Click for next page ( 144


The National Academies | 500 Fifth St. N.W. | Washington, D.C. 20001
Copyright © National Academy of Sciences. All rights reserved.
Terms of Use and Privacy Statement



Below are the first 10 and last 10 pages of uncorrected machine-read text (when available) of this chapter, followed by the top 30 algorithmically extracted key phrases from the chapter as a whole.
Intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text on the opening pages of each chapter. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.

Do not use for reproduction, copying, pasting, or reading; exclusively for search engines.

OCR for page 143
References Achyuthan, K. E., A. M. Achyuthan, P. D. Adams, S. M. Dirk, J. C. Harper, B. A. Simmons, and A. K. Singh. 2010. Supramolecular self-assembled chaos: polyphenolic lignin's bar- rier to cost-effective lignocellulosic biofuels. Molecules 15(12):8641-8688. Adamczyk, B., T. Tharmalingam, and P. M. Rudd. 2011. Glycans as cancer biomarkers. Bio- chimica et Biophysica Acta 1820(9):1347-1353. Albersheim, P., A. Darvill, K. Roberts, R. Sederoff, and A. Staehelin. 2010. Plant Cell Walls. New York: Garland Science, Taylor & Francis Group, LLC. Antoine, T., B. Priem, A. Heyraud, L. Greffe, M. Gilbert, B. W. Wakarchuk, J. S. Lam, and E. Samain. 2003. Large-scale in vivo synthesis of the carbohydrate moieties of gangliosides GM1 and GM2 by metabolically engineered Escherichia coli. ChemBioChem 4(5):406-412. Antoine, T., A. Heyraud, C. Bosso, and E. Samain. 2005. Highly efficient biosynthesis of the oligosaccharide moiety of the GD3 ganglioside by using metabolically engineered Escherichia coli. Angewandte Chemie--International Edition 44(9):1350-1352. Aoki, K. F., A. Yamaguchi, Y. Okuno, T. Akutsu, N. Ueda, M. Kanehisa, and H. Mamitsuka. 2003. Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform 14:134-143. Aoki, K. F., H. Mamitsuka, T. Akutsu, and M. Kanehisa. 2005. A score matrix to reveal the hidden links in glycans. Bioinformatics 21(8):1457-1463. Aoki-Kinoshita, K., N. Ueda, H. Mamitsuka, and M. Kanehisa. 2006. ProfilePSTMM: Cap- turing tree-structure motifs in carbohydrate sugar chains. Bioinformatics 22(14):25-34. Aoki-Kinoshita, K. F. 2010. Glycome Informatics: Methods and Applications. Boca Raton, FL: CRC Press. Arnold, J. N., M. R. Wormald, R. B. Sim, P. M. Rudd, and R. A. Dwek. 2007. The impact of glycosylation on the biological function and structure of human immunoglobulins. Annual Review of Immunology 25:21-50. Astronomo, R. D., and D. R. Burton. 2010. Carbohydrate vaccines: Developing sweet solu- tions to sticky situations? Nature Reviews Drug Discovery 9(4):308-324. 143

OCR for page 143
144 TRANSFORMING GLYCOSCIENCE Avci, U., S. Pattathil, J. S. Miller, and M. G. Hahn. 2011. Immunological approaches to cell wall and biomass characterization. In: Biomass Conversion: Methods and Protocols. M. Himmel, ed. Athens, GA: Humana Press. Banin, E., Y. Neuberger, Y. Altshuler, A. Halevi, O. Inbar, D. Nir, and A. Dukler. 2002. A novel linear code(r) nomenclature for complex carbohydrates. Trends in Glycoscience and Glycotechnology 14:127-137. Bar-Peled, M., and M. A. O'Neill. 2011. Plant nucleotide sugar formation, interconversion, and salvage by sugar recycling. Annual Review of Plant Biology 62:127-155. Bardoel, B. W., and J. A. G. van Strijp. 2011. Molecular battle between host and bacterium: Recognition in innate immunity. Journal of Molecular Recognition 24(6):1077-1086. Barreiro, O., and F. Sanchez-Madrid. 2009. Molecular basis of leukocyte-endothelium inter- actions during the inflammatory response. Revista Espanola De Cardiologia 62(5):552-562. Bendiak, B., T. T. Fang, and D. N. M. Jones. 2002. An effective strategy for structural elucida- tion of oligosaccharides through NMR spectroscopy combined with peracetylation us- ing doubly C-13-labeled acetyl groups. Canadian Journal of Chemistry--Revue Canadienne De Chimie 80(8):1032-1050. Bishop, J. R., and P. Gagneux. 2007. Evolution of carbohydrate antigens--microbial forces shaping host glycomes? Glycobiology 17(5):23R-34R. Bishop, J. R., M. Schuksz, and J. D. Esko. 2007. Heparan sulphate proteoglycans fine-tune mammalian physiology. Nature 446(7139):1030-1037. Blixt, O., K. Allin, O. Bohorov, X. Liu, H. Andersson-Sand, J. Hoffmann, and N. Razi. 2008. Glycan microarrays for screening sialyltransferase specificities. Glycoconjugate Journal 25(1):59-68. Boeggeman, E., B. Ramakrishnan, C. Kilgore, N. Khidekel, L. C. Hsieh-Wilson, J. T. Simpson, and P. K. Qasba. 2007. Direct identification of nonreducing GlcNAc residues on N- glycans of glycoproteins using a novel chemoenzymatic method. Bioconjugate Chemistry 18(3):806-814. Bohne-Lang, A., E. Lang, T. Frster, and C. W. von der Lieth. 2001. LINUCS: Linear notation for unique description of carbohydrate sequences. Carbohydrate Research 336(1):1-11. Boltje, T. J., T. Buskas, and G. J. Boons. 2009. Opportunities and challenges in synthetic oli- gosaccharide and glycoconjugate research. Nature Chemistry 1(8):611-622. Bose-Basu, B., J. Zajicek, G. Bondo, S. Zhao, M. Kubsch, I. Carmichael, and A. S. Serianni. 2000. Deuterium nuclear spin-lattice relaxation times and quadrupolar coupling constants in isotopically labeled saccharides. Journal of Magnetic Resonance 144(10828189):207-216. Bozell, J. J., and G. R. Petersen. 2010. Technology development for the production of bio- based products from biorefinery carbohydrates--the US Department of Energy's "Top 10" revisited. Green Chemistry 12(4):539-554. Broekhuizen, L. N., H. L. Mooij, J. J. P. Kastelein, E. S. G. Stroes, H. Vink, and M. Nieuwdorp. 2009. Endothelial glycocalyx as potential diagnostic and therapeutic target in cardio- vascular disease. Current Opinion in Lipidology 20(1):57-62. Brown, J. R., F. Yang, A. Sinha, B. Ramakrishnan, Y. Tor, P. K. Qasba, and J. D. Esko. 2009. Deoxygenated disaccharide analogs as specific inhibitors of beta 1-4-galactos- yltransferase 1 and selectin-mediated tumor metastasis. Journal of Biological Chemistry 284(8):4952-4959. Buskas, T., P. Thompson, and G. J. Boons. 2009. Immunotherapy for cancer: Synthetic carbo- hydrate-based vaccines. Chemical Communications 36:5335-5349. Butters, T. D. 2007. Gaucher disease. Current Opinion in Chemical Biology 11(4):412-418. Carroll, A., and C. Somerville. 2009. Cellulosic biofuels. Annual Review of Plant Biology 60:165-182. Celie, J., R. H. J. Beelen, and J. van den Born. 2009. Heparan sulfate proteoglycans in extrava- sation: Assisting leukocyte guidance. Frontiers in Bioscience 14:4932-4949.

