Processes 2018, 6,38
53. Downs, T.R.; Wilfinger, W.W. Fluorometric quantification of DNA in cells and tissue. Anal. Biochem. 1983,
131, 538–547. [CrossRef]
54. Beck, A.E.; Bernstein, H.C.; Carlson, R.P. Stoichiometric network analysis of cyanobacterial acclimation to
photosynthesis-associated stresses identifies heterotrophic niches. Processes 2017, 5, 32. [CrossRef]
55. Sigma-Aldrich. DNA Quantitation Kit, Fluorescence Assay: Technical Bulletin; Sigma-Aldrich: St. Louis,
MO, USA, 2009.
56. Hoiczyk, E.; Hansel, A. Cyanobacterial cell walls: News from an unusual prokaryotic envelope. J. Bacteriol.
2000, 182, 1191–1199. [CrossRef][PubMed]
57. Izard, J.; Limberger, R.J. Rapid screening method for quantitation of bacterial cell lipids from whole cells.
J. Microbiol. Methods 2003, 55, 411–418. [CrossRef]
58. Bligh, E.G.; Dyer, W.J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 1959,
37, 911–917. [CrossRef][PubMed]
59. Sheng, J.; Vannela, R.; Rittrnann, B.E. Evaluation of methods to extract and quantify lipids from Synechocystis
PCC 6803. Bioresour. Technol. 2011, 102, 1697–1703. [CrossRef][PubMed]
60. Sheng, J.; Vannela, R.; Rittmann, B.E. Disruption of Synechocystis PCC 6803 for lipid extraction. Water Sci. Technol.
2012, 65, 567–573. [CrossRef][PubMed]
61. Archanaa, S.; Moise, S.; Suraishkumar, G.K. Chlorophyll interference in microalgal lipid quantification
through the Bligh and Dyer method. Biomass Bioenergy 2012, 46, 805–808. [CrossRef]
62. Vier, B.; Rogge, G.; Voigt, B. Production of lipids from a thermoacidophilic Bacillus strain. 1. Lipids from
Bacillus acidocaldarius ZIMET 11274. Acta Biotechnol. 1992, 12, 37–40. [CrossRef]
63. Noble, J.E.; Knight, A.E.; Reason, A.J.; Di Matola, A.; Bailey, M.J.A. A comparison of protein quantitation
assays for biopharmaceutical applications. Mol. Biotechnol. 2007, 37, 99–111. [CrossRef][PubMed]
64. Noble, J.E.; Bailey, M.J.A. Quantitation of protein. In Guide to Protein Purification, 2nd ed.; Burgess, R.R.,
Deutscher, M.P., Eds.; Elsevier Science & Technology Books: New York, NY, USA, 2009; Vol. 463, pp. 73–95.
65. Fountoulakis, M.; Lahm, H.W. Hydrolysis and amino acid composition analysis of proteins. J. Chromatogr. A
1998, 826, 109–134. [CrossRef]
66. Henderson, J.W.; Ricker, R.D.; Bidlingmeyer, B.A.; Woodward, C. Rapid, Accurate, Sensitive, and Reproducible
HPLC Analysis of Amino Acids; Agilent Technologies: Santa Clara, CA, USA, 2000.
67. Benthin, S.; Nielsen, J.; Villadsen, J. A simple and reliable method for the determination of cellular RNA
content. Biotechnol. Tech. 1991, 5, 39–42. [CrossRef]
68. Imam, S.; Yilmaz, S.; Sohmen, U.; Gorzalski, A.S.; Reed, J.L.; Noguera, D.R.; Donohue, T.J. iRsp1095:
A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC Syst. Biol. 2011, 5, 116.
