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Title: Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria

 [1]; ORCiD logo [2]
  1. Chemical & Biomolecular Engineering, Vanderbilt University, Nashville Tennessee
  2. Chemical & Biomolecular Engineering, Vanderbilt University, Nashville Tennessee, Molecular Physiology & Biophysics, Vanderbilt University, Nashville Tennessee
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Publisher's Accepted Manuscript
Journal Name:
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
Additional Journal Information:
Journal Name: Wiley Interdisciplinary Reviews: Systems Biology and Medicine Journal Volume: 12 Journal Issue: 3; Journal ID: ISSN 1939-5094
Wiley Blackwell (John Wiley & Sons)
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Country unknown/Code not available

Citation Formats

Babele, Piyoosh Kumar, and Young, Jamey D. Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria. Country unknown/Code not available: N. p., 2019. Web. doi:10.1002/wsbm.1472.
Babele, Piyoosh Kumar, & Young, Jamey D. Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria. Country unknown/Code not available. doi:10.1002/wsbm.1472.
Babele, Piyoosh Kumar, and Young, Jamey D. Mon . "Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria". Country unknown/Code not available. doi:10.1002/wsbm.1472.
title = {Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria},
author = {Babele, Piyoosh Kumar and Young, Jamey D.},
abstractNote = {},
doi = {10.1002/wsbm.1472},
journal = {Wiley Interdisciplinary Reviews: Systems Biology and Medicine},
number = 3,
volume = 12,
place = {Country unknown/Code not available},
year = {2019},
month = {12}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1002/wsbm.1472

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Works referenced in this record:

Advances in mass spectrometry-based metabolomics for investigation of metabolites
journal, January 2018

  • Ren, Jun-Ling; Zhang, Ai-Hua; Kong, Ling
  • RSC Advances, Vol. 8, Issue 40
  • DOI: 10.1039/C8RA01574K

Carbon recycling by cyanobacteria: improving CO2 fixation through chemical production
journal, August 2017

  • Zhang, Angela; Carroll, Austin L.; Atsumi, Shota
  • FEMS Microbiology Letters, Vol. 364, Issue 16
  • DOI: 10.1093/femsle/fnx165

Synthetic and systems biology for microbial production of commodity chemicals
journal, April 2016

  • Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J.
  • npj Systems Biology and Applications, Vol. 2, Issue 1
  • DOI: 10.1038/npjsba.2016.9

Metabolite Measurement: Pitfalls to Avoid and Practices to Follow
journal, June 2017

INCA: a computational platform for isotopically non-stationary metabolic flux analysis
journal, January 2014

Metabolic engineering of cyanobacteria for the synthesis of commodity products
journal, June 2015

  • Angermayr, S. Andreas; Gorchs Rovira, Aleix; Hellingwerf, Klaas J.
  • Trends in Biotechnology, Vol. 33, Issue 6
  • DOI: 10.1016/j.tibtech.2015.03.009

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods
journal, April 2018

Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice
journal, December 2018

Lipid production and molecular dynamics simulation for regulation of accD gene in cyanobacteria under different N and P regimes
journal, April 2017

  • Kumar, Roshan; Biswas, Koushik; Singh, Puneet Kumar
  • Biotechnology for Biofuels, Vol. 10, Issue 1
  • DOI: 10.1186/s13068-017-0776-2

Metabolomics tools for the synthetic biology of natural products
journal, December 2018

Imaging the Unimaginable: Desorption Electrospray Ionization – Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research
journal, January 2018

  • Parrot, Delphine; Papazian, Stefano; Foil, Daniel
  • Planta Medica, Vol. 84, Issue 09/10
  • DOI: 10.1055/s-0044-100188

The challenge and potential of photosynthesis: unique considerations for metabolic flux measurements in photosynthetic microorganisms
journal, November 2018

  • Sake, Cara L.; Metcalf, Alexander J.; Boyle, Nanette R.
  • Biotechnology Letters, Vol. 41, Issue 1
  • DOI: 10.1007/s10529-018-2622-4

Photoheterotrophic Fluxome in Synechocystis sp. Strain PCC 6803 and Its Implications for Cyanobacterial Bioenergetics
journal, December 2014

  • You, Le; He, Lian; Tang, Yinjie J.
  • Journal of Bacteriology, Vol. 197, Issue 5
  • DOI: 10.1128/JB.02149-14

Understanding metabolism with flux analysis: From theory to application
journal, September 2017

An LC–MS-Based Chemical and Analytical Method for Targeted Metabolite Quantification in the Model Cyanobacterium Synechococcus sp. PCC 7002
journal, May 2011

  • Bennette, Nicholas B.; Eng, John F.; Dismukes, G. Charles
  • Analytical Chemistry, Vol. 83, Issue 10
  • DOI: 10.1021/ac200108a