OCR for page 143
REFERENCES 145 Ceroni, A., K. Maass, H. Geyer, R. Geyer, A. Dell, and S. M. Haslam. 2008. GlycoWorkbench: A tool for the computer-assisted annotation of mass spectra of glycans. Journal of Pro- teome Research 7(4):1650-1659. Chabre, Y. M., D. Giguere, B. Blanchard, J. Rodrigue, S. Rocheleau, M. Neault, S. Rauthu, A. Papadopoulos, A. A. Arnold, A. Imberty, and R. Roy. 2011. Combining glycomi- metic and multivalent strategies toward designing potent bacterial lectin inhibitors. Chemistry--A European Journal 17(23):6545-6562. Chang, P. V., J. A. Prescher, E. M. Sletten, J. M. Baskin, I. A. Miller, N. J. Agard, A. Lo, and C. R. Bertozzi. 2010. Copper-free click chemistry in living animals. Proceedings of the National Academy of Sciences of the United States of America 107(5):1821-1826. Chiba, Y., and Y. Jigami. 2007. Production of humanized glycoproteins in bacteria and yeasts. Current Opinion in Chemical Biology 11(6):670-676. Chichlowski, M., J. B. German, C. B. Lebrilla, and D. A. Mills. 2011. The influence of milk oligosaccharides on microbiota of infants: Opportunities for formulas. Annual Review of Food Science and Technology 2:331-351. Chuck, G. S., C. Tobias, L. Sun, F. Kraemer, C. L. Li, D. Dibble, R. Arora, J. N. Bragg, J. P. Vogel, S. Singh, B. A. Simmons, M. Pauly, and S. Hake. 2011. Overexpression of the maize Corngrass1 micro-RNA prevents flowering, improves digestibility, and increases starch content of switchgrass. Proceedings of the National Academy of Sciences of the United States of America 108(42):17550-17555. Clark, R. J., P. M. McDonough, E. Swanson, S. U. Trost, M. Suzuki, M. Fukuda, and W. H. Dillmann. 2003. Diabetes and the accompanying hyperglycemia impairs cardiomyo- cyte calcium cycling through increased nuclear O-GlcNAcylation. Journal of Biological Chemistry 278(45):44230-44237. Cohen, M., and A. Varki. 2010. The Sialome--Far more than the sum of its parts. OMICS: A Journal of Integrative Biology 14(4):455-464. Comelli, E. M., S. R. Head, T. Gilmartin, T. Whisenant, S. M. Haslam, S. J. North, N. K. Wong, T. Kudo, H. Narimatsu, J. D. Esko, K. Drickamer, A. Dell, and J. C. Paulson. 2006. A focused microarray approach to functional glycomics: Transcriptional regulation of the glycome. Glycobiology 16(2):117-131. Cooper, C. A., H. J. Joshi, M. J. Harrison, M. R. Wilkins, and N. H. Packer. 2003. GlycoSuit- eDB: A curated relational database of glycoprotein glycan structures and their biologi- cal sources; 2003 update. Nucleic Acids Research 31(1):511-513. Copeland, R. J., J. W. Bullen, and G. W. Hart. 2008. Cross-talk between GlcNAcylation and phosphorylation: Roles in insulin resistance and glucose toxicity. American Journal of Physiology--Endocrinology and Metabolism 295(1):E17-28. Costantino, P., R. Rappuoli, and F. Berti. 2011. The design of semi-synthetic and synthetic glycoconjugate vaccines. Expert Opinion on Drug Discovery 6(10):1045-1066. Coutinho, M. F., L. Lacerda, and S. Alves. 2012. Glycosaminoglycan storage disorders: A review. Biochemistry Research International 2012:471325. Cox, T. M., and M. B. Cachon-Gonzalez. 2012. The cellular pathology of lysosomal diseases. Journal of Pathology 226(2):241-254. Coxon, B. 2009. Developments in the Karplus equation as they relate to the NMR coupling constants of carbohydrates. Advances in Carbohydrate Chemistry and Biochemistry, Vol. 62. D. Horton, ed. San Diego: Elsevier Academic Press. Crocker, P. R., J. C. Paulson, and A. Varki. 2007. Siglecs and their roles in the immune system. Nature Reviews Immunology 7(4):255-266. Crocker, P. R., and P. Redelinghuys. 2008. Siglecs as positive and negative regulators of the immune system. Biochemical Society Transactions 36:1467-1471. Culyba, E. K., J. L. Price, S. R. Hanson, A. Dhar, C.-H. Wong, M. Gruebele, E. T. Powers, and J. W. Kelly. 2011. Protein native-state stabilization by placing aromatic side chains in N-glycosylated reverse turns. Science 331(6017):571-575.

OCR for page 143
146 TRANSFORMING GLYCOSCIENCE Cummings, R. D. 2009. The repertoire of glycan determinants in the human glycome. Mo- lecular BioSystems 5(10):1087-1104. Dai, H., and X. M. Gao. 2011. Elevated levels of serum antibodies against alpha-1, 6-glucan in patients with systemic lupus erythematosus or rheumatoid arthritis. Protein and Cell 2(9):739-744. Dehnert, K. W., J. M. Baskin, S. T. Laughlin, B. J. Beahm, N. N. Naidu, S. L. Amacher, and C. R. Bertozzi. 2012. Imaging the sialome during zebrafish development with copper-free click chemistry. ChemBioChem 13(3):353-357. Dell, A., and H. R. Morris. 2001. Glycoprotein structure determination by mass spectrometry. Science 291(5512):2351-2356. Dell, A., A. J. Reason, K. H. Khoo, M. Panico, R. A. McDowell, and H. R. Morris. 1994. Mass spectrometry of carbohydrate-containing biopolymers. Methods in Enzymology 230:108-132. Demotte, N., V. Stroobant, P. J. Courtoy, P. Van Der Smissen, D. Colau, I. F. Luescher, C. Hivroz, J. Nicaise, J. L. Squifflet, M. Mourad, D. Godelaine, T. Boon, and P. van der Bruggen. 2008. Restoring the association of the T-cell receptor with CD8 reverses anergy in human tumor-infiltrating lymphocytes. Immunity 28(3):414-424. Dennis, J. W., M. Granovsky, and C. E. Warren. 1999. Glycoprotein glycosylation and cancer progression. Biochimica et Biophysica Acta--General Subjects 1473(1):21-34. Dias, W. B., and G. W. Hart. 2007. O-GlcNAc modification in diabetes and Alzheimer's disease. Molecular BioSystems 3(11):766-772. Ding, S.-Y., Q. Xu, M. Crowley, Y. Zeng, M. Nimlos, R. Lamed, E. A. Bayer, and M. E. Himmel. 2008. A biophysical perspective on the cellulosome: New opportunities for biomass conversion. Current Opinion in Biotechnology 19(3):218-227. DOE (U.S. Department of Energy). 2006. Breaking the Biological Barriers to Cellulose Ethanol--A Joint Research Agenda. Report from the December 2005 Workshop, DOE/SC-0095. U.S. Department of Energy Office of Science, Washington, D.C. DOE. 2011. U.S. Billion-Ton Update: Biomass Supply for a Bioenergy and Bioproducts Industry . R. D. Perlack and B. J. Stokes (Leads), ORNL/TM-2011/224. Oak Ridge National Labo- ratory, Oak Ridge, TN. 227 pp. Drake, P. M., W. Cho, B. S. Li, A. Prakobphol, E. Johansen, N. L. Anderson, F. E. Regnier, B. W. Gibson, and S. J. Fisher. 2010. Sweetening the pot: Adding glycosylation to the biomarker discovery equation. Clinical Chemistry 56(2):223-236. Drouillard, S., H. Driguez, and E. Samain. 2006. Large-scale synthesis of H-antigen oligo- saccharides by expressing Helicobacter pylori alpha 1,2-fucosyltransferase in met- abolically engineered Escherichia coli cells. Angewandte Chemie, International Edition 45(11):1778-1780. Drozdova, A., P. Bojarova, K. Krenek, L. Weignerova, B. Henssen, L. Elling, H. Christensen, H. H. Jensen, H. Pelantova, M. Kuzma, K. Bezouska, M. Krupova, D. Adamek, K. Slamova, and V. Kren. 2011. Enzymatic synthesis of dimeric glycomimetic ligands of NK cell activation receptors. Carbohydrate Research 346(12):1599-1609. Dube, D. H., and C. R. Bertozzi. 2005. Glycans in cancer and inflammation: Potential for therapeutics and diagnostics. Nature Reviews Drug Discovery 4(6):477-488. Duus, J., C. H. Gotfredsen, and K. Bock. 2000. Carbohydrate structural determination by NMR spectroscopy: Modern methods and limitations. Chemical Reviews 100(12):4589-4614. Dwek, R. A. 1996. Glycobiology: Toward understanding the function of sugars. Chemical Reviews 96(2):683-720. Dykhuizen, E. C., J. F. May, A. Tongpenyai, and L. L. Kiessling. 2008. Inhibitors of UDP- galactopyranose mutase thwart mycobacterial growth. Journal of the American Chemical Society 130(21):6706-6707. Erbacher, A., F. Gieseke, R. Handgretinger and I. Muller. 2009. Dendritic cells: Functional aspects of glycosylation and lectins. Human Immunology 70(5):308-312.