[CrossRef][PubMed]
69. Liao, Y.C.; Huang, T.W.; Chen, F.C.; Charusanti, P.; Hong, J.S.J.; Chang, H.Y.; Tsai, S.F.; Palsson, B.O.;
Hsiung, C.A. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae
MGH 78578, iYL1228. J. Bacteriol. 2011, 193, 1710–1717. [CrossRef][PubMed]
70. Liu, Z.J.; Gao, Y.; Chen, J.; Imanaka, T.; Bao, J.; Hua, Q. Analysis of metabolic fluxes for better understanding
of mechanisms related to lipid accumulation in oleaginous yeast Trichosporon cutaneum. Bioresour. Technol.
2013, 130, 144–151. [CrossRef][PubMed]
71. Carnicer, M.; Baumann, K.; Toplitz, I.; Sanchez-Ferrando, F.; Mattanovich, D.; Ferrer, P.; Albiol, J.
Macromolecular and elemental composition analysis and extracellular metabolite balances of Pichia pastoris
growing at different oxygen levels. Microb. Cell Fact. 2009, 8, 65. [CrossRef][PubMed]
72. Van Veen, J.A.; Paul, E.A. Conversion of bio-volume measurements of soil organisms, grown under various
moisture tensions, to biomass and their nutrient content. Appl. Environ. Microbiol. 1979, 37, 686–692. [PubMed]
73. Whyte, J.N.C. Biochemical composition and energy content of 6 species of phytoplankton used in mariculture
of bivalves. Aquaculture 1987, 60, 231–241. [CrossRef]
74. Carlson, R.; Srienc, F. Fundamental Escherichia coli biochemical pathways for biomass and energy production:
Creation of overall flux states. Biotechnol. Bioeng. 2004, 86, 149–162. [CrossRef][PubMed]
75. Vu, T.T.; Stolyar, S.M.; Pinchuk, G.E.; Hill, E.A.; Kucek, L.A.; Brown, R.N.; Lipton, M.S.; Osterman, A.;
Fredrickson, J.K.; Konopka, A.E.; et al. Genome-scale modeling of light-driven reductant partitioning and
carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput. Biol.
2012, 8, e1002460. [CrossRef][PubMed]
179
53. Downs, T.R.; Wilfinger, W.W. Fluorometric quantification of DNA in cells and tissue. Anal. Biochem. 1983,
131, 538–547. [CrossRef]
54. Beck, A.E.; Bernstein, H.C.; Carlson, R.P. Stoichiometric network analysis of cyanobacterial acclimation to
photosynthesis-associated stresses identifies heterotrophic niches. Processes 2017, 5, 32. [CrossRef]
55. Sigma-Aldrich. DNA Quantitation Kit, Fluorescence Assay: Technical Bulletin; Sigma-Aldrich: St. Louis,
MO, USA, 2009.
56. Hoiczyk, E.; Hansel, A. Cyanobacterial cell walls: News from an unusual prokaryotic envelope. J. Bacteriol.
2000, 182, 1191–1199. [CrossRef][PubMed]
57. Izard, J.; Limberger, R.J. Rapid screening method for quantitation of bacterial cell lipids from whole cells.
J. Microbiol. Methods 2003, 55, 411–418. [CrossRef]
58. Bligh, E.G.; Dyer, W.J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 1959,
37, 911–917. [CrossRef][PubMed]
59. Sheng, J.; Vannela, R.; Rittrnann, B.E. Evaluation of methods to extract and quantify lipids from Synechocystis
PCC 6803. Bioresour. Technol. 2011, 102, 1697–1703. [CrossRef][PubMed]
60. Sheng, J.; Vannela, R.; Rittmann, B.E. Disruption of Synechocystis PCC 6803 for lipid extraction. Water Sci. Technol.