Sustainable consumption within a sustainable economy – beyond green growth and green economies
journal, January 2014

Meeting Report for Synthetic Biology for Natural Products 2017: The Interface of (Meta)Genomics, Machine Learning, and Natural Product Discovery
journal, February 2017

The future of NMR-based metabolomics
journal, February 2017

Metabolomics Applied to Diabetes Research: Moving From Information to Knowledge
journal, October 2009

  • Bain, J. R.; Stevens, R. D.; Wenner, B. R.
  • Diabetes, Vol. 58, Issue 11
  • DOI: 10.2337/db09-0580

Metabolic engineering tools in model cyanobacteria
journal, November 2018

OpenMebius: An Open Source Software for Isotopically Nonstationary 13 C-Based Metabolic Flux Analysis
journal, January 2014

  • Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio
  • BioMed Research International, Vol. 2014
  • DOI: 10.1155/2014/627014

The plasticity of cyanobacterial metabolism supports direct CO2 conversion to ethylene
journal, April 2015

Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes
journal, March 2019

Unlocking the photobiological conversion of CO 2 to ( R )-3-hydroxybutyrate in cyanobacteria
journal, January 2018

  • Wang, Bo; Xiong, Wei; Yu, Jianping
  • Green Chemistry, Vol. 20, Issue 16
  • DOI: 10.1039/C8GC01208C

Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris
journal, September 2017

  • Zuñiga, Cristal; Levering, Jennifer; Antoniewicz, Maciek R.
  • Plant Physiology, Vol. 176, Issue 1
  • DOI: 10.1104/pp.17.00605

Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13 C metabolic flux analysis : Rerouting of Carbon Flux in a Glycogen Mutant
journal, June 2017

  • Hendry, John I.; Prasannan, Charulata; Ma, Fangfang
  • Biotechnology and Bioengineering, Vol. 114, Issue 10
  • DOI: 10.1002/bit.26350

Kinetic flux profiling for quantitation of cellular metabolic fluxes
journal, July 2008

  • Yuan, Jie; Bennett, Bryson D.; Rabinowitz, Joshua D.
  • Nature Protocols, Vol. 3, Issue 8
  • DOI: 10.1038/nprot.2008.131

Recent applications of metabolomics to advance microbial biofuel production
journal, February 2017

A roadmap for interpreting 13 C metabolite labeling patterns from cells
journal, August 2015

Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient 13 C-Labeling Data
journal, December 2018

  • Hendry, John I.; Gopalakrishnan, Saratram; Ungerer, Justin
  • Plant Physiology, Vol. 179, Issue 2
  • DOI: 10.1104/pp.18.01357

Tracing metabolism from lignocellulosic biomass and gaseous substrates to products with stable-isotopes
journal, February 2017

Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria
journal, March 2017

  • Kanno, Masahiro; Carroll, Austin L.; Atsumi, Shota
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms14724

Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels
journal, December 2016

Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis
journal, November 2017

Effects of Environmental Factors and Nutrient Availability on the Biochemical Composition of Algae for Biofuels Production: A Review
journal, September 2013

  • Juneja, Ankita; Ceballos, Ruben; Murthy, Ganti
  • Energies, Vol. 6, Issue 9
  • DOI: 10.3390/en6094607

Engineering the methylerythritol phosphate pathway in cyanobacteria for photosynthetic isoprene production from CO 2
journal, January 2016

  • Gao, Xiang; Gao, Fang; Liu, Deng
  • Energy & Environmental Science, Vol. 9, Issue 4
  • DOI: 10.1039/C5EE03102H

Insights into isoprene production using the cyanobacterium Synechocystis sp. PCC 6803
journal, April 2016

Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production
journal, July 2017

Metabolomics and Isotope Tracing
journal, May 2018

Microscale LC-MS-NMR Platform Applied to the Identification of Active Cyanobacterial Metabolites
journal, November 2008

  • Lin, Yiqing; Schiavo, Susan; Orjala, Jimmy
  • Analytical Chemistry, Vol. 80, Issue 21
  • DOI: 10.1021/ac801049k

Integration of the information from gene expression and metabolic fluxes for the analysis of the regulatory mechanisms in Synechocystis
journal, May 2002

Engineering cyanobacteria as photosynthetic feedstock factories
journal, February 2014

Integrated Metabolic Flux and Omics Analysis of Synechocystis sp. PCC 6803 under Mixotrophic and Photoheterotrophic Conditions
journal, June 2014

  • Nakajima, Tsubasa; Kajihata, Shuichi; Yoshikawa, Katsunori
  • Plant and Cell Physiology, Vol. 55, Issue 9
  • DOI: 10.1093/pcp/pcu091

