Genomics and milk

Australian Journal of Dairy Technology

Volumn 64, Issue 1, 2009, Pages 94-101

  German, J Bruce ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 63749113539     PISSN: 00049433     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (112)

1. Adkins, Y. and Lönnerdal, B. (2003), Potential host-defense role of a human milk vitamin B-12-binding protein, haptocorrin, in the gastrointestinal tract of breastfed infants, as assessed with porcine haptocorrin in vitro. Am. J. Clin. Nutr. 77, 1234-1240.
2. Admyre, C. Johansson, S.M. Qazi KR, Filén JJ, Lahesmaa R, Norman M, Neve EP, Scheynius A, Gabrielsson S. (2007); Exosomes with immune modulatory features are present in human breast milk. J. Immunol. 179, 1969-78.
3. Alberti, G. (2001), Noncommunicable diseases: tomorrow's pandemics, Bull. World Health Organ. 79, 907.
4. Anderle, P. Duval, M. Draghici, S. Kuklin, A. Littlejohn, T.G. Medrano, J.F. Vilanova, D. and Roberts, M.A. (2003), Gene expression databases and data mining. Biotechniques, Suppl. 36-44.
5. Argov, N. Lemay, D.G. and German, J.B. (2008), Milk fat globule structure and function: nanoscience comes to milk production Trends Food Sci. Technol. (in press)
6. Asakuma, S. Urashima, T. Akahori, M. Obayashi, H. Nakamura, T. Kimura, K. Watanabe, Y. Arai, I. and Sanai, Y. (2007) Eur. J. Clin. Nutr. 62, 488-94.
7. Baldi, A., Ioannis, P., Chiara, P., Eleonora, F., Roubini, C., and Vittorio, D. (2005), Biological effects of milk proteins and their peptides with emphasis on those related to the gastrointestinal ecosystem. J. Dairy Res. 72, Spec No., 66-72.
8. Bateson, P. Barker, D. Clutton-Brock, T. Deb, D. D'Udine, B., Foley, R.A. Gluckman, P. Godfrey, K. Kirkwood, T. Lahr, M.M. McNamara, J. Metcalfe, N.B. Monaghan, P. Spencer H.G. and Sultan, S.E. (2004), Developmental plasticity and human health, Nature. 430(6998), 419-421.
9. Bode, L. (2006), Recent advances on structure, metabolism, and function of human milk oligosaccharides. J. Nutr. 136, 2127-2130.
10. Bruin, S. and Jongen, Th.R.G (2003), Food process engineering: the last 25 years and the challenges ahead, Crit. Rev. Food Sci. Food Safety. 2, 42-81.
11. Castillo, C. Atalah, E. Riumallo, J. and Castro, R. (1996), Breast-feeding and the nutritional status of nursing children in Chile. Bulletin of the Pan American Health Organization, 30, 125-133.
12. Catchpole, G.S. Beckmann, M. Enot, D.P. Mondhe, M. Zywicki, B. Taylor, J. Hardy, N. Smith, A. King, R.D. Kell, D.B. Fiehn, O. and Draper, J. (2005), Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops, Proc. Natl. Acad. Sci. USA. 102, 14458-14462.
13. Chamaillard, M. et al. (2003), An essential role for Nodi in host recognition of bacterial peptidoglycan containing diaminopimelic acid. Nature Immunol. 4, 702-707
14. Charlwood, J. Tolson, D. Dwek, M. Camilleri, P. (1999), Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry. Analytical Biochemistry., 273, 261-277.
15. Collins, F.S. Green, E.D. Guttmacher, A.E. Guyer, M.S. US National Human Genome Research Institute. (2003), A vision for the future of genomics research. Nature. 24. 422(6934):835-47.
16. Coppa, G.V. Gabrielli, O. Pierani, P. Catassi, C. Carlucci, A. Giorgi, P.L. (1993), Pediatrics, 91, 637-641.
17. de Campo, L. Yaghmur, A. Sagalowicz, L. Leser, M.E. Watzke, H. Glatter, O. (2004), Reversible phase transitions in emulsified nanostructured lipid systems. Langmuir. 20(13), 5254-61.