OCR for page 143
REFERENCES 147 Ernst, B., and J. L. Magnani. 2009. From carbohydrate leads to glycomimetic drugs. Nature Reviews Drug Discovery 8(8):661-677. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8(3):186-194. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 8(3):175-185. Fadda, E., and R. J. Woods. 2010. Molecular simulations of carbohydrates and protein- carbohydrate interactions: Motivation, issues and prospects. Drug Discovery Today 15(15-16):596-609. Fang, T. T., and B. Bendiak. 2007. The stereochemical dependence of unimolecular dissocia- tion of monosaccharide-glycolaldehyde anions in the gas phase: A basis for assignment of the stereochemistry and anomeric configuration of monosaccharides in oligosac- charides by mass spectrometry via a key discriminatory product ion of disaccharide fragmentation, m/z 221. Journal of the American Chemical Society 129(31):9721-9736. Fattal I., N. Shental, D. Mevorach, J. M. Anaya, A. Livneh, P. Langevitz, G. Zandman- Goddard, R. Pauzner, M. Lerner, M. Blank, M. E. Hincapie, U. Gafter, Y. Naparstek, Y. Shoenfeld, E. Domany, and I. R. Cohen. 2010. An antibody profile of systemic lupus erythematosus detected by antigen microarray. Immunology 130(3):337-343. Frank, M., and S. Schloissnig. 2010. Bioinformatics and molecular modeling in glycobiology. Cellular and Molecular Life Sciences 67(16):2749-2772. Freeze, H. H., and B. G. Ng. 2011. Golgi glycosylation and human inherited diseases. Cold Spring Harbor Perspectives in Biology 3(9):a005371. Freeze, H. H., and V. Sharma. 2010. Metabolic manipulation of glycosylation disorders in humans and animal models. Seminars in Cell & Developmental Biology 21(6):655-662. Fulop, N., M. M. Mason, K. Dutta, P. P. Wang, A. J. Davidoff, R. B. Marchase, and J. C. Chatham. 2007. Impact of Type 2 diabetes and aging on cardiomyocyte function and O-linked N-acetylglucosamine levels in the heart. American Journal of Physiology--Cell Physiology 292(4):C1370-C1378. Galan, M. C., D. Benito-Alifonso, and G. M. Watt. 2011. Carbohydrate chemistry in drug discovery. Organic & Biomolecular Chemistry 9(10):3598-3610. Gantt, R. W., P. Peltier-Pain, W. J. Cournoyer, and J. S. Thorson. 2011a. Using simple donors to drive the equilibria of glycosyltransferase-catalyzed reactions. Nature Chemical Biol- ogy 7(10):685-691. Gantt, R. W., P. Peltier-Pain, and J. S. Thorson. 2011b. Enzymatic methods for glyco(diversification/randomization) of drugs and small molecules. Natural Product Reports 28(11):1811-1853. Garber, K. C. A., K. Wangkanont, E. E. Carlson, and L. L. Kiessling. 2010. A general glyco- mimetic strategy yields non-carbohydrate inhibitors of DC-SIGN. Chemical Communica- tions 46(36):6747-6749. Garcia, I., M. Marradi, and S. Penades. 2010. Glyconanoparticles: Multifunctional nanoma- terials for biomedical applications. Nanomedicine 5(5):777-792. Ghaderi, D., R. E. Taylor, V. Padler-Karavani, S. Diaz, and A. Varki. 2010. Implications of the presence of N-glycolylneuraminic acid in recombinant therapeutic glycoproteins. Nature Biotechnology 28(8):863-867. Gilbert, M., R. Bayer, A. M. Cunningham, S. Defrees, Y. H. Gao, D. C. Watson, N. M. Young, and W. W. Wakarchuk. 1998. The synthesis of sialylated oligosaccharides using a CMP- Neu5Ac synthetase/sialyltransferase fusion. Nature Biotechnology 16(8):769-772. Godfrey, C., A. R. Foley, E. Clement, and F. Muntoni. 2011. Dystroglycanopathies: Coming into focus. Current Opinion in Genetics & Development 21(3):278-285. Golks, A., T. T. T. Tran, J. F. Goetschy, and D. Guerini. 2007. Requirement for O-linked N-acetyl- glucosaminyltransferase in lymphocytes activation. EMBO Journal 26(20):4368-4379.

OCR for page 143
148 TRANSFORMING GLYCOSCIENCE Gomord, V., P. Chamberlain, R. Jefferis, and L. Faye. 2005. Biopharmaceutical production in plants: Problems, solutions and opportunities. Trends in Biotechnology 23(11):559-565. Gray, G. R. 1990. Linkage analysis using reductive cleavage method. Methods in Enzymology 193:573-587. Greene, R. V. 2011. Basic energy sciences (BES) perspective. Presentation to the Committee on Assessing the Importance and Impact of Glycomics and Glycosciences, October 11, Washington, DC. Gross, B. J., B. C. Kraybill, and S. Walker. 2005. Discovery of O-GlcNAc transferase inhibitors. Journal of the American Chemical Society 127(42):14588-14589. Guerrini, M., D. Beccati, Z. Shriver, A. Naggi, K. Viswanathan, A. Bisio, I. Capila, J. C. Lansing, S. Guglieri, B. Fraser, A. Al-Hakim, N. S. Gunay, Z. Zhang, L. Robinson, L. Buhse, M. Nasr, J. Woodcock, R. Langer, G. Venkataraman, R. J. Linhardt, B. Casu, G. Torri, and R. Sasisekharan. 2008. Oversulfated chondroitin sulfate is a contaminant in heparin associated with adverse clinical events. Nature Biotechnology 26(6):669-675. Habibi, Y., L. A. Lucia, and O. J. Rojas. 2010. Cellulose nanocrystals: Chemistry, self-assem- bly, and applications. Chemical Reviews 110(6):3479-3500. Hakomori, S. 1964. A rapid permethylation of glycolipid, and polysaccharide catalyzed by methylsulfinyl carbanion in dimethyl sulfoxide. Journal of Biological Chemistry 55: 205-208. Hakomori, S. 2002. Glycosylation defining cancer malignancy: New wine in an old bottle. Proceedings of the National Academy of Sciences of the United States of America 99(16): 10231-10233. Haltiwanger, R. S., and J. B. Lowe. 2004. Role of glycosylation in development. Annual Review of Biochemistry 73:491-537. Hancock, S. M., M. D. Vaughan, and S. G. Withers. 2006. Engineering of glycosidases and glycosyltransferases. Current Opinion in Chemical Biology 10(5):509-519. Hanson, S. R., E. K. Culyba, T.-L. Hsu, C.-H. Wong, J. W. Kelly, and E. T. Powers. 2009. The core trisaccharide of an N-linked glycoprotein intrinsically accelerates folding and enhances stability. Proceedings of the National Academy of Sciences of the United States of America 106(9):3131-3136. Hart, G. W., and R. J. Copeland. 2010. Glycomics hits the big time. Cell 143(5):672-676. Hart, G. W., M. P. Housley, and C. Slawson. 2007. Cycling of O-linked beta-N-acetylglucos- amine on nucleocytoplasmic proteins. Nature 446(7139):1017-1022. Hart, G. W., C. Slawson, G. Ramirez-Correa, and O. Lagerlof. 2011. Cross talk between O-glcNAcylation and phosphorylation: Roles in signaling, transcription, and chronic disease. Annual Review of Biochemistry 80:825-858. Hashimoto, K., K. F. Aoki-Kinoshita, N. Ueda, M. Kanehisa, and H. Mamitsuka. 2008a. A new efficient probabilistic model for mining labeled ordered trees applied to glycobiol- ogy. ACM Transactions on Knowledge Discovery from Data 2(1):1-30. Hashimoto, K., I. Takigawa, M. Shiga, M. Kanehisa, and H. Mamitsuka. 2008b. Mining significant tree patterns in carbohydrate sugar chains. Bioinformatics 24(16):167-173. Heimburg-Molinaro, J., M. Lum, G. Vijay, M. Jain, A. Almogren, and K. Rittenhouse-Olson. 2011. Cancer vaccines and carbohydrate epitopes. Vaccine 29(48):8802-8826. Helm, J. S., Y. N. Hu, L. Chen, B. Gross, and S. Walker. 2003. Identification of active-site inhibitors of MurG using a generalizable, high-throughput glycosyltransferase screen. Journal of the American Chemical Society 125(37):11168-11169. Hennet, T. 2012. Diseases of glycosylation beyond classical congenital disorders of glycosyl- ation. Biochimica et Biophysica Acta 1820(9):1306-1317. Hennet, T., and L. G. Ellies. 1999. The remodeling of glycoconjugates in mice. Biochimica et Biophysica Acta--General Subjects 1473(1):123-136.