Defining the Metabolome: Size, Flux, and Regulation
journal, May 2015

Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analyses of 13C-labeled metabolic product isotopomers
journal, March 2007

Metabolic Flux Analysis in Synechocystis Using Isotope Distribution from 13C-Labeled Glucose
journal, July 2002

Ambient Mass Spectrometry
journal, March 2006

Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942
journal, August 2014

  • Triana, Julián; Montagud, Arnau; Siurana, Maria
  • Metabolites, Vol. 4, Issue 3
  • DOI: 10.3390/metabo4030680

Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models
journal, May 2018

Lignocellulosic biomass: a sustainable platform for the production of bio-based chemicals and polymers
journal, January 2015

  • Isikgor, Furkan H.; Becer, C. Remzi
  • Polymer Chemistry, Vol. 6, Issue 25
  • DOI: 10.1039/C5PY00263J

Metabolomics and fluxomics approaches
journal, September 2008

It Is All about Metabolic Fluxes
journal, December 2003

Quantifying Biomass Composition by Gas Chromatography/Mass Spectrometry
journal, September 2014

  • Long, Christopher P.; Antoniewicz, Maciek R.
  • Analytical Chemistry, Vol. 86, Issue 19
  • DOI: 10.1021/ac502734e

Metabolic networks in motion: 13 C‐based flux analysis
journal, January 2006

Flux balance analysis of photoautotrophic metabolism: Uncovering new biological details of subsystems involved in cyanobacterial photosynthesis
journal, April 2017

  • Qian, Xiao; Kim, Min Kyung; Kumaraswamy, G. Kenchappa
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1858, Issue 4
  • DOI: 10.1016/j.bbabio.2016.12.007

Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis
journal, November 2011

  • Young, Jamey D.; Shastri, Avantika A.; Stephanopoulos, Gregory
  • Metabolic Engineering, Vol. 13, Issue 6
  • DOI: 10.1016/j.ymben.2011.08.002

Measuring the Composition and Stable-Isotope Labeling of Algal Biomass Carbohydrates via Gas Chromatography/Mass Spectrometry
journal, April 2016

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142
journal, April 2012

Rapid, colorimetric quantification of lipid from algal cultures
journal, March 2010

An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis
journal, February 2008

  • Young, Jamey D.; Walther, Jason L.; Antoniewicz, Maciek R.
  • Biotechnology and Bioengineering, Vol. 99, Issue 3
  • DOI: 10.1002/bit.21632

Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production
journal, October 2015

Cyanobacterial metabolic engineering for biofuel and chemical production
journal, December 2016

  • Oliver, Neal J.; Rabinovitch-Deere, Christine A.; Carroll, Austin L.
  • Current Opinion in Chemical Biology, Vol. 35
  • DOI: 10.1016/j.cbpa.2016.08.023

Influence of long term nitrogen limitation on lipid, protein and pigment production of Euglena gracilis in photoheterotrophic cultures
journal, January 2019

  • Tossavainen, Marika; Ilyass, Usman; Ollilainen, Velimatti
  • PeerJ, Vol. 7
  • DOI: 10.7717/peerj.6624

Recent Applications of Metabolomics Toward Cyanobacteria
journal, February 2013

Synthetic Biology Toolbox for Controlling Gene Expression in the Cyanobacterium Synechococcus sp. strain PCC 7002
journal, September 2014

  • Markley, Andrew L.; Begemann, Matthew B.; Clarke, Ryan E.
  • ACS Synthetic Biology, Vol. 4, Issue 5
  • DOI: 10.1021/sb500260k

13C flux analysis of cyanobacterial metabolism
journal, October 2014

  • Adebiyi, Adeola O.; Jazmin, Lara J.; Young, Jamey D.
  • Photosynthesis Research, Vol. 126, Issue 1
  • DOI: 10.1007/s11120-014-0045-1

Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence: Cyanobacterial Carbon Metabolism
journal, March 2017

  • Wan, Ni; DeLorenzo, Drew M.; He, Lian
  • Biotechnology and Bioengineering, Vol. 114, Issue 7
  • DOI: 10.1002/bit.26287

Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production
journal, November 2012

  • Varman, Arul M.; Xiao, Yi; Pakrasi, Himadri B.
  • Applied and Environmental Microbiology, Vol. 79, Issue 3
  • DOI: 10.1128/AEM.02827-12

Metabolomics: beyond biomarkers and towards mechanisms
journal, March 2016

  • Johnson, Caroline H.; Ivanisevic, Julijana; Siuzdak, Gary
  • Nature Reviews Molecular Cell Biology, Vol. 17, Issue 7
  • DOI: 10.1038/nrm.2016.25