Sample amount alternatives for data adjustment in comparative cyanobacterial metabolomics

Analytical and Bioanalytical Chemistry

Volumn 399, Issue 10, 2011, Pages 3503-3517

  Huege, Jan ^a,d   Krall, Leonard ^a   Steinhauser, Marie Caroline ^a   Giavalisco, Patrick ^a   Rippka, Rosmarie ^b   Tandeau De Marsac, Nicole ^b,c   Steinhauser, Dirk ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b CNRS   (France)

^c AIX MARSEILLE UNIVERSITÉ   (France)

^d LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

Comparative metabolomics; Nostoc; Oscillatoria; Spectral adjustment; Synechocystis

Indexed keywords

METABOLOMICS; NOSTOC; OSCILLATORIA; SPECTRAL ADJUSTMENT; SYNECHOCYSTIS;

ADHESION; BIOMOLECULES; CARBOHYDRATES; CHEMICAL ANALYSIS; CHLOROPHYLL; GAS CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; METABOLITES; STATISTICAL TESTS;

STRAIN;

BACTERIAL PROTEIN; CHLOROPHYLL; GLYCOGEN;

ARTICLE; CHEMISTRY; CYANOBACTERIUM; GROWTH, DEVELOPMENT AND AGING; MASS FRAGMENTOGRAPHY; METABOLISM; METABOLOMICS; METHODOLOGY; STATISTICAL ANALYSIS;

BACTERIAL PROTEINS; CHLOROPHYLL; CYANOBACTERIA; DATA INTERPRETATION, STATISTICAL; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GLYCOGEN; METABOLOMICS; RESEARCH DESIGN;

CYANOBACTERIA; NOSTOC; OSCILLATORIA; SYNECHOCYSTIS;

EID: 79954426747     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-011-4678-z     Document Type: Article

References (52)