18. Delmer, D.P. (2005), Agriculture in the developing world: Connecting innovations in plant research to downstream applications, Proc. Natl. Acad. Sci. USA. 102, 15739-15746.
19. Dewey, K.G. (1998), Growth characteristics of breast-fed compared to formula-fed infants. Biology of the Neonate, 74, 94-105.
20. European Plant Science Organization (2005), European plant science: a field of opportunities, J. Exp. Bot. 56, 1699-709.
21. Fernandez, M.I. et al. Anti-inflammatory role for intracellular dimeric immunoglobulin A by neutralization of lipopolysaccharide in epithelial cells. Immunity 18, 739-749 (2003).
22. Fetherston, C.M. Lee, C.S. and Hartmann, P.E. (2001), Mammary gland defense: the role of colostrum, milk and involution secretion. Advances Nutrit. Res. 10, 67-98.
23. Fiehn, O. Kopka, J. Dormann, P. Altmann, T. Trethewey, R.N. and Willmitzer, L. (2000), Metabolite profiling for plant functional genomics. Nature Biotechnol. 18, 1157-1161.
24. FitzGerald, R.J. Murray, B.A. and Walsh, D.J. (2004), Hypotensive peptides from milk proteins. J. Nutr. 134(4) 980S-8S.
25. German, J.B., Schanbacher, F.L., Lönnerdal, B., Medrano, J., McGuire, M.A., McManaman, J.L., Rocke, D.M., Smith, T.P., Neville, M.C., Donnelly, P., Lange M.C. and Ward, R.E. (2006), International milk genomics consortium, Trends Food Sci. Technol. 17, 656-661.
26. German, J.B., Hammock, B.D. and Watkins, S.M. (2005a), Metabolomics: building on a century of biochemistry to guide human health, Metabolomics 1, 3-8.
27. German, J.B. Yeretzian, C. and Watzke, H.J. (2005b), Personalizing foods for health and preference, Food Technol. 58, 26-31.
28. German, J.B., Watkins, S.M. and Fay, L.-B. (2005), Metabolomics in practice: emerging knowledge to guide future dietetic advice toward individualized health, J. Am. Dietetics Assoc. 105, 1425-1432.
29. German, J.B., Dillard, C.J. and Ward, R.E. (2002) Bioactive components in milk. Curr. Opinion Clin. Nutrit. Metabolic Care 5, 653-658.
30. Goldman, A.S., Chheda, S. and Garofalo, R. (1998), Evolution of immunologic functions of the mammary gland and the postnatal development of immunity. Pediatric Res. 43, 155-162.
31. Gould, G.W. (2000), Preservation: past, present and future. Br. Med. Bull. 56, 84-96.
32. Grigorov M. G. (2005), Global properties of biological networks, Drug Discov. Today 10, 365-372.
33. Harmsen, H.J.M., Wildeboer-Veloo, A.C.M., Raangs, G. C., Wagendorp, A.A., Klijn, N., Bindels, J.G. and Welling, G.W. (2000). J. Pediat. Gastroenterol. Nutrit, 30, 61-67.
34. Holland, M.S. and Holland, R.E. (2005), The cellular perspective on mammary gland development: stem/progenitor cells and beyond. J. Dairy Sci, 88, Suppl. 1, E1-8.
35. Hood, L. (2003), Systems biology: Integrating technology, biology, and computation. Mechan. Ageing Develop. 124, 9-16.
36. Hooper, L.V., Midtvedt, T. and Gordon, J.I. (2002), How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22, 283-307.
37. International Council for Science. (2006), New genetics, food and agriculture: Scientific discoveries - societal dilemmas. Internet: http://www.doylefoundation.org/icsu/glossary.htm (accessed March 13, 2006).
