Processes 2018, 6,38
30. Kanehisa, M.; Goto, S.; Sato, Y.; Furumichi, M.; Tanabe, M. KEGG for integration and interpretation of
large-scale molecular data sets. Nucleic Acids Res. 2012, 40, D109–D114. [CrossRef][PubMed]
31. Schomburg, I.; Chang, A.; Placzek, S.; Sohngen, C.; Rother, M.; Lang, M.; Munaretto, C.; Ulas, S.; Stelzer, M.;
Grote, A.; et al. BRENDA in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease
classification: New options and contents in BRENDA. Nucleic Acids Res. 2013, 41, D764–D772. [CrossRef]
[PubMed]
32. Neidhardt, F.C.; Ingraham, J.L.; Schaechter, M. Physiology of the Bacterial Cell: A Molecular Approach; Sinauer
Associates: Sunderland, MA, USA, 1990.
33. De Rosa, M.; Gambacorta, A.; Minale, L.; Bu’Lock, J. Cyclohexane fatty acids from a thermophilic bacterium.
J. Chem. Soc. D Chem. Commun. 1971, 21, 1334a. [CrossRef]
34. Goto, K.; Tanaka, T.; Yamamoto, R.; Suzuki, T.; Tokuda, H. Characteristics of Alicyclobacillus.I nAlicyclobacillus;
Springer: Berlin, Germany, 2007; pp. 9–48.
35. Trinh, C.T.; Wlaschin, A.; Srienc, F. Elementary mode analysis: A useful metabolic pathway analysis tool for
characterizing cellular metabolism. Appl. Microbiol. Biotechnol. 2009, 81, 813–826. [CrossRef][PubMed]
36. Terzer, M.; Stelling, J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics
2008, 24, 2229–2235. [CrossRef][PubMed]
37. Farrand, S.G.; Jones, C.W.; Linton, J.D.; Stephenson, R.J. The effect of temperature and pH on the growth
efficiency of the thermoacidophilic bacterium Bacillus acidocaldarius in continuous culture. Arch. Microbiol.
1983, 135, 276–283. [CrossRef]
38. Lloyd, L. HPLC Determination of Carbohydrates in Food and Drink; Agilent Technologies: Santa Clara, CA, USA,
2011; Vol. SI-01407.
39. ASTM E1758-01. Standard method for the determination of carbohydrates by HPLC. In 2003 Annual Book of
ASTM Standards; American Society for Testing and Materials, International: Philadelphia, PA, USA, 2003.
40. Chaplin, M.F. Carbohydrate Analysis: A Practical Approach; IRL Press: Washington, DC, USA, 1986; p. 228.
41. Dubois, M.; Gilles, K.A.; Hamilton, J.K.; Rebers, P.A.; Smith, F. Colorimetric method for determination of
sugars and related substances. Anal. Chem. 1956, 28, 350–356. [CrossRef]
42. Taylor, K. A modification of the phenol sulfuric acid assay for total carbohydrates giving more comparable
absorbances. Appl. Biochem. Biotechnol. 1995, 53, 207–214. [CrossRef]
43. Trevelyan, W.E.; Harrison, J.S. Studies on yeast metabolism. 1. Fractionation and microdetermination of cell
carbohydrates. Biochem. J. 1952, 50, 298–303. [CrossRef][PubMed]
44. Beck, C.; Knoop, H.; Axmann, I.M.; Steuer, R. The diversity of cyanobacterial metabolism: Genome analysis
of multiple phototrophic microorganisms. BMC Genom. 2012, 13, 56. [CrossRef][PubMed]
45. Folsom, J.P.; Carlson, R.P. Physiological, biomass elemental composition and proteomic analyses of
Escherichia coli ammonium-limited chemostat growth, and comparison with iron- and glucose-limited
chemostat growth. Microbiology 2015, 161, 1659–1670. [CrossRef][PubMed]
46. Vu, T.T.; Hill, E.A.; Kucek, L.A.; Konopka, A.E.; Beliaev, A.S.; Reed, J.L. Computational evaluation of
Synechococcus sp. PCC 7002 metabolism for chemical production. Biotechnol. J. 2013, 8, 619–630. [CrossRef]
[PubMed]
47. Van Handel, E. Rapid determination of glycogen and sugars in mosquitos. J. Am. Mosq. Control Assoc. 1985,
1, 299–301. [PubMed]
48. Del Don, C.; Hanselmann, K.W.; Peduzzi, R.; Bachofen, R. Biomass composition and methods for the
determination of metabolic reserve polymers in phototrophic sulfur bacteria. Aquat. Sci. 1994, 56, 1–15.
[CrossRef]
49. Sattler, L.; Zerban, F.W. The Dreywood anthrone reaction as affected by carbohydrate structure. Science 1948,
108, 207. [CrossRef][PubMed]
50. De Mey, M.; Lequeux, G.; Maertens, J.; De Maeseneire, S.; Soetaert, W.; Vandamme, E. Comparison of DNA
and RNA quantification methods suitable for parameter estimation in metabolic modeling of microorganisms.
