Profiling techniques in nutrition and health research

Current Opinion in Biotechnology

Volumn 19, Issue 2, 2008, Pages 83-99

  Kussmann, Martin ^a   Rezzi, Serge ^a   Daniel, Hannelore ^b  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; MEDICAL PROBLEMS; METABOLISM; PEPTIDES;

METABOLIC CHARACTERIZATION; METABOLOMICS; PROTEOMICS; TRANSCRIPTOMICS;

NUTRITION;

BIOLOGICAL MARKER; MESSENGER RNA; PROTEOME; TRANSCRIPTOME;

DNA FINGERPRINTING; GEL CHROMATOGRAPHY; HEALTH; HUMAN; INFORMATION PROCESSING; MASS SPECTROMETRY; MEDICAL RESEARCH; METABOLOMICS; MICROARRAY ANALYSIS; NUTRITION; NUTRITIONAL SCIENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTAKE; PROTEOMICS; REVIEW; TRANSCRIPTOMICS;

BIOMEDICAL RESEARCH; DIETETICS; GENE EXPRESSION PROFILING; HUMANS; MODELS, THEORETICAL; NUTRITION PHYSIOLOGY; PROTEOMICS;

EID: 42449157075     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2008.02.003     Document Type: Review

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116. Siffert W. G protein polymorphisms in hypertension, atherosclerosis, and diabetes. Annu Rev Med 56 (2005) 17-28. Excellent review on metabolically and clinically relevant polymorphisms in G proteins.
117. Chen Y., Rollins J., Paigen B., and Wang X. Genetic and genomic insights into the molecular basis of atherosclerosis. Cell Metab 6 (2007) 164-179
118. Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian Jr. R.K., Jones A.R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., et al. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25 (2007) 887-893
119. Orchard S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stümpflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P., et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 25 (2007) 894-898
120. Lindon J.C., Nicholson J.K., Holmes E., Keun H.C., Craig A., Pearce J.T.M., Bruce S.J., Hardy N., Sansone S.A., Antti H., et al. Summary recommendations for standardization and reporting of metabolic analysis. Nat Biotechnol 23 (2005) 833-838
121. Nicholson J.K., Lindon J.C., and Holmes E. Metabonomics: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29 (1999) 1181-1189
122. Nicholson J.K., Holmes E., Lindon J.C., and Wilson I.D. The challenges of modeling mammalian biocomplexity. Nat Biotechnol 22 (2004) 1268-1274. Addresses the unmet challenge of how to deal with the different time scales at which Omics events take place, that is transcription, protein expression and metabolite generation.
123. Rezzi S., Ramadan Z., Fay L.B., and Kochhar S. Nutritional metabonomics: applications and perspectives. J Proteome Res 6 (2007) 513-525. Puts metabonomics, 'traditionally' rather associated with toxicity and safety studies, into a nutritional perspective.
124. Nicholson J.K., and Wilson I.D. Opinion: understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2 (2003) 668-676
125. Gavaghan C.L., Holmes E., Lenz E., Wilson I.D., and Nicholson J.K. An NMR-based metabonomic approach to investigate the biochemical consequences of genetic strain differences: application to the C57BL10J and Alpk: ApfCD mouse. FEBS Lett 484 (2000) 169-174
126. Lindon J.C., Holmes E., and Nicholson J.K. Pattern recognition methods and applications in biomedical magnetic resonance. Prog Nucl Mag Res Sp 39 (2001) 1-40
127. Lindon J.C., Holmes E., Bollard M.E., Stanley E.G., and Nicholson J.K. Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis. Biomarkers 9 (2004) 1-31
128. Fiehn O., Kopka J., Dormann P., Altmann T., Trethewey R.N., and Willmitzer L. Metabolite profiling for plant functional genomics. Nat Biotechnol 18 (2000) 1157-1161
129. Watkins S.M., and German J.B. Toward the implementation of metabolomic assessments of human health and nutrition. Curr Opin Biotechnol 13 (2002) 512-516
130. Plumb R.S., Granger J.H., Stumpf C.L., Johnson K.A., Smith B.W., Gaulitz S., Wilson I.D., and Castro-Perez J. A rapid screening approach to metabonomics using UPLC and oa-TOF mass spectrometry: application to age, gender and diurnal variation in normal/Zucker obese rats and black, white and nude mice. Analyst 130 (2005) 844-849
131. 1H NMR studies of vertebrate blood and plasma. Biochem J 211 (1983) 605-615
132. 1H NMR spectroscopy of biological fluids. Prog Nucl Mag Res Sp 21 (1989) 449-501
133. Beckonert O., Keun H.C., Ebbels T.M., Bundy J., Holmes E., Lindon J.C., and Nicholson J.K. Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2 (2007) 2692-2703. Essential guide and laboratory instruction on how to perform metabolomics in body fluids and tissue samples.
134. Trygg J., and Wold S. Orthogonal projections to latent structures O-PLS. J Chemom 16 (2002) 119-128
135. Shulaev V. Metabolomics technology and bioinformatics. Brief Bioinform 7 (2006) 128-139
136. Lee J.M., Gianchandani E.P., and Papin J.A. Flux balance analysis in the era of metabolomics. Brief Bioinform 7 (2006) 140-150
137. Martin F.P., Dumas M.E., Wang Y., Legido-Quigley C., Yap I.K., Tang H., Zirah S., Murphy G.M., Cloarec O., Lindon J.C., et al. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol 3 (2007) 112. Pioneering study of a complex mammalian ecosystem, namely of the interaction between the heterogeneous bacterial gut population and its host.