38. Kagnoff, M.F. and Eckmann, L. (1997), Epithelial cells as sensors for microbial infection. J. Clin. Invest. 100, 6-10.
39. Kell, D.B. and King, R.D. (2000), On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: The need for machine learning. Trends in Biotechnol. 18, 93-98.
40. Krauss, R.M. (2001), Dietary and genetic effects on low-density lipoprotein heterogeneity, Ann. Rev. Nutr. 21, 283-295.
41. Kunz, C., Rudloff, S., Baier, W., Klein, N., Strobel, S. (2000), Ann. Rev. Nutr., 20, 699-722.
42. Lai, C.Q., Tai, E.S., Tan, C.E., Cutter, J.S., Chew, K., Zhu, Y.P., Adiconis, X. and Ordovas, J.M. (2003), The apolipoprotein A5 locus is a strong determinant of plasma triglyceride concentrations across ethnic groups in Singapore, J. Lipid Res. 44, 2365-2373.
43. Lange, M.C., Lemay D.A. and German, J.B. (2007), Multi-ontology framework to guide agriculture and food toward diet and health, J. Sci. Food Agric. 87, 8, 1427-1434.
44. Lehrer, R.I. and Ganz, T. (2002), Defensins of vertebrate animals. Curr. Opin. Immunol. 14, 96-102
45. Lemay, D.G., Dillard, C.J. and German, J.B. (2006), Nutrition and Food Structure In Food Colloids Self-Assembly and Material Science. (Eds Eric Dickinson and Martin Leser). Royal Society of Chemistry, London UK.
46. Lemay, D.G., Neville M.C., Rudolph, M.C., Pollard, K.S. and German, J.B. (2007), Gene regulatory networks in lactation: identification of global principles using bioinformatics BMC Systems Biol. 27, 1:56.
47. Lemay, D.G., Zivkovic, A.G. and German, J.B. (2007), Building the Bridges to Bioinformatics in Nutrition Research. Am. J. Clin. Nutr. 86, 1261-1268
48. Leser, M.E., Sagalowicz, L., Michel, M. and Watzke, H.J. (2006) Self-assembly of polar food lipids. Adv Colloid Interface Sci. 16, 125-36.
49. Lönnerdal, B. (2003), Nutritional and physiologic significance of human milk proteins. Am. J. Clin. Nutr., 77, 1537S-1543S.
50. Lönnerdal, B. (2004), Human milk proteins-key components for the biological activity of human milk. Adv. Expert. Biol. Med., 554, 423-426.
51. Macpherson, A.J. and Harris, N.L. (2004), Interactions between commensal intestinal bacteria and the immune system. Nature Rev. Immunol. 4, 478-485.
52. MacPherson, A.J. and Uhr, T. (2004), Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303, 1662-1665.
53. Martinez, J.A., Corbalan, M.S., Sanchez-Villegas, A., Forga, L., Marti, A. and Martinez-Gonzalez, M.A. (2003), Obesity risk is associated with carbohydrate intake in women carrying the Gln27Glu beta2-adrenoceptor polymorphism, J. Nutr. 133, 2549-2554.
54. McCarthy, F.M., Wang, N., Magee, G.B., Nanduri, B., Lawrence, M.L., Camon, E.B., Barrell, D.G., Hill, D.P., Dolan, M.E., Williams, W.P., Luthe, D.S., Bridges, S.M. and Burgess, S.C. (2006), AgBase: a functional genomics resource for agriculture. BMC Genomics, 7, 229-237.
55. McManaman, J.L. and Neville, M.C. (2003), Mammary physiology and milk secretion. Adv. Drug Delivery Rev. 55, 629-641.
56. McManaman, J.L., Palmer, C.A., Anderson, S., Schwertfeger, K. and Neville, M.C. (2004), Regulation of milk lipid formation and secretion in the mouse mammary gland. Adv. Expert. Med. Biol. 554, 263-279.