OCR for page 143
REFERENCES 149 Henrissat, B., A. Surolia, and P. Stanley. 2009. A genomic view of glycobiology. In Essentials of Glycobiology. A. Varki, R. D. Cummings, J. D. Esko, H. H. Freeze, P. Stanley, C. R. Bertozzi, G. W. Hart, M. E. Etzler, eds. New York: Cold Spring Harbor. Herget, S., R. Ranzinger, K. Maass, and C. W. Lieth. 2008. GlycoCT--a unifying sequence format for carbohydrates. Carbohydrate Research 343(12):2162-2171. Hess, M. A., R. Sczyrba, T.-W. Egan, H. Kim, H. Chokhawala, G. Schroth, S. Luo, D. S. Clark, F. Chen, T. Zhang, R. I. Machie, L. A. Pennacchio, S. G. Tringe, A. Visel, T. Woyke, Z. Wang, and E. M. Rubin. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463-467. Himmel, M. E., ed. 2008. Front matter. Biomass Recalcitrance: Deconstructing the Cell Wall for Bioenergy. United Kingdom: Blackwell Publishing, John Wiley & Sons. Himmel, M. E., S. Y. Ding, D. K. Johnson, W. S. Adney, M. R. Nimlos, J. W. Brady, and T. D. Foust. 2007. Biomass recalcitrance: Engineering plants and enzymes for biofuels pro- duction. Science 315(5813):804-807. Hizukuri, Y., Y. Yamanishi, O. Nakamura, F. Yagi, S. Goto, and M. Kanehisa. 2005. Extraction of leukemia-specific glycan motifs in humans by computational glycomics. Carbohydrate Research 340(14):2270-2278. Horton, D., and J. D. Wander. 1980. Naturally occurring amino sugars. Pp. 726-760 in The Carbohydrates, Chemistry and Biochemistry. W. Pigman, D. Horton, and J. D. Wander, eds. New York: Academic Press. Hossler, P., B. C. Mulukutla, and W.-S. Hu. 2007. Systems analysis of N-glycan processing in mammalian cells. PLoS ONE 2(8):e713. Hsu, C. H., S. C. Hung, C. Y. Wu, and C. H. Wong. 2011. Toward automated oligosaccharide synthesis. Angewandte Chemie, International Edition 50(50):11872-11923. Hu, Y., J. Suarez, E. Fricovsky, H. Wang, B. T. Scott, S. A. Trauger, W. L. Han, M. O. Oyeleye, and W. H. Dillmann. 2009. Increased enzymatic O-GlcNAcylation of mitochondrial proteins impairs mitochondrial function in cardiac myocytes exposed to high glucose. Journal of Biological Chemistry 284(1):547-555. Huang, Y. L., and C. Y. Wun. 2010. Carbohydrate-based vaccines: Challenges and opportuni- ties. Expert Review of Vaccines 9(11):1257-1274. Imberty, A., Y. M. Chabre, and R. Roy. 2008. Glycomimetics and glycodendrimers as high- affinity microbial anti-adhesins. Chemistry--A European Journal 14(25):7490-7499. Jaeken, J. 2011. Congenital disorders of glycosylation (CDG): It's (nearly) all in it! Journal of Inherited Metabolic Disease 34(4):853-858. Jaipuri, F. A., and N. L. Pohl. 2008. Toward solution-phase automated iterative synthesis: Fluorous-tag assisted solution-phase synthesis of linear and branched mannose oligo- mers. Organic & Biomolecular Chemistry 6(15):2686-2691. Jandus, C., H. U. Simon, and S. von Gunten. 2011. Targeting siglecs--a novel pharmaco- logical strategy for immuno- and glycotherapy. Biochemical Pharmacology 82(4):323-332. Jang-Lee J., S. J. North, M. Sutton-Smith, D. Goldberg, M. Panico, H. Morris, S. Haslam, and A. Dell. 2006. Glycomic profiling of cells and tissues by mass spectrometry: Fingerprint- ing and sequencing methodologies. Methods in Enzymology 415:59-86. Jefferis, R. 2009. Glycosylation as a strategy to improve antibody-based therapeutics. Nature Reviews Drug Discovery 8(3):226-234. Jeffrey, G. A., and M. Sundaralingam. 1985. Bibliography of crystal-structures of carbohy- drates, nucleosides, and nucleotides for 1979 and 1980--addenda and errata for 1970- 1978--and index for 1935-1980. Advances in Carbohydrate Chemistry and Biochemistry 43:203-421. Jiang, D. H., J. R. Liang, and P. W. Noble. 2011a. Hyaluronan as an immune regulator in hu- man diseases. Physiological Reviews 91(1):221-264. Jiang, H., K. F. Aoki-Kinoshita, and W. K. Ching. 2011b. Extracting glycan motifs using a biochemically weighted kernel. Bioinformation 7(8):405-412.

OCR for page 143
150 TRANSFORMING GLYCOSCIENCE Johnson, R. A. 2012. Emerging trends and drivers in the global biotechnology industry. Available at www.unog.ch/bwc/meeting [accessed August 1, 2012]. Jokela, T. A., K. M. Makkonen, S. Oikari, R. Karna, E. Koli, G. W. Hart, R. H. Tammi, C. Carlberg, and M. I. Tammi. 2011. Cellular content of UDP-N-acetylhexosamines con- trols hyaluronan synthase 2 expression and correlates with O-linked N-acetylglucos- amine modification of transcription factors YY1 and SP1. Journal of Biological Chemistry 286(38):33632-33640. Jones, S. P. 2005. A bittersweet modification O-GlcNAc and cardiac dysfunction. Circulation Research 96(9):925-926. Kaddurah-Daouk, R., B. S. Kristal, and R. M. Weinshilboum. 2008. Metabolomics: A global biochemical approach to drug response and disease. Annual Review of Pharmacology and Toxicology 48:653-683. Kaeothip, S., and A. V. Demchenko. 2011. Expeditious oligosaccharide synthesis via selective, semi-orthogonal, and orthogonal activation. Carbohydrate Research 346(12):1371-1388. Kaida, K., T. Ariga, and R. K. Yu. 2009. Antiganglioside antibodies and their pathophysi- ological effects on Guillain-Barr syndrome and related disorders--a review. Glycobiol- ogy 19(7):676-692. Karlsson, K. A. 1998. Meaning and therapeutic potential of microbial recognition of host glycoconjugates. Molecular Microbiology 29(1):1-11. Karr, J. R., J. C. Sanghvi, D. N. Macklin, M. V. Gutschow, J. M. Jacobs, B. Bolival, N. Assad- Garcia, J. I. Glass, and M. W. Covert. 2012. A whole-cell computational model predicts phenotype from genotype. Cell 150(2):389-401. Kawano, S., K. Hashimoto, T. Miyama, S. Goto, and M. Kanehisa. 2005. Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinfor- matics 21(21):3976-3982. Khidekel, N., S. B. Ficarro, E. C. Peters, and L. C. Hsieh-Wilson. 2004. Exploring the O- GlcNAc proteome: Direct identification of O-GlcNAc-modified proteins from the brain. Proceedings of the National Academy of Sciences of the United States of America 101(36): 13132-13137. Kiessling, L. L., and R. A. Splain. 2010. Chemical approaches to glycobiology. Annual Review of Biochemistry 79:619-653. Klemm, D., B. Heublein, H. P. Fink, and A. Bohn. 2005. Cellulose: Fascinating biopolymer and sustainable raw material. Angewandte Chemie--International Edition 44(22):3358-3393. Klemm D., F. Kramer, S. Moritz, T. Lindstrom, M. Ankerfors, D. Gray, and A. Dorris. 2011. Nanocelluloses: A new family of nature-based materials. Angewandte Chemie Interna- tional Edition 50:5438-5466. Kobayashi, M., M. Fukuda, and J. Nakayama. 2009a. Role of sulfated O-glycans expressed by high endothelial venule-like vessels in pathogenesis of chronic inflammatory gas- trointestinal diseases. Biological & Pharmaceutical Bulletin 32(5):774-779. Kobayashi, M., H. Lee, J. Nakayama, and M. Fukuda. 2009b. Roles of gastric mucin-type O-glycans in the pathogenesis of Helicobacter pylori infection. Glycobiology 19(5):453-461. Kochlamazashvili, G., O. Senkov, S. Grebenyuk, C. Robinson, M. F. Xiao, K. Stummeyer, R. Gerardy-Schahn, A. K. Engel, L. Feig, A. Semyanov, V. Suppiramaniam, M. Schachner, and A. Dityatev. 2010. Neural cell adhesion molecule-associated polysialic acid regu- lates synaptic plasticity and learning by restraining the signaling through GluN2B- containing NMDA receptors. Journal of Neuroscience 30(11):4171-4183. Koeller, K. M., and C. H. Wong. 2001. Enzymes for chemical synthesis. Nature 409(6817): 232-240. Kolarich, D., B. Lepenies, and P. H. Seeberger. 2012. Glycomics, glycoproteomics and the immune system. Current Opinion in Chemical Biology 16(1-2):214-220. Kornfeld, S. 2010. A fascination with sugars. Molecular Biology of the Cell 21(22):3773-3775.