1. O Fiehn J Kopka P Dormann T Altmann RN Trethewey L Willmitzer 2000 Metabolite profiling for plant functional genomics Nat Biotechnol 18 11 1157 1161 10.1038/81137 1:CAS:528:DC%2BD3cXotVSmtL0%3D
2. J Lisec N Schauer J Kopka L Willmitzer AR Fernie 2006 Gas chromatography mass spectrometry-based metabolite profiling in plants Nat Protoc 1 1 387 396 10.1038/nprot.2006.59 1:CAS:528:DC%2BD28XhtFOitbnN
3. K Dettmer PA Aronov BD Hammock 2007 Mass spectrometry-based metabolomics Mass Spectrom Rev 26 1 51 78 10.1002/mas.20108 1:CAS:528:DC%2BD2sXht1anur8%3D (Pubitemid 46051813)
4. WB Dunn 2008 Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes Phys Biol 5 1 011001 10.1088/1478-3975/5/1/011001 (Pubitemid 351570983)
5. MR Mashego K Rumbold M De Mey E Vandamme W Soetaert JJ Heijnen 2007 Microbial metabolomics: past, present and future methodologies Biotechnol Lett 29 1 1 16 10.1007/s10529-006-9218-0 1:CAS:528:DC%2BD28Xht12gsL7I (Pubitemid 44950152)
6. Knoll AH (2008) Cyanobacteria and earth history. In: Herrero A, Flores E (eds) The cyanobacteria: molecular biology, genomics and evolution. Caister Academic, pp 1-19
7. R Rippka J Deruelles JB Waterbury M Herdman RY Stanier 1979 Generic assignments, strain histories and properties of pure cultures of cyanobacteria J Gen Microbiol 111 1 1 61 (Pubitemid 9142236)
8. Stal LJ (2000) Cyanobacterial mats and stromatolites. In: Whitton BA, Potts M (eds) The ecology of cyanobacteria. Kluwer Academic, Dordrecht, pp 61-120
9. C Yang Q Hua K Shimizu 2002 Metabolic flux analysis in Synechocystis using isotope distribution from 13C-labeled glucose Metab Eng 4 3 202 216 10.1006/mben.2002.0226 1:CAS:528:DC%2BD3sXkvVCrtw%3D%3D (Pubitemid 35474127)
10. M Eisenhut J Huege D Schwarz H Bauwe J Kopka M Hagemann 2008 Metabolome phenotyping of inorganic carbon limitation in cells of the wild type and photorespiratory mutants of the cyanobacterium Synechocystis sp. strain PCC 6803 Plant Physiol 148 4 2109 2120 10.1104/pp.108.129403 1:CAS:528: DC%2BD1cXhsFemtrfO (Pubitemid 352847463)
11. T Rezanka I Dor A Prell VM Dembitsky 2003 Fatty acid composition of six freshwater wild cyanobacterial species Folia Microbiol 48 1 71 75 10.1007/BF02931279 1:CAS:528:DC%2BD3sXisVart7k%3D (Pubitemid 37027639)
12. T Rezanka VM Dembitsky 2006 Metabolites produced by cyanobacteria belonging to several species of the family Nostocaceae Folia Microbiol 51 3 159 182 10.1007/BF02932119 1:CAS:528:DC%2BD28XovFynt7Y%3D (Pubitemid 44338154)
13. KP Narayan TS Shalini S Pabbi DW Dhar 2006 Biodiversity analysis of selected cyanobacteria Curr Sci 91 7 947 951 (Pubitemid 44654615)
14. L Krall J Huege G Catchpole D Steinhauser L Willmitzer 2009 Assessment of sampling strategies for gas chromatography-mass spectrometry (GC-MS) based metabolomics of cyanobacteria J Chromatogr B 877 27 2952 2960 10.1016/j.jchromb.2009.07.006 1:CAS:528:DC%2BD1MXhtFams7rN
15. JW Allwood A Erban S de Koning WB Dunn A Luedemann A Lommen L Kay R Loscher J Kopka R Goodacre 2009 Inter-laboratory reproducibility of fast gas chromatography-electron impact-time of flight mass spectrometry (GC-EI-TOF/MS) based plant metabolomics Metabolomics 5 4 479 496 10.1007/s11306-009-0169-z 1:CAS:528:DC%2BD1MXhsFGrurfO
16. MM Koek B Muilwijk MJ van der Werf T Hankemeier 2006 Microbial metabolomics with gas chromatography/mass spectrometry Anal Chem 78 4 1272 1281 10.1021/ac051683+ 1:CAS:528:DC%2BD28Xis1yrtg%3D%3D (Pubitemid 43271861)
17. AB Canelas C Ras A ten Pierick JC van Dam JJ Heijnen WM van Gulik 2008 Leakage-free rapid quenching technique for yeast metabolomics Metabolomics 4 3 226 239 10.1007/s11306-008-0116-4 1:CAS:528:DC%2BD1cXhtVyis7bO
18. CL Winder WB Dunn S Schuler D Broadhurst R Jarvis GM Stephens R Goodacre 2008 Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites Anal Chem 80 8 2939 2948 10.1021/ac7023409 1:CAS:528:DC%2BD1cXjtVSiu7o%3D (Pubitemid 351556459)