57. Medzhitov, R. and Janeway, C.A. (2002), Decoding the patterns of self and non-self by the innate immune system. Science 296, 298-300
58. Meisel, H. and FitzGerald, R.J. (2003), Biofunctional peptides from milk proteins: mineral binding and cytomodulatory effects. Curr. Pharm. Des. 9(16) 1289-95.
59. Meisel, H. and FitzGerald, R.J. (2000) Opioid peptides encrypted in intact milk protein sequences. Br. J. Nutr. 84 Suppl 1:S27-31.
60. Meisel, H. (2005), Biochemical properties of peptides encrypted in bovine milk proteins. Current Med. Chem. 12, 1905-1919.
61. Meisel, H., and FitzGerald, R.J. (2000), Opioid peptides encrypted in intact milk protein sequences. Br. J. Nutr. 84, Suppl. 1, S27-S31.
62. Miller, W., Makova, K.D., Nekrutenko. A. and Hardison, R.C. (2004), Comparative genomics, Annu. Rev. Genomics Hum. Genet. 5, 15-56.
63. Morris, R.M. (2006), Environmental genomics: exploring ecological sequence space, Curr. Biol. 6, R499-501.
64. Moskowitz, H.R., German, J.B. and Saguy, I.S. (2005), Unveiling health attitudes and creating good-for-you foods: the genomics metaphor, consumer innovative web-based technologies, Crit. Rev. Food Sci. Nutr. 45, 165-191.
65. Musumeci, M., Simpore, J., D'Agata, A., Sotgiu, S. and Musumeci, S. (2006), J. Pediatr Gastroenterol Nutr, 43, 372-378.
66. Nakhla, T., Fu, D.T., Zopf, D., Brodsky, N.L. and Hurt, H. (1999) Neutral oligosaccharide content of preterm human milk. Br. J. Nutri, 82, 361-367.
67. Neish, A.S. (2000), Prokaryotic regulation of epithelial responses by inhibition of IB-ubiquitination. Science 289, 1560-1563.
68. Neville, M.C., McFadden, T.B. and Forsyth, I.J. (2002), Hormonal regulation of mammary differentiation and milk secretion. J. Mammary Gland Biol. Neoplasia. 7, 49-66.
69. Newburg, D.S., Ruiz-Palacios, G.M. and Morrow, A.L. (2005), Human milk glycans protect infants against enteric pathogens. Ann Rev Nutr, 25, 37-58.
70. Newburg, D.S. (Ed.) (2001), Bioactive Components of Human Milk, in Advances in Experimental Medicine and Biology: Kluwer Academic/Plenum Publishers, New York.
71. Nicholson, J.K. and Wilson, I.D. (2003), Opinion: understanding 〈global〉 systems biology: metabonomics and the continuum of metabolism, Nat. Rev. Drug Discov. 2, 668-676.
72. Ninonuevo, M.R., Park, Y., Yin, H., Zhang, J., Ward, R.E., Clowers, B.H., German, J.B., Freeman, S.L., Killeen, K., Grimm, R. and Lebrilla, C.B. (2006), A strategy for annotating the human milk glycome. J. Agric. Food Chem. 54, 7471-7480.
73. Ninonuevo, M.R., Perkins, P.D., Francis, J., Lamotte, L., LoCascio, R.G., German, J.B., Freeman, S.L., Grimm, R. and Lebrilla, C.B. (2008), Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry. J. Agric Food Chem. 56(12) 4854-4861.
74. Ninonuevo, M.R., Ward, R.E., Locascio, R.G., German, J.B., Freeman, S.L., Barboza, M., Mills, D.A. and Lebrilla, C.B. (2007), The title for the reference is Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry. Anal Biochem. 361, 15-23.
75. Ninonuevo, M., An, H., Yin, H., Killeen, K., Grimm, R., Ward, R., German, B. and Lebrilla, C. (2005), Nanoliquid chromatography-mass spectrometry of oligosaccharides employing graphitized carbon chromatography on microchip with a high-accuracy mass analyzer. Electrophoresis, 26, 3641-3649.
