Albermann & Georg A. Sprenger

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  1. Michael Weiner
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  2. Julia Tröndle
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  3. Christoph Albermann
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  4. Georg A. Sprenger
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  5. Dirk Weuster-Botz
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Correspondence to Dirk Weuster-Botz .

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Editors and Affiliations

  1. State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China

    Jie Bao

  2. State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China

    Qin Ye

  3. School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Jian-Jiang Zhong

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Weiner, M., Tröndle, J., Albermann, C., Sprenger, G.A., Weuster-Botz, D. (2015). Perturbation Experiments: Approaches for Metabolic Pathway Analysis in Bioreactors. In: Bao, J., Ye, Q., Zhong, JJ. (eds) Bioreactor Engineering Research and Industrial Applications II. Advances in Biochemical Engineering/Biotechnology, vol 152. Springer, Berlin, Heidelberg. https://doi.org/10.1007/10_2015_326

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