19. CJ Bolten P Kiefer F Letisse JC Portais C Wittmann 2007 Sampling for metabolome analysis of microorganisms Anal Chem 79 10 3843 3849 10.1021/ac0623888 1:CAS:528:DC%2BD2sXjvFKgtr0%3D (Pubitemid 46799081)
20. JC Ewald S Heux N Zamboni 2009 High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format Anal Chem 81 9 3623 3629 10.1021/ac900002u 1:CAS:528:DC%2BD1MXjs1ahtb0%3D
21. S Laurent H Chen S Bedu F Ziarelli L Peng CC Zhang 2005 Nonmetabolizable analogue of 2-oxoglutarate elicits heterocyst differentiation under repressive conditions in Anabaena sp. PCC 7120 Proc Natl Acad Sci USA 102 28 9907 9912 10.1073/pnas.0502337102 1:CAS:528:DC%2BD2MXmsFaru7g%3D (Pubitemid 40993666)
22. N Tandeau de Marsac J Houmard 1988 Complementary chromatographic adaption: physiological conditions and action spectra Meth Enzymol 167 318 328 10.1016/0076-6879(88)67037-6 1:CAS:528:DyaL1MXitVyrtL4%3D
23. JH Hendriks A Kolbe Y Gibon M Stitt P Geigenberger 2003 ADP-glucose pyrophosphorylase is activated by posttranslational redox-modification in response to light and to sugars in leaves of Arabidopsis and other plant species Plant Physiol 133 2 838 849 10.1104/pp.103.024513 1:CAS:528: DC%2BD3sXosVaqtbY%3D (Pubitemid 37325692)
24. LL Campbell Jr 1955 Purification and properties of an alpha-amylase from facultative thermophilic bacteria Arch Biochem 54 1 154 161 10.1016/0003- 9861(55)90018-7 1:CAS:528:DyaG2MXisVGjsA%3D%3D
25. WM Fogarty CP Benson 1983 Purification and properties of a thermophilic amyloglucosidase from Aspergillus niger Eur J Appl Microbiol Biotechnol 18 5 271 278 10.1007/BF00500491 1:CAS:528:DyaL2cXotFOhtg%3D%3D (Pubitemid 14178385)
26. JL Parrou J Francois 1997 A simplified procedure for a rapid and reliable assay of both glycogen and trehalose in whole yeast cells Anal Biochem 248 1 186 188 10.1006/abio.1997.2138 1:CAS:528:DyaK2sXjsVGmtLc%3D (Pubitemid 27218240)
27. J Kopka N Schauer S Krueger C Birkemeyer B Usadel E Bergmuller P Dormann W Weckwerth Y Gibon M Stitt L Willmitzer AR Fernie D Steinhauser 2005 GMD@CSB.DB: the golm metabolome database Bioinformatics (Oxford, England) 21 8 1635 1638 10.1093/bioinformatics/bti236 1:CAS:528:DC%2BD2MXjtlGgsrg%3D (Pubitemid 40542722)
28. J Hummel N Strehmel J Selbig D Walther J Kopka 2010 Decision tree supported substructure prediction of metabolites from GC-MS profiles Metabolomics 6 2 322 333 10.1007/s11306-010-0198-7 1:CAS:528: DC%2BC3cXmtlKhs7g%3D
29. R Development Core Team (2009) R: A language and environment for statistical computing. - R foundation for statistical computing. Vienna
30. Sokal RR, Rohlf FJ (1995) Biometry: the principles and practice of statistics in biological research, vol 3. W.H. Freeman and Company, New York
31. W Stacklies H Redestig M Scholz D Walther J Selbig 2007 pcaMethods-a bioconductor package providing PCA methods for incomplete data Bioinformatics (Oxford, England) 23 9 1164 1167 10.1093/bioinformatics/btm069 1:CAS:528:DC%2BD2sXmtVKqu7g%3D (Pubitemid 47050571)
32. Y Benjamini Y Hochberg 1995 Controlling the false discovery rate-a practical and powerful approach to multiple testing J R Stat Soc B Methodol 57 1 289 300
33. Cox TF, Cox MAA (1994) Multidimensional scaling. Monographs on statistics and applied probability, vol 88. Chapman and Hall/CRC, Boca Raton
34. PJ Rousseeuw 1987 Silhouettes: a graphical aid to the interpretation and validation of cluster analysis J Comput Appl Math 20 1 53 65 10.1016/0377-0427(87)90125-7 (Pubitemid 18528483)
35. R Breitling P Armengaud A Amtmann P Herzyk 2004 Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments FEBS Lett 573 1-3 83 92 10.1016/j.febslet.2004.07.055 1:CAS:528:DC%2BD2cXmvFyrtr4%3D (Pubitemid 39141040)