76. Oddy, W.H. (2001), Breastfeeding protects against illness and infection in infants and children: a review of the evidence. Breastfeeding Rev. 9, 11-18.
77. Ordovas, J.M. (2003), Cardiovascular disease genetics: a long and winding road, Curr. Opin. Lipidol. 14, 47-54.
78. Petrovici, D.A. and Ritson, C. (2006), Factors influencing consumer dietary health preventative behaviours, BMC Public Health 6, 222-228.
79. Pfenninger, A., Karas, M., Finke, B. and Stahl, B. (2002) Structural analysis of underivatized neutral human milk oligosaccharides in the negative ion mode by nano-electrospray MS(n) (part 1: methodology), J. Am. Soc. Mass Spectrom. 13, 1331-1340.
80. Pharkya, P., Burgard, A.P. and Maranas, C.D. (2004) OptStrain: a computational framework for redesign of microbial production systems. Genome Res. 14(11), 2367-76.
81. Pickart, C.M. and Eddins, M.J. (2004), Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta. 1695 (1-3):55-72.
82. Politis, I. and Chronopoulou, R. (2008), Milk peptides and immune response in the neonate. Adv. Exp. Med. Biol. 606, 253-69.
83. Popkin, B.M. (2006), Global nutrition dynamics: the world is shifting rapidly toward a diet linked with noncommunicable diseases, Am. J. Clin. Nutr. 84, 289-298.
84. Quam, L. Smith, R. and Yach, D. (2006), Rising to the global challenge of the chronic disease epidemic, Lancet, 368, 1221-1223.
85. Raamsdonk, L.M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M.C., Berden, J. A., Brindle, K.M., Kell, D.B., Rowland, J.J., Westerhoff, H.V., van Dam, K. and Oliver, S.G. (2001), A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations, Nat. Biotechnol. 19, 45-50.
86. Rahoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S. and Medzhitov, R. (2004), Recognition of commensal microflora by Toll-like receptors is required for intestinal homeostasis. Cell 118, 229-241.
87. Rantala, M., Rantala, T.T., Savolainen, M.J., Friedlander Y. and Kesaniemi, Y.A. (2000), Apolipoprotein B gene polymorphisms and serum lipids: meta-analysis of the role of genetic variation in responsiveness to diet, Am. J. Clin. Nutr. 71, 713-724.
88. Rescigno, M. et al. (2001), Dendritic cells express tight junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nature Immunol. 2, 361-367
89. Rescigno, M., Rotta, G., Valzasina, B. and Ricciardi-Castagnoli, P. (2001), Dendritic cells shuttle microbes across gut epithelial monolayers. Immunobiol. 204, 572-581.
90. Rubaltelli, F.F., Biadaiol, R., Pecile, P. and Nicoletti, P. (1998), Intestinal flora in breast-and bottle-fed infants. J. Perinatal Med. 26, 186-191.
91. Ruiz-Palacios, G.M., Cervantes, L.E., Ramos, P., Chavez-Munguia, B. and Newburg, D.S. (2003) Campylobacter jejuni binds intestinal H(O) antigen (Fuc alpha 1, 2Gal beta 1, 4GIcNAc), and fucosyloligosaccharides of human milk inhibit its binding and infection. J. Biol. Chem, 278, 14112-14120.
92. Rutherfur, K.J. and Gill, H.S. (2000), Peptides affecting coagulation. Br. J. Nutr. 84 Suppl 1:S99-102.
93. Rutherfurd-Markwick, K.J. and Moughan, R.J. (2005), Bioactive peptides derived from food. J. AOAC Int. 88, 955-966.
94. Sagalowicz, L., Leser, M.E., Watzke, H.J. and Michel, M. (2006), Monoglyceride self-assembly structures as delivery vehicles, Trends Food Sci. Technol. 17, 204-214.