OCR for page 143
REFERENCES 151 Korpos, E., C. Wu, and L. Sorokin. 2009. Multiple roles of the extracellular matrix in inflam- mation. Current Pharmaceutical Design 15(12):1349-1357. Krambeck, F. J., S. V. Bennun, S. Narang, S. Choi, K. J. Yarema, and M. J. Betenbaugh. 2009. A mathematical model to derive N-glycan structures and cellular enzyme activities from mass spectrometric data. Glycobiology 19(11):1163-1175. Kremer, R. M. D., and C. Gallo-Rodriguez. 2004. Naturally occurring monosaccharides: Properties and synthesis. Advances in Carbohydrate Chemistry and Biochemistry 59:9-67. Kuboyama, T., K. Hirata, K. Aoki-Kinoshita, H. Kashima, and H. Yasuda. 2006. A gram distribution kernel applied to glycan classification and motif extraction. Genome Inform 17(2):25-34. Kudlow, J. E. 2006. Post-translational modification by O-GlcNAc: Another way to change protein function. Journal of Cellular Biochemistry 98(5):1062-1075. Lachmann, R. H. 2003. Miglustat. Oxford GlycoSciences/Actelion. Current Opinion in Inves- tigational Drugs 4(4):472-479. Lairson, L. L., B. Henrissat, G. J. Davies, and S. G. Withers. 2008. Glycosyltransferases: Struc- tures, functions, and mechanisms. Annual Review of Biochemistry 77:521-555. Langer, H. F., and T. Chavakis. 2009. Leukocyte-endothelial interactions in inflammation. Journal of Cellular and Molecular Medicine 13(7):1211-1220. Laubli, H., and L. Borsig. 2010. Selectins promote tumor metastasis. Seminars in Cancer Biol- ogy 20(3):169-177. Laughlin, S. T., and C. R. Bertozzi. 2009. Imaging the glycome. Proceedings of the National Academy of Sciences of the United States of America 106(1):12-17. Lazarus, B. D., D. C. Love, and J. A. Hanover. 2009. O-GlcNAc cycling: Implications for neurodegenerative disorders. International Journal of Biochemistry & Cell Biology 41(11):2134-2146. Lee, S. U., A. Grigorian, J. Pawling, I. J. Chen, G. Gao, T. Mozaffar, C. McKerlie, and M. Demetriou. 2007. N-glycan processing deficiency promotes spontaneous inflam- matory demyelination and neurodegeneration. Journal of Biological Chemistry 282(46): 33725-33734. Lepenies, B., and P. H. Seeberger. 2010. The promise of glycomics, glycan arrays and car- bohydrate-based vaccines. Immunopharmacology and Immunotoxicology 32(2):196-207. Li, D., T. Mallory, and S. Satomura. 2001. AFP-L3: A new generation of tumor marker for hepatocellular carcinoma. Clinica Chimica Acta 313(1-2):15-19. Li, M., L. J. Song, and X. Y. Qin. 2010. Glycan changes: Cancer metastasis and anti-cancer vaccines. Journal of Biosciences 35(4):665-673. Liang, P. H., C. Y. Wu, W. A. Greenberg, and C. H. Wong. 2008. Glycan arrays: Biological and medical applications. Current Opinion in Chemical Biology 12(1):86-92. Lindberg, B., and J. Lonngren. 1978. Methylation analysis of complex carbohydrates: General procedure and application for sequence analysis. Methods in Enzymology 50:3-33. Liu, Q. P., G. Sulzenbacher, H. Yuan, E. P. Bennett, G. Pietz, K. Saunders, J. Spence, E. Nudelman, S. B. Levery, T. White, J. M. Neveu, W. S. Lane, Y. Bourne, M. L. Olsson, B. Henrissat, and H. Clausen. 2007. Bacterial glycosidases for the production of universal red blood cells. Nature Biotechnology 25(4):454-464. Loss, A., P. Bunsmann, A. Bohne, E. Schwarzer, E. Lang, and C. W. von der Lieth. 2002. SWEET-DB: An attempt to create annotated data collections for carbohydrates. Nucleic Acids Research 30(1):405-408. Loss, A., R. Stenutz, E. Schwarzer, and C. von der Lieth. 2006. GlyNest and CASPER: Two in- dependent approaches to estimate 1H and 13C NMR shifts of glycans available through a common Web interface. Nucleic Acids Research 34(Web server issue):W733-W737.

OCR for page 143
152 TRANSFORMING GLYCOSCIENCE Louthrenoo, W., N. Kasitanon, R. Wichainun, S. Wangkaew, W. Sukitawut, S. Kuwata, and F. Takeuchi. 2010. Anti-agalactosyl IgG antibodies in Thai patients with rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis. Clinical Rheumatology 29(3):241-246. Lowe, J. B., and J. D. Marth. 2003. A genetic approach to mammalian glycan function. Annual Review of Biochemistry 72:643-691. Lu, Y. P., Y. H. P. Zhang, and L. R. Lynd. 2006. Enzyme-microbe synergy during cellulose hydrolysis by Clostridium thermocellum. Proceedings of the National Academy of Sciences of the United States of America 103(44):16165-16169. Ltteke, T., A. Bohne-Lang, A. Loss, T. Goetz, M. Frank, and C. von der Lieth. 2006. GLYCOSCIENCES.de: An Internet portal to support glycomics and glycobiology re- search. Glycobiology 16(5):71R-81R. Lux, A., and F. Nimmerjahn. 2011. Impact of differential glycosylation on IgG activity. Ad- vances in Experimental Medicine and Biology 780:113-124. Lynd, L. R. 2010. Bioenergy: In search of clarity. Energy & Environmental Science 3(9):1150-1152. Lynd, L. R., and C. H. D. Cruz. 2010. Make way for ethanol. Science 330(6008):1176-1176. Lynd, L. R., M. S. Laser, D. Brandsby, B. E. Dale, B. Davison, R. Hamilton, M. Himmel, M. Keller, J. D. McMillan, J. Sheehan, and C. E. Wyman. 2008. How biotech can transform biofuels. Nature Biotechnology 26(2):169-172. Macnaughtan, M. A., F. Tian, S. Liu, L. Meng, S. Park, P. Azadi, K. W. Moremen, and J. H. Prestegard. 2008. (13)C-sialic acid labeling of glycans on glycoproteins using ST6Gal-I. Journal of the American Chemical Society 130(36):11864-11865. Magnani, J. L., and B. Ernst. 2009. Glycomimetic drugs--a new source of therapeutic op- portunities. Discovery Medicine 8(43):247-252. Marino, K., J. Bones, J. J. Kattla, and P. M. Rudd. 2010. A systematic approach to protein glycosylation analysis: A path through the maze. Nature Chemical Biology 6(10):713-723. Marth, J. D., and P. K. Grewal. 2008. Mammalian glycosylation in immunity. Nature Reviews Immunology 8(11):874-887. Martin-Pastor, M., A. Canales-Mayordomo, and J. Jimenez-Barbero. 2003. NMR experiments for the measurement of proton-proton and carbon-carbon residual dipolar couplings in uniformly labelled oligosaccharides. Journal of Biomolecular NMR 26(4):345-353. McEver, R. P. 2010. Rolling back neutrophil adhesion. Nature Immunology 11(4):282-284. McEver, R. P., and C. Zhu. 2010. Rolling cell adhesion. Annual Review of Cell and Developmen- tal Biology 26:363-396. McGowan E. D., and K. Bowman. 2010. Background Paper on Glycosciences and Glycomics in the United States. Board on Chemical Sciences and Technology and Board on Life Sciences, National Research Council. McLellan J. S., M. Pancera, C. Carrico, J. Gorman, J. P. Julien, R. Khayat, R. Louder, R. Pejchal, M. Sastry, K. Dai, S. O'Dell, N. Patel, S. Shahzad-ul-Hussan, Y. Yang, B. Zhang, T. Zhou, J. Zhu, J. C. Boyington, G. Y. Chuang, D. Diwanji, I. Georgiev, Y. D. Kwon, D. Lee, M. K. Louder, S. Moquin, S. D. Schmidt, Z. Y. Yang, M. Bonsignori, J. A. Crump, S. H. Kapiga, N. E. Sam, B. F. Haynes, D. R. Burton, W. C. Koff, L. M. Walker, S. Phogat, R. Wyatt, J. Orwenyo, L. X. Wang, J. Arthos, C. A. Bewley, J. R. Mascola, G. J. Nabel, W. R. Schief, A. B. Ward, I. A. Wilson, and P. D. Kwong. 2011. Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature 480(7377):336-343. Meany, D. L., and D. W. Chan. 2011. Aberrant glycosylation associated with enzymes as cancer biomarkers. Clinical Proteomics 8(1):7. Mendonca, S., R. B. Cole, J. Zhu, Y. Cai, A. D. French, G. P. Johnson, and R. A. Laine. 2003. Incremented alkyl derivatives enhance collision induced glycosidic bond cleavage in mass spectrometry of disaccharides. Journal of the American Society for Mass Spectrometry 14(1):63-78.