36. Rousseeuw PJ, Leroy AM (2003) Robust regression and outlier detection. Wiley Series in Probability and Statistics. Wiley-VCH
37. Boone DR, Castenholz RW, Garrity GM (2001) Bergey's manual of systematic bacteriology, vol 1. Springer, New York
38. Dawson RMC, Elliott DC, Elliot WH, Jones KM (1986) Data for biochemical research. Oxford University Press, Oxford
39. MM Bradford 1976 A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal Biochem 72 248 254 10.1016/0003-2697(76)90527-3 1:CAS:528: DyaE28XksVehtrY%3D
40. T Zor Z Selinger 1996 Linearization of the Bradford protein assay increases its sensitivity: theoretical and experimental studies Anal Biochem 236 2 302 308 10.1006/abio.1996.0171 1:CAS:528:DyaK28Xislaju7w%3D (Pubitemid 26136110)
41. S Liotenberg D Campbell R Rippka J Houmard NT de Marsac 1996 Effect of the nitrogen source on phycobiliprotein synthesis and cell reserves in a chromatically adapting filamentous cyanobacterium Microbiology (Reading, England) 142 Pt 3 611 622 10.1099/13500872-142-3-611 1:CAS:528: DyaK28XhvVSnsbk%3D (Pubitemid 26093647)
42. MM Allen 1988 Inclusions: cyanophycin Meth Enzymol 16 207 213 10.1016/0076-6879(88)67022-4
43. M Stitt RM Lilley R Gerhardt HW Heldt 1989 Metabolite levels in specific cells and subcellular compartments of plant leaves Meth Enzymol 174 518 552 10.1016/0076-6879(89)74035-0 1:CAS:528:DyaK3cXitFentb0%3D (Pubitemid 20046307)
44. Carr NG (1988) Nitrogen reserves and dynamic reservoirs in cyanobacteria. In: Rogers LJ, Gallon JR (eds) Biochemistry of the algae and cyanobacteria. Clarendon, Oxford, pp 13-39
45. AH Mackerras NM De Chazal GD Smith 1990 Transient accumulations of cyanophycin in Anabaena cylindrica and Synechocystis 6803 J Gen Microbiol 136 10 2057 2065 1:CAS:528:DyaK3MXlvVKhuw%3D%3D (Pubitemid 20350969)
46. Y Elbahloul M Krehenbrink R Reichelt A Steinbuchel 2005 Physiological conditions conducive to high cyanophycin content in biomass of Acinetobacter calcoaceticus strain ADP1 Appl Environ Microbiol 71 2 858 866 10.1128/AEM.71.2.858-866.2005 1:CAS:528:DC%2BD2MXhsVKgsbc%3D (Pubitemid 40223573)
47. M Drath N Kloft A Batschauer K Marin J Novak K Forchhammer 2008 Ammonia triggers photodamage of photosystem II in the cyanobacterium Synechocystis sp. strain PCC 6803 Plant Physiol 147 1 206 215 10.1104/pp.108.117218 1:CAS:528:DC%2BD1cXms1eksLs%3D (Pubitemid 352844356)
48. B Desortova 1981 Relationship between chlorophyll-alpha concentration and phytoplankton biomass in several reservoirs in Czechoslovakia Int Rev Gesamten Hydrobiol Hydrograph 66 2 153 169 10.1002/iroh.19810660202 1:CAS:528: DyaL3MXlsFKitr8%3D
49. LJ Stal H van Gemerden WE Krumbein 1984 The simultaneous assay of chlorophyll and bacteriochlorophyll in natural microbial communities J Microbiol Meth 2 6 295 306 10.1016/0167-7012(84)90048-4 1:CAS:528:DyaL2cXlsVOit7w%3D
50. J Sauer M Gorl K Forchhammer 1999 Nitrogen starvation in Synechococcus PCC 7942: involvement of glutamine synthetase and NtcA in phycobiliprotein degradation and survival Arch Microbiol 172 4 247 255 10.1007/s002030050767 1:CAS:528:DyaK1MXmvFehsL0%3D (Pubitemid 29470802)
51. AR Grossman MR Schaefer GG Chiang JL Collier 1993 The phycobilisome, a light-harvesting complex responsive to environmental conditions Microbiol Rev 57 3 725 749 1:CAS:528:DyaK3sXmsVGnuro%3D (Pubitemid 23262516)
52. DS Wishart C Knox AC Guo R Eisner N Young B Gautam DD Hau N Psychogios E Dong S Bouatra R Mandal I Sinelnikov J Xia L Jia JA Cruz E Lim CA Sobsey S Shrivastava P Huang P Liu L Fang J Peng R Fradette D Cheng D Tzur M Clements A Lewis A De Souza A Zuniga M Dawe Y Xiong D Clive R Greiner A Nazyrova R Shaykhutdinov L Li HJ Vogel I Forsythe 2009 HMDB: a knowledgebase for the human metabolome Nucleic Acids Res 37 Database issue D603 D610 10.1093/nar/gkn810 1:CAS:528:DC%2BD1cXhsFejt7fO