95. Sajda P. (2006), Machine learning for detection and diagnosis of disease, Annu. Rev. Biomed. Eng. 8, 537-565.
96. Sansonetti, P.J. (2001), Rupture, invasion and inflammatory destruction of the intestinal barrier by Shigella, making sense of prokaryote-eukaryote cross-talk. FEMS Microbiol. Rev. 25, 3-14.
97. Schanbacher, F.L., Talhouk, R.S. and Murray, F.A. (1997), Biology and origin of bioactive peptides in milk. Livestock Prod. Sci. 50, 105-123.
98. Sela David A. Chapman J., Adeuya A., Kim J.H., Chen F., Whitehead T.R., Lapidus A., Rokhsar D.S., Lebrilla C.B., German J.B, Price N.P., Richardson P.M Mills D.A. *The Complete Genome Sequence of Bifidobacterium longum subsp. infantis Reveals Adaptations for Milk Utilization within the Infant Microbiome. Proceedings of the National Academy USA Dec 2; 105(48): 18964-9
99. Severin, S. and Wenshui, X. (2005), Milk biologically active components as nutraceuticals. Crit. Rev. Food Sci. Nutrit. 45, 645-656.
100. Sharp, J.A., Lefevre, C. and Nicholas, K.R. (2008), Lack of functional alpha-lactalbumin prevents involution in Cape fur seals and identifies the protein is an apoptotic milk factor in mammary gland involution BMC Biol. 6(1) 48-55.
101. Shen, Z.J., Warren, C.D. and Newburg, D.S. (2000), High-performance capillary electrophoresis of sialylated oligosaccharides of human milk. Analytical Biochem. 279, 37-45.
102. Stefanon, B., Colitti, M., Gabai, G., Knight, C.H. and Wilde, C.J. (2002), Mammary apoptosis and lactation persistency in dairy animals. J. Dairy Res. 69, 37-52.
103. Stelwagen, K., Carpenter, E., Haigh, B., Hodgkinson, A. and Wheeler, T.T. (2008), Immune Components of Bovine Colostrum and Milk J. Anim. Sci. 24 (ahead of print).
104. Sumiyoshi, W., Urashima, T., Nakamura, T., Arai, I., Saito, T., Tsumura, N., Wang, B., Brand-Miller, J., Watanabe, Y. and Kimura, K. (2003), Determination of each neutral oligosaccharide in the milk of Japanese women during the course of lactation. Br. J. Nutrit. 89, 61-69.
105. Suzuki, M. and Suzuki, A. (2001), Structural characterization of fucose-containing oligosaccharides by high-performance liquid chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Biol. Chem. 382, 251-257.
106. Thurl, S. MullerWerner, B. Sawatzki, G. (1996) Quantification of individual oligosaccharide compounds from human milk using high-pH anion-exchange chromatography. Analytical Biochem. 235, 202-206.
107. Wagner, C.L., Taylor, S.N. and Johnson, D. (2008), Host factors in amniotic fluid and breast milk that contribute to gut maturation. Clin. Rev. Allergy Immunol. 34(2) 191-204.
108. Ward, R.E., Watzke, H.J., Jiménez-Flores R. and German, J.B. (2004), Bioguided processing: a paradigm change in food production, Food Technol. 58, 44-48.
109. Ward, R.E. and German, J.B. (2004), Understanding milk's bioactive components: a goal for the genomics toolbox. J. Nutr. 134, 962S-7S.
110. Ward, R.E., Ninonuevo, M., Mills, D.A., Lebrilla, C.B. and German, J.B. (2006), In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri. Appl. Environ. Microbiol. 72, 4497-4499.
111. Whetstine, J.R. Witt, T.L. and Matherly, L.H. (2002), The human reduced folate carrier gene is regulated by the AP2 and sp1 transcription factor families and a functional 61-base pair polymorphism, J. Biol. Chem. 277, 43873-43880.
112. Womack, J.E. (2005), Advances in livestock genomics: opening the barn door. Genome Res. 15, 1699-705.