OCR for page 143
REFERENCES 153 Moon, R. J., A. Martini, J. Nairn, J. Simonsen, and J. Youngblood. 2011. Cellulose nano- materials review: Structure, properties and nanocomposites. Chemical Society Reviews 40(7):3941-3994. Morelle, W., and J. C. Michalski. 2005. The mass spectrometric analysis of glycoproteins and their glycan structures. Current Analytical Chemistry 1(1):29-57. Morelli, L., L. Poletti, and L. Lay. 2011. Carbohydrates and immunology: Synthetic oligo- saccharide antigens for vaccine formulation. European Journal of Organic Chemistry 29:5723-5777. Morgan, W. T. J., and W. M. Watkins. 1969. Genetic and biochemical aspects of human blood group A- B- H- LEA- and LEB- specificity. British Medical Bulletin 25(1):30. Muntoni, F., S. Torelli, D. J. Wells, and S. C. Brown. 2011. Muscular dystrophies due to gly- cosylation defects: Diagnosis and therapeutic strategies. Current Opinion in Neurology 24(5):437-442. Narimatsu, H. 2006. Human glycogene cloning: Focus on beta 3-glycosyltransferase and beta 4-glycosyltransferase families. Current Opinion in Structural Biology 16(5):567-575. National Research Council. 2011. Life Science and Related Fields: Trends Relevant to the Biological Weapons Convention. Washington, DC: National Academies Press. Newburg, D. S., G. M. Ruiz-Palacios, and A. L. Morrow. 2005. Human milk glycans protect infants against enteric pathogens. Annual Review of Nutrition 25:37-58. Nieuwdorp, M., M. C. Meuwese, H. Vink, J. B. L. Hoekstra, J. J. P. Kastelein, and E. S. G. Stroes. 2005. The endothelial glycocalyx: A potential barrier between health and vas- cular disease. Current Opinion in Lipidology 16(5):507-511. Nyame, A. K., Z. S. Kawar, and R. D. Cummings. 2004. Antigenic glycans in parasitic infec- tions: Implications for vaccines and diagnostics. Archives of Biochemistry and Biophysics 426(2):182-200. Ohtsubo, K., and J. D. Marth. 2006. Glycosylation in cellular mechanisms of health and disease. Cell 126(5):855-867. Ohtsubo, K., M. Z. Chen, J. M. Olefsky, and J. D. Marth. 2011. Pathway to diabetes through attenuation of pancreatic beta cell glycosylation and glucose transport. Nature Medicine 17(9):1067-1075. Okahisa Y., A. Yoshida, S. Miyaguch, and H. Yano. 2009. Optically transparent wood cel- lulose nanocomposites as a base substrate for flexible organic light-emitting diode displays. Composites Science and Technology 69:1958-1961. Olson, D. G., J. E. McBride, A. J. Shaw, and L. R. Lynd. 2011. Recent progress in consolidated bioprocessing. Current Opinion in Biotechnology 23(3):396-405. Olsson, M. L., and H. Clausen. 2008. Modifying the red cell surface: Towards an ABO- universal blood supply. British Journal of Haematology 140(1):3-12. O'Reilly, M. K., and J. C. Paulson. 2009. Siglecs as targets for therapy in immune-cell- mediated disease. Trends in Pharmacological Sciences 30(5):240-248. Packer, N., C. von der Lieth, K. Aoki-Kinoshita, C. Lebrilla, J. Paulson, R. Raman, P. Rudd, R. Sasisekharan, N. Taniguchi, and W. York. 2008. Frontiers in glycomics: Bioinformatics and biomarkers in disease. Proteomics 8(1):8-20. Palcic, M. M. 2011. Glycosyltransferases as biocatalysts. Current Opinion in Chemical Biology 15(2):226-233. Park, Y. M., and C. B. Lebrilla. 2005. Application of Fourier transform ion cyclotron reso- nance mass spectrometry to oligosaccharides. Mass Spectrometry Reviews 24(2):232-264. Pejchal R., K. J. Doores, L. M. Walker, R. Khayat, P. S. Huang, S. K. Wang, R. L. Stanfield, J. P. Julien, A. Ramos, M. Crispin, R. Depetris, U. Katpally, A. Marozsan, A. Cupo, S. Maloveste, Y. Liu, R. McBride, Y. Ito, R. W. Sanders, C. Ogohara, J. C. Paulson, T. Feizi, C. N. Scanlan, C. H. Wong, J. P. Moore, W. C. Olson, A. B. Ward, P. Poignard, W. R. Schief, D. R. Burton, and I. A. Wilson. 2011. A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield. Science 334(6059):1097-1103.

OCR for page 143
154 TRANSFORMING GLYCOSCIENCE Perlack, R. D., L. L. Wright, A. F. Turhollow, R. L. Graham, B. J. Stokes, and D. C. Erbach. Biomass as Feedstock for a Bioenergy and Bioproducts Industry: The Technical Feasibility of a Billion-Ton Annual Supply (U.S. Department of Energy and U.S. Department of Agri- culture, April 2005; Available at feedstockreview.ornl.gov/pdf/billion_ton_vision.pdf [accessed August 1, 2012]). Petitou, M., and C. A. van Boeckel. 2004. A synthetic antithrombin III binding pentasac- charide is now a drug! What comes next? Angewandte Chemie, International Edition in English 43(24):3118-3133. Pieters, R. J. 2011. Carbohydrate mediated bacterial adhesion. Bacterial Adhesion: Chemistry, Biology and Physics 715:227-240. Pinho, S. S., R. Seruca, F. Gartner, Y. Yamaguchi, J. G. Gu, N. Taniguchi, and C. A. Reis. 2011. Modulation of E-cadherin function and dysfunction by N-glycosylation. Cellular and Molecular Life Sciences 68(6):1011-1020. Porter, A., T. Yue, L. Heeringa, S. Day, E. Suh, and B. B. Haab. 2010. A motif-based analysis of glycan array data to determine the specificities of glycan-binding proteins. Glycobiol- ogy 20(3):369-380. Price, J. L., D. Shental-Bechor, A. Dhar, M. J. Turner, E. T. Powers, M. Gruebele, Y. Levy, and J. W. Kelly. 2010. Context-dependent effects of asparagine glycosylation on pin WW folding kinetics and thermodynamics. Journal of the American Chemical Society 132(43):15359-15367. Qua, E. H., P. R. Hornsby, H. S. S. Sharma, and G. Lyons. 2011. Preparation and characterisa- tion of cellulose nanofibres. Journal of Materials Science 46(18): 6029-6045. Rabinovich, G. A., and M. A. Toscano. 2009. Turning "sweet" on immunity: Galectin-glycan interactions in immune tolerance and inflammation. Nature Reviews Immunology 9(5): 338-352. Rabinovich, G. A., M. A. Toscanol, S. S. Jackson, and G. R. Vasta. 2007. Functions of cell surface galectin-glycoprotein lattices. Current Opinion in Structural Biology 17(5):513-520. Raju, T. S. 2008. Terminal sugars of Fc glycans influence antibody effector functions of IgGs. Current Opinion in Immunology 20(4):471-478. Rambaruth, N. D. S., and M. V. Dwek. 2011. Cell surface glycan-lectin interactions in tumor metastasis. Acta Histochemica 113(6):591-600. Ramirez-Correa, G. A., W. H. Jin, Z. H. Wang, X. Zhong, W. D. Gao, W. B. Dias, C. Vecoli, G. W. Hart, and A. M. Murphy. 2008. O-Linked GlcNAc modification of cardiac myo- filament proteins. Circulation Research 103(12):1354-1358. Ramya, T. N. C., E. Weerapana, L. Liao, Y. Zeng, H. Tateno, L. Liao, J. R. Yates III, B. F. Cravatt, and J. C. Paulson. 2010. In situ trans ligands of CD22 identified by glycan-protein photocross-linking-enabled proteomics. Molecular and Cellular Proteomics 9(6):1339-1351. Ranzinger, R., S. Herget, C. W. von der Lieth, and M. Frank. 2011. GlycomeDB--a unified da- tabase for carbohydrate structures. Nucleic Acids Research 39(Database issue):D373-D376. Raska, M., and J. Novak. 2010. Involvement of envelope-glycoprotein glycans in HIV-1 biology and infection. Archivum Immunologiae et Therapiae Experimentalis 58(3):191-208. Rehm, B. H. A. 2010. Bacterial polymers: Biosynthesis, modifications and applications. Na- ture Reviews Microbiology 8(8):578-592. Reis, C. A., H. Osorio, L. Silva, C. Gomes, and L. David. 2010. Alterations in glycosylation as biomarkers for cancer detection. Journal of Clinical Pathology 63(4):322-329. Rexach, J. E., P. M. Clark, D. E. Mason, R. L. Neve, E. C. Peters, and L. C. Hsieh-Wilson. 2012. Dynamic O-GlcNAc modification regulates CREB-mediated gene expression and memory formation. Nature Chemical Biology 8(3):253-261. Rich, J. R., and S. G. Withers. 2009. Emerging methods for the production of homogeneous human glycoproteins. Nature Chemical Biology 5(4):206-215. Rillahan, C. D., and J. C. Paulson. 2011. Glycan microarrays for decoding the glycome. An- nual Review of Biochemistry 80:797-823.