Anal. Biochem. 2006, 353, 198–203. [CrossRef][PubMed]
51. Burton, K. Study of the conditions and mechanism of the diphenylamine reaction for the colorimetric
estimation of deoxyribonucleic acid. Biochem. J. 1956, 62, 315–323. [CrossRef][PubMed]
52. Gorokhova, E.; Kyle, M. Analysis of nucleic acids in Daphnia: Development of methods and ontogenetic
variations in RNA-DNA content. J. Plankton Res. 2002, 24, 511–522. [CrossRef]
178
30. Kanehisa, M.; Goto, S.; Sato, Y.; Furumichi, M.; Tanabe, M. KEGG for integration and interpretation of
large-scale molecular data sets. Nucleic Acids Res. 2012, 40, D109–D114. [CrossRef][PubMed]
31. Schomburg, I.; Chang, A.; Placzek, S.; Sohngen, C.; Rother, M.; Lang, M.; Munaretto, C.; Ulas, S.; Stelzer, M.;
Grote, A.; et al. BRENDA in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease
classification: New options and contents in BRENDA. Nucleic Acids Res. 2013, 41, D764–D772. [CrossRef]
[PubMed]
32. Neidhardt, F.C.; Ingraham, J.L.; Schaechter, M. Physiology of the Bacterial Cell: A Molecular Approach; Sinauer
Associates: Sunderland, MA, USA, 1990.
33. De Rosa, M.; Gambacorta, A.; Minale, L.; Bu’Lock, J. Cyclohexane fatty acids from a thermophilic bacterium.
J. Chem. Soc. D Chem. Commun. 1971, 21, 1334a. [CrossRef]
34. Goto, K.; Tanaka, T.; Yamamoto, R.; Suzuki, T.; Tokuda, H. Characteristics of Alicyclobacillus.I nAlicyclobacillus;
Springer: Berlin, Germany, 2007; pp. 9–48.
35. Trinh, C.T.; Wlaschin, A.; Srienc, F. Elementary mode analysis: A useful metabolic pathway analysis tool for
characterizing cellular metabolism. Appl. Microbiol. Biotechnol. 2009, 81, 813–826. [CrossRef][PubMed]
36. Terzer, M.; Stelling, J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics
2008, 24, 2229–2235. [CrossRef][PubMed]
37. Farrand, S.G.; Jones, C.W.; Linton, J.D.; Stephenson, R.J. The effect of temperature and pH on the growth
efficiency of the thermoacidophilic bacterium Bacillus acidocaldarius in continuous culture. Arch. Microbiol.
1983, 135, 276–283. [CrossRef]
38. Lloyd, L. HPLC Determination of Carbohydrates in Food and Drink; Agilent Technologies: Santa Clara, CA, USA,
2011; Vol. SI-01407.
39. ASTM E1758-01. Standard method for the determination of carbohydrates by HPLC. In 2003 Annual Book of
ASTM Standards; American Society for Testing and Materials, International: Philadelphia, PA, USA, 2003.
40. Chaplin, M.F. Carbohydrate Analysis: A Practical Approach; IRL Press: Washington, DC, USA, 1986; p. 228.
41. Dubois, M.; Gilles, K.A.; Hamilton, J.K.; Rebers, P.A.; Smith, F. Colorimetric method for determination of
sugars and related substances. Anal. Chem. 1956, 28, 350–356. [CrossRef]
42. Taylor, K. A modification of the phenol sulfuric acid assay for total carbohydrates giving more comparable
absorbances. Appl. Biochem. Biotechnol. 1995, 53, 207–214. [CrossRef]
43. Trevelyan, W.E.; Harrison, J.S. Studies on yeast metabolism. 1. Fractionation and microdetermination of cell
carbohydrates. Biochem. J. 1952, 50, 298–303. [CrossRef][PubMed]
44. Beck, C.; Knoop, H.; Axmann, I.M.; Steuer, R. The diversity of cyanobacterial metabolism: Genome analysis
of multiple phototrophic microorganisms. BMC Genom. 2012, 13, 56. [CrossRef][PubMed]
45. Folsom, J.P.; Carlson, R.P. Physiological, biomass elemental composition and proteomic analyses of
Escherichia coli ammonium-limited chemostat growth, and comparison with iron- and glucose-limited
chemostat growth. Microbiology 2015, 161, 1659–1670. [CrossRef][PubMed]
46. Vu, T.T.; Hill, E.A.; Kucek, L.A.; Konopka, A.E.; Beliaev, A.S.; Reed, J.L. Computational evaluation of
Synechococcus sp. PCC 7002 metabolism for chemical production. Biotechnol. J. 2013, 8, 619–630. [CrossRef]
[PubMed]
47. Van Handel, E. Rapid determination of glycogen and sugars in mosquitos. J. Am. Mosq. Control Assoc. 1985,
1, 299–301. [PubMed]
48. Del Don, C.; Hanselmann, K.W.; Peduzzi, R.; Bachofen, R. Biomass composition and methods for the
determination of metabolic reserve polymers in phototrophic sulfur bacteria. Aquat. Sci. 1994, 56, 1–15.
[CrossRef]
49. Sattler, L.; Zerban, F.W. The Dreywood anthrone reaction as affected by carbohydrate structure. Science 1948,
108, 207. [CrossRef][PubMed]
50. De Mey, M.; Lequeux, G.; Maertens, J.; De Maeseneire, S.; Soetaert, W.; Vandamme, E. Comparison of DNA
and RNA quantification methods suitable for parameter estimation in metabolic modeling of microorganisms.
Anal. Biochem. 2006, 353, 198–203. [CrossRef][PubMed]
51. Burton, K. Study of the conditions and mechanism of the diphenylamine reaction for the colorimetric
estimation of deoxyribonucleic acid. Biochem. J. 1956, 62, 315–323. [CrossRef][PubMed]
52. Gorokhova, E.; Kyle, M. Analysis of nucleic acids in Daphnia: Development of methods and ontogenetic
variations in RNA-DNA content. J. Plankton Res. 2002, 24, 511–522. [CrossRef]
178