138. Kochhar S., Jacobs D., Ramadan Z., Berruex F., Fuerholz A., and Fay L.B. Probing gender-specific metabolism differences in humans by nuclear magnetic resonance-based metabonomics. Anal Biochem 352 (2006) 274-281
139. Stella C., Beckwith-Hall B., Cloarec O., Holmes E., Lindon J.C., Powell J., vanderOuderaa F., Bingham S., Cross A.J., and Nicholson J.K. Susceptibility of human metabolic phenotypes to dietary modulation. J Proteome Res 5 (2006) 2780-2788
140. Lenz E.M., Bright J., Wilson I.D., Hughes A., Morrisson J., Lindberg H., and Lockton A. Metabonomics, dietary influences and cultural differences: a 1H NMR-based study of urine samples obtained from healthy British and Swedish subjects. J Pharm Biomed Anal 36 (2004) 841-849
141. Rezzi S., Ramadan Z., Martin F.P., Fay L.B., van Bladeren P., Lindon J.C., Nicholson J.K., and Kochhar S. Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals. J Proteome Res 6 (2007) 4469-4477. Innovative approach to associate a metabolic fingerprint to either chocolate liking or indifference. It remains to be seen whether the metabolic signature is a cause or rather a result of dietary preference.
142. Dumas M.E., Barton R.H., Toye A., Cloarec O., Blancher C., Rothwell A., Fearnside J., Tatoud R., Blanc V., Lindon J.C., et al. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A 103 (2006) 12511-12516. One of the emerging examples of how gut-residing bacteria can exert an important influence on the host's overall metabolism.
143. Nicholson J.K., Holmes E., and Wilson I.D. Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3 (2005) 431-438
144. Marchesi J.R., Holmes E., Khan F., Kochhar S., Scanlan P., Shanahan F., Wilson I.D., and Wang Y. Rapid and non-invasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 6 (2007) 546-551
145. Goodacre R., Broadhurst D., Smilde A.K., Kristal B.S., Baker J.D., Beger R., Bessant C., Connor S., Calmani G., Craig A., et al. Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics 3 (2007) 231-241
146. Noguchi Y., Sakai R., and Kimura T. Metabolomics and its potential for assessment of adequacy and safety of amino acid intake. J Nutr 133 (2003) 2097S-2100S
147. Matsuzaki K., Kato H., Sakai R., Toue S., Amao M., and Kimura T. Transcriptomics and metabolomics of dietary leucine excess. J Nutr 135 (2005) 1571S-1575S
148. Watson A.D. Lipidomics: A global approach to lipid analysis in biological systems. J Lipid Res 47 (2006) 2101-2111
149. Watkins S.M., Zhu X., and Zeisel S.H. Phosphatidylethanolamine-N-methyltransferase activity and dietary choline regulate liver-plasma lipid flux and essential fatty acid metabolism in mice. J Nutr 133 (2003) 3386-3391
150. Lee W.N., and Go V.L. Nutrient-gene interaction: tracer-based metabolomics. J Nutr 135 (2005) 3027S-3032S
151. Selman C., Kerrison N.D., Cooray A., Piper M.D., Lingard S.J., Barton R.H., Schuster E.F., Blanc E., Gems D., Nicholson J.K., et al. Coordinated multi-tissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice. Physiol Genom 27 (2006) 187-200
152. Wang Y., Lawler D., Larson B., Ramadan Z., Kochhar S., Holmes E., and Nicholson J.K. Metabonomic investigations of aging and caloric restriction in a life-long dog study. J Proteome Res 6 (2007) 1846-1854
153. Solanky K.S., Bailey N.J., Holmes E., Lindon J.C., Davis A.L., Mulder T.P., Van Duynhoven J.P., and Nicholson J.K. NMR-based metabonomic studies on the biochemical effects of epicatechin in the rat. J Agric Food Chem 51 (2003) 4139-4145
154. Wang Y., Holmes E., Tang H., Lindon J.C., Sprenger N., Turini M.E., Bergonzelli G., Fay L.B., Kochhar S., and Nicholson J.K. Experimental metabonomic model of dietary variation and stress interactions. J Proteome Res 5 (2006) 1535-1542
155. 1H NMR and HPLC-TOF MS. Mol Biosyst 1 (2005) 166-175
156. Nicholls A.W., Mortishire-Smith R.J., and Nicholson J.K. NMR spectroscopic-based metabonomic studies of urinary metabolite variation in acclimatizing germ-free rats. Chem Res Toxicol 16 (2003) 1395-1404
157. 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study. Anal Chem 78 (2006) 2199-2208
158. Walsh M.C., Brennan L., Malthouse J.P., Roche H.M., and Gibney M.J. Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans. Am J Clin Nutr 84 (2006) 531-539
159. 1H nuclear magnetic resonance-based metabonomic techniques for the analysis of the biochemical effects of dietary isoflavones on human plasma profile. Anal Biochem 323 (2003) 197-204
160. 1H NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans. J Nutr Biochem 16 (2005) 236-244
161. Van Dorsten F.A., Daykin C.A., Mulder T.P.J., and Van Duynhoven J.P.M. Metabonomics approach to determine metabolic differences between green tea and black tea consumption. J Agr Food Chem 54 (2006) 6929-6938
162. Wang Y., Tang H., Nicholson J.K., Hylands P.J., Sampson J., and Holmes E. A metabonomic strategy for the detection of the metabolic effects of chamomile (Matricaria recutita L.) ingestion. J Agric Food Chem 53 (2005) 191-196
163. Drewnowski A. Taste preferences and food intake. Annu Rev Nutr 17 (1997) 237-253
164. Drewnowski A., Henderson S.A., Levine A., and Hann C. Taste and food preferences as predictors of dietary practices in young women. Public Health Nutr 2 (1999) 513-519
165. Breen F.M., Plomin R., and Wardle J. Heritability of food preferences in young children. Physiol Behav 88 (2006) 443-447