OCR for page 143
REFERENCES 155 Rillahan, C. D., S. J. Brown, A. C. Register, H. Rosen, and J. C. Paulson. 2011. High-through- put screening for inhibitors of sialyl- and fucosyltransferases. Angewandte Chemie, International Edition 50(52):12534-12537. Roy, D., M. Semsarilar, J. T. Guthrie, and S. Perrier. 2009. Cellulose modification by polymer grafting: A review. Chemical Society Reviews 38(7):2046-2064. Rubin, E. M. 2008. Genomics of cellulosic biofuels. Nature 454:841-845. Rudd, P. M., and R. A. Dwek. 1997. Glycosylation: Heterogeneity and the 3D structure of proteins. Critical Reviews in Biochemistry and Molecular Biology 32(1):1-100. Sackstein, R. 2009. Glycosyltransferase-Programmed Stereosubstitution (GPS) to create HCELL: Engineering a roadmap for cell migration. Immunological Reviews 230:140-163 Sahoo, S., C. Thomas, A. Sheth, C. Henson, and W. York. 2005. GLYDE--an expressive XML standard for the representation of glycan structure. Carbohydrate Research 340(18):2802-2807. Satoh, T., Y. Kanai, M. H. Wu, H. Yokozeki, R. Kannagi, J. B. Lowe, and K. Nishioka. 2005. Synthesis of alpha(1,3) fucosyltransferases IV- and VII-dependent eosinophil selectin ligand and recruitment to the skin. American Journal of Pathology 167(3):787-796. Satoh, M., S. Iida, and K. Shitara. 2006. Non-fucosylated therapeutic antibodies as next- generation therapeutic antibodies. Expert Opinion on Biological Therapy 6(11):1161-1173. Sauerzapfe, B., K. Krenek, J. Schmiedel, W. W. Wakarchuk, H. Pelantova, V. Kren, and L. Elling. 2009. Chemo-enzymatic synthesis of poly-N-acetyllactosamine (poly-LacNAc) structures and their characterization for CGL2-galectin-mediated binding of ECM gly- coproteins to biomaterial surfaces. Glycoconjugate Journal 26(2):141-159. Schaffer, R. 1972. Occurrence, properties, and preparation of naturally occurring monosac- charides (including 6-deoxy sugars). Pp. 69-111 in The Carbohydrates, Chemistry and Biochemistry. W. Pigman and D. Horton, eds. New York: Academic Press. Schauer, R. 2009. Sialic acids as regulators of molecular and cellular interactions. Current Opinion in Structural Biology 19(5):507-514. Schmaltz, R. M., S. R. Hanson, and C. H. Wong. 2011. Enzymes in the synthesis of glycocon- jugates. Chemical Reviews 111(7):4259-4307. Schulze, H., and K. Sandhoff. 2011. Lysosomal lipid storage diseases. Cold Spring Harbor Perspectives in Biology 3(6). Seeberger, P. H. 2008. Automated oligosaccharide synthesis. Chemical Society Reviews 37(1):19-28. Seeberger, P. H., and D. B. Werz. 2007. Synthesis and medical applications of oligosaccha- rides. Nature 446(7139):1046-1051. Sethuraman, N., and T. A. Stadheim. 2006. Challenges in therapeutic glycoprotein produc- tion. Current Opinion in Biotechnology 17(4):341-346. Sharon, N., and H. Lis. 2004. History of lectins: From hemagglutinins to biological recogni- tion molecules. Glycobiology 14(11):53R-62R. Shriver, Z., S. Raguram, and R. Sasisekharan. 2004. Glycomics: A pathway to a class of new and improved therapeutics. Nature Reviews Drug Discovery 3(10):863-873. Silva, Z., K. Konstantopoulos, and P. A. Videira. 2012. The role of sugars in dendritic cell trafficking. Annals of Biomedical Engineering 40(4):777-789. Skorobogatko, Y. V., J. Deuso, J. Adolf-Bergfoyle, M. G. Nowak, Y. S. Gong, C. F. Lippa, and K. Vosseller. 2011. Human Alzheimer's disease synaptic O-GlcNAc site map- ping and iTRAQ expression proteomics with ion trap mass spectrometry. Amino Acids 40(3):765-779. Skrisovska, L., M. Schubert, and F. H. T. Allain. 2010. Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins. Journal of Biomolecular NMR 46(1):51-65. Slawson, C., and G. W. Hart. 2011. O-GlcNAc signalling: Implications for cancer cell biology. Nature Reviews Cancer 11(9):678-684.

OCR for page 143
156 TRANSFORMING GLYCOSCIENCE Slawson, C., R. J. Copeland, and G. W. Hart. 2010. O-GlcNAc signaling: A metabolic link between diabetes and cancer? Trends in Biochemical Sciences 35(10):547-555. Sletten, E. M., and C. R. Bertozzi. 2011. From mechanism to mouse: A tale of two bioorthogo- nal reactions. Accounts of Chemical Research 44(9):666-676. Smith, D. F., X. Z. Song, and R. D. Cummings. 2010. Use of glycan microarrays to explore specificity of glycan-binding proteins. Methods in Enzymology 480:417-444. Solomon, S. S., G. Majumdar, A. Martinez-Hernandez, and R. Raghow. 2008. A critical role of Sp1 transcription factor in regulating gene expression in response to insulin and other hormones. Life Sciences 83(9-10):305-312. Sorokin, L. 2010. The impact of the extracellular matrix on inflammation. Nature Reviews Immunology 10(10):712-723. Sperandio, M., C. A. Gleissner, and K. Ley. 2009. Glycosylation in immune cell trafficking. Immunological Reviews 230(1):97-113. St Hill, C. A. 2011. Interactions between endothelial selectins and cancer cells regulate me- tastasis. Frontiers in Bioscience-Landmark 16:3233-3251. Stanford, K. I., J. R. Bishop, E. M. Foley, J. C. Gonzales, I. R. Niesman, J. L. Witztum, and J. D. Esko. 2009. Syndecan-1 is the primary heparan sulfate proteoglycan mediating hepatic clearance of triglyceride-rich lipoproteins in mice. Journal of Clinical Investiga- tion 119(11):3236-3245. Stevens, J., O. Blixt, J. C. Paulson, and I. A. Wilson. 2006. Glycan microarray technolo- gies: Tools to survey host specificity of influenza viruses. Nature Reviews Microbiology 4(11):857-864. Stockert, R. J. 1995. The asialoglycoprotein receptor--relationships between structure, func- tion, and expression. Physiological Reviews 75(3):591-609. Tallent, M. K., N. Varghis, Y. Skorobogatko, L. Hernandez-Cuebas, K. Whelan, D. J. Vocadlo, and K. Vosseller. 2009. In vivo modulation of O-GlcNAc levels regulates hippocampal synaptic plasticity through interplay with phosphorylation. Journal of Biological Chem- istry 284(1):174-181. Tannock, L. R., and V. L. King. 2008. Proteoglycan mediated lipoprotein retention: A mecha- nism of diabetic atherosclerosis. Reviews in Endocrine & Metabolic Disorders 9(4):289-300. Tao, N. A., S. A. Wu, J. Kim, H. J. An, K. Hinde, M. L. Power, P. Gagneux, J. B. German, and C. B. Lebrilla. 2011. Evolutionary glycomics: Characterization of milk oligosaccharides in primates. Journal of Proteome Research 10(4):1548-1557. Taylor, M. E., and K. Drickamer. 2007. Paradigms for glycan-binding receptors in cell adhe- sion. Current Opinion in Cell Biology 19(5):572-577. Taylor, M. E., and K. Drickamer. 2009. Structural insights into what glycan arrays tell us about how glycan-binding proteins interact with their ligands. Glycobiology 19(11):1155-1162. Teo, C. F., E. E. Wollaston-Hayden, and L. Wells. 2010. Hexosamine flux, the O-GlcNAc modification, and the development of insulin resistance in adipocytes. Molecular and Cellular Endocrinology 318(1-2):44-53. Tillett, W. S., and T. Francis. 1929. Cutaneous reactions to the polysaccharides and proteins of pneumococcus in lobar pneumonia. Journal of Experimental Medicine 50(5):687-701. Tilman, D., R. Socolow, J. A. Foley, J. Hill, E. Larson, L. Lynd, S. Pacala, J. Reilly, T. Search- inger, C. Somerville, and R. Williams. 2009. Beneficial biofuels--the food, energy, and environment trilemma. Science 325(5938):270-271. Tumpey, T. M., T. R. Maines, N. Van Hoeven, L. Glaser, A. Solorzano, C. Pappas, N. J. Cox, D. E. Swayne, P. Palese, J. M. Katz, and A. Garcia-Sastre. 2007. A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission. Science 315(5812):655-659. Van de Vyver S., J. Geboers, P. A. Jacobs, and B. F. Sels. 2011. Recent advances in the catalytic conversion of cellulose. ChemCatChem 3:82-94.

