Repository » Data AccessID 90
Detail View - Data AccessID 90

Back

General Information
Manuscript title Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8
PubMed ID 24909362
Journal Metabolic Engineering
Year 2014
Authors Aditi Swarup, Jimg Lu, Kathleen C. DeWoody, Maciek R. Antoniewicz
Affiliations Department of Chemical & Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark DE 19716, USA
Keywords Extremophile, Thermophilic bacterium, Optimal growth, Metabolic network model, Isotopic labeling
Full text article Swarup_2014.pdf
Project name not specified


Experiment Description
Organism Thermus thermophilus
Strain HB8 (ATCC 27634)
Data type flux measurements
Data units % substrate uptake
Execution date not specified


Experimental Details
Temperature (°C) 70
pH 7.9
Carbon source glucose,
Culture mode batch
Process condition aerobic
Dilution rate (h⁻¹)
Working volume (L) 0.01
Biomass concentration (g/L) 0.39 (g/L)/OD600 cell dry weight and 25.3 g/C-mol for the molecular weight of dry biomass
Medium composition

Glucose stock solutions were prepared at 20 wt% in distilled water. The optimized minimum medium contained (per liter of medium): 0.50 g K2HPO4, 0.30 g KH2PO4, 0.50 g NH4Cl, 0.50 g NaCl, 0.20 g MgCl2.6H2O, 0.04 g CaSO4.2H2O, 40 mL of 1 M Tris, 5 mL of Wolfe׳s minerals, and 5 mL of Wolfe׳s vitamins.

General protocol information Flux analysis method: 13C constrained MFA

Platform: GC-MS

Methods description - Notes

13C-Metabolic flux analysis - 13C –MFA was performed using the Metran software [1,2], which is based on the elementary metabolite units (EMU) framework [3,4]. Fluxes were estimated by minimizing the variance-weighted sum of squared residuals (SSR) between the experimentally ...

----------------References-----------------
[1] S.B. Crown, M.R. Antoniewicz,Metab. Eng., 20 (2013), pp. 42–48. http://doi.org/7td
[2] H. Yoo, M.R. Antoniewicz, G. Stephanopoulos, J.K. Kelleher, J. Biol. Chem., 283 (2008), pp. 20621–20627. http://doi.org/fsrtj5
[3] M.R. Antoniewicz, J.K. Kelleher, G. Stephanopoulos, Metab. Eng., 9 (2007), pp. 68–86. http://doi.org/b97p7s
[4] J.D. Young, J.L. Walther, M.R. Antoniewicz, H. Yoo, G. Stephanopoulos, Biotechnol. Bioeng., 99 (2008), pp. 686–699. http://doi.org/crmdfw
[5] M.R. Antoniewicz, J.K. Kelleher, G. Stephanopoulos, Metab. Eng., 8 (2006), pp. 324–337. http://doi.org/fbgz85
[6] R. Caspi, T. Altman, K. Dreher, C.A. Fulcher, P. Subhraveti, I.M. Keseler, A. Kothari, M. Krummenacker, M. Latendresse, L.A. Mueller, Q. Ong, S. Paley, A. Pujar, A.G. Shearer, M. Travers, D. Weerasinghe, P. Zhang, P.D. Karp, Nucleic Acids Res., 40 (2012), pp. http://doi.org/ckb6fjD742–D753
[7] M. Kanehisa, S. Goto, Nucleic Acids Res., 28 (2000), pp. 27–30. http://doi.org/b9st54
[8] M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, M. Tanabe, Nucleic Acids Res., 40 (2012), pp. D109–D114. http://doi.org/c4vgkr

Read more
Data file
KIMODATAID90_v0.xlsx Preview file
Alternative format(s)
no file uploaded
Export metadata
RDF: metadataDataEntryID90.rdf
XML: metadataDataEntryID90.xml
Plain text: metadataDataEntryID90.txt
Share | Cite Data EntryID 90



Submission and curation

Entered by: Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data

Created: 2015-09-22 12:48:07 UTC

Updated: 2020-04-24 16:10:35 UTC

Version: 0

Status: (reviewed) 2015-09-22 13:06:46 UTC

Views: 2

Downloads: 0




Associated Models

Here we can find relevant models associated with Data EntryID 90:

Model
EntryID
Model name Category Model Type Data used for Access Json



Associate models to data

- Several models can be associated.

New Model



Back | Top