2012, 65, 567–573. [CrossRef][PubMed]
61. Archanaa, S.; Moise, S.; Suraishkumar, G.K. Chlorophyll interference in microalgal lipid quantification
through the Bligh and Dyer method. Biomass Bioenergy 2012, 46, 805–808. [CrossRef]
62. Vier, B.; Rogge, G.; Voigt, B. Production of lipids from a thermoacidophilic Bacillus strain. 1. Lipids from
Bacillus acidocaldarius ZIMET 11274. Acta Biotechnol. 1992, 12, 37–40. [CrossRef]
63. Noble, J.E.; Knight, A.E.; Reason, A.J.; Di Matola, A.; Bailey, M.J.A. A comparison of protein quantitation
assays for biopharmaceutical applications. Mol. Biotechnol. 2007, 37, 99–111. [CrossRef][PubMed]
64. Noble, J.E.; Bailey, M.J.A. Quantitation of protein. In Guide to Protein Purification, 2nd ed.; Burgess, R.R.,
Deutscher, M.P., Eds.; Elsevier Science & Technology Books: New York, NY, USA, 2009; Vol. 463, pp. 73–95.
65. Fountoulakis, M.; Lahm, H.W. Hydrolysis and amino acid composition analysis of proteins. J. Chromatogr. A
1998, 826, 109–134. [CrossRef]
66. Henderson, J.W.; Ricker, R.D.; Bidlingmeyer, B.A.; Woodward, C. Rapid, Accurate, Sensitive, and Reproducible
HPLC Analysis of Amino Acids; Agilent Technologies: Santa Clara, CA, USA, 2000.
67. Benthin, S.; Nielsen, J.; Villadsen, J. A simple and reliable method for the determination of cellular RNA
content. Biotechnol. Tech. 1991, 5, 39–42. [CrossRef]
68. Imam, S.; Yilmaz, S.; Sohmen, U.; Gorzalski, A.S.; Reed, J.L.; Noguera, D.R.; Donohue, T.J. iRsp1095:
A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC Syst. Biol. 2011, 5, 116.
[CrossRef][PubMed]
69. Liao, Y.C.; Huang, T.W.; Chen, F.C.; Charusanti, P.; Hong, J.S.J.; Chang, H.Y.; Tsai, S.F.; Palsson, B.O.;
Hsiung, C.A. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae
MGH 78578, iYL1228. J. Bacteriol. 2011, 193, 1710–1717. [CrossRef][PubMed]
70. Liu, Z.J.; Gao, Y.; Chen, J.; Imanaka, T.; Bao, J.; Hua, Q. Analysis of metabolic fluxes for better understanding
of mechanisms related to lipid accumulation in oleaginous yeast Trichosporon cutaneum. Bioresour. Technol.
2013, 130, 144–151. [CrossRef][PubMed]
71. Carnicer, M.; Baumann, K.; Toplitz, I.; Sanchez-Ferrando, F.; Mattanovich, D.; Ferrer, P.; Albiol, J.
Macromolecular and elemental composition analysis and extracellular metabolite balances of Pichia pastoris
growing at different oxygen levels. Microb. Cell Fact. 2009, 8, 65. [CrossRef][PubMed]
72. Van Veen, J.A.; Paul, E.A. Conversion of bio-volume measurements of soil organisms, grown under various
moisture tensions, to biomass and their nutrient content. Appl. Environ. Microbiol. 1979, 37, 686–692. [PubMed]
73. Whyte, J.N.C. Biochemical composition and energy content of 6 species of phytoplankton used in mariculture
of bivalves. Aquaculture 1987, 60, 231–241. [CrossRef]
74. Carlson, R.; Srienc, F. Fundamental Escherichia coli biochemical pathways for biomass and energy production:
Creation of overall flux states. Biotechnol. Bioeng. 2004, 86, 149–162. [CrossRef][PubMed]
75. Vu, T.T.; Stolyar, S.M.; Pinchuk, G.E.; Hill, E.A.; Kucek, L.A.; Brown, R.N.; Lipton, M.S.; Osterman, A.;
Fredrickson, J.K.; Konopka, A.E.; et al. Genome-scale modeling of light-driven reductant partitioning and
carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput. Biol.
2012, 8, e1002460. [CrossRef][PubMed]
179