OCR for page 143
REFERENCES 157 van Kooyk, Y., and G. A. Rabinovich. 2008. Protein-glycan interactions in the control of in- nate and adaptive immune responses. Nature Immunology 9(6):593-601. Varki, A. 1993. Biological roles of oligosaccharides--all of the theories are correct. Glycobiol- ogy 3(2):97-130. Varki, A. 2006. Nothing in glycobiology makes sense, except in the light of evolution. Cell 126(5):841-845. Varki, A. 2007. Glycan-based interactions involving vertebrate sialic-acid-recognizing pro- teins. Nature 446(7139):1023-1029. Varki, A. 2011. Since there are PAMPs and DAMPs, there must be SAMPs? Glycan "self- associated molecular patterns" dampen innate immunity, but pathogens can mimic them. Glycobiology 21(9):1121-1124. Varki, A., R. D. Cummings, J. D. Esko, H. H. Freeze, P. Stanley, C. R. Bertozzi, G. W. Hart, and M. E. Etzler. 2009. Essentials of Glycobiology. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Vartiainen J., T. Pohler, K. Sirola, L. Pylkkanen, H. Alenius, J. Hokkinen, U. Tapper, P. Lahtinen, A. Kapanen, K. Putkisto, P. Hiekkataipale, P. Eronen, J. Ruokolainen, and A. Laukkanen 2011. Health and environmental safety aspects of fiction grinding and spray drying of microfibrillated cellulose. Cellulose 18:775-786. Vasiliu, D., N. Razi, Y. Zhang, N. Jacobsen, K. Allin, X. Liu, J. Hoffmann, O. Bohorov, and O. Blixt. 2006. Large-scale chemoenzymatic synthesis of blood group and tumor- associated poly-N-acetyllactosamine antigens. Carbohydrate Research 341(10):1447-1457. Voet, D., and J. G. Voet. 2010. Biochemistry, 4th Edition. John Wiley & Sons Viswanathan, K., A. Chandrasekaran, A. Srinivasan, R. Raman, V. Sasisekharan, and R. Sasisekharan. 2010. Glycans as receptors for influenza pathogenesis. Glycoconjugate Journal 27(6):561-570. Wagner R., R. J. Moon, and A. Raman. 2011. Uncertainty quantification in nanomechanical measurements using the atomic force microscope. Nanotechnology 22(45):455703. Walker L. M., D. Sok, Y. Nishimura, O. Donau, R. Sadjadpour, R. Gautam, M. Shingai, R. Pejchal, A. Ramos, M. D. Simek, Y. Geng, I. A. Wilson, P. Poignard, M. A. Martin, and D. R. Burton. 2011. Rapid development of glycan-specific, broad, and potent anti-HIV-1 gp120 neutralizing antibodies in an R5 SIV/HIV chimeric virus infected macaque. Proceedings of the National Academy of Sciences of the United States of America 108(50):20125-20129. Walsh, G., and R. Jefferis. 2006. Post-translational modifications in the context of therapeutic proteins. Nature Biotechnology 24(10):1241-1252. Wang, C. C., J. C. Lee, S. Y. Luo, S. S. Kulkarni, Y. W. Huang, C. C. Lee, K. L. Chang, and S. C. Hung. 2007. Regioselective one-pot protection of carbohydrates. Nature 446(7138): 896-899. Wang, A. M., C. de la Motte, M. Lauer, and V. Hascall. 2011. Hyaluronan matrices in patho- biological processes. FEBS Journal 278(9):1412-1418. Wang, L.-X., and J. V. Lomino. 2012. Emerging technologies for making glycan-defined glycoproteins. ACS Chemical Biology 7(1):110-122. Wetterstrand, K. A. 2012. DNA Sequencing Costs: Data from the NHGRI Large-Scale Ge- nome Sequencing Program. Available at www.genome.gov/sequencingcosts [accessed August 16, 2012]. Werz, D. B., R. Ranzinger, S. Herget, A. Adibekian, C. W. von der Lieth, and P. H. Seeberger. 2007. Exploring the structural diversity of mammalian carbohydrates ("Glycospace") by statistical databank analysis. ACS Chemical Biology 2(10):685-691. Williams, N. R., and J. D. Wander. 1980. Deoxy and branched-chain sugars. Pp. 761-798 in The Carbohydrates, Chemistry and Biochemistry. W. Pigman, D. Horton, and J. D. Wander, eds. New York: Academic Press.

OCR for page 143
158 TRANSFORMING GLYCOSCIENCE Wu, C. Y., P. H. Liang, and C. H. Wong. 2009. New development of glycan arrays. Organic & Biomolecular Chemistry 7(11):2247-2254. Xu, Y., S. Masuko, M. Takieddin, H. Xu, R. Liu, J. Jing, S. A. Mousa, R. J. Linhardt, and J. Liu. 2011. Chemoenzymatic synthesis of homogeneous ultralow molecular weight heparins. Science 334(6055):498-501. Yamada, T. 2011. Therapeutic monoclonal antibodies. The Keio Journal of Medicine 60(2):37-46. Yu, F., and J. H. Prestegard. 2006. Structural monitoring of oligosaccharides through 13C enrichment and NMR observation of acetyl groups. Biophysical Journal 91(5):1952-1959. Yu, H., S. Huang, H. Chokhawala, M. Sun, H. Zheng, and X. Chen. 2006. Highly efficient che- moenzymatic synthesis of naturally occurring and non-natural alpha-2,6-linked sialo- sides: A P. damsela alpha-2,6-sialyltransferase with extremely flexible donor-substrate specificity. Angewandte Chemie, International Edition 45(24):3938-3944. Yuzwa, S. A., X. Shan, M. S. Macauley, T. Clark, Y. Skorobogatko, K. Vosseller, and D. J. Vocadlo. 2012. Increasing O-GlcNAc slows neurodegeneration and stabilizes tau against aggregation. Nature Chemical Biology 8:393-399. Zaia, J. 2004. Mass spectrometry of oligosaccharides. Mass Spectrum Reviews 23(3):161-227. Zarbock, A., K. Ley, R. P. McEver, and A. Hidalgo. 2011. Leukocyte ligands for endothelial selectins: Specialized glycoconjugates that mediate rolling and signaling under flow. Blood 118(26):6743-6751. Zhang, H., S. Singh, and V. N. Reinhold. 2005. Congruent strategies for carbohydrate se- quencing. 2. FragLib: An MSn spectral library. Analytical Chemistry 77(19):6263-6270. Zhang, N., L. Liu, C. D. Dumitru, R. N. Cummings, M. Cukan, Y. Jiang, Y. Li, F. Li, T. Mitchell, M. R. Mallem, Y. Ou, R. N. Patel, K. Vo, H. Wang, I. Burnina, B. K. Choi, H. E. Huber, T. A. Stadheim, and D. Zha. 2011. Glycoengineered Pichia produced anti-HER2 is comparable to trastuzumab in preclinical study. mAbs 3(3):289-298. Zheng, T., H. Jiang, M. Gros, D. S. del Amo, S. Sundaram, G. Lauvau, F. Marlow, Y. Liu, P. Stanley, and P. Wu. 2011. Tracking N-acetyllactosamine on cell-surface glycans in vivo. Angewandte Chemie, International Edition 50(18):4113-4118. Zhu, X. M., and R. R. Schmidt. 2009. New principles for glycoside-bond formation. Ange- wandte Chemie, International Edition 48(11):1900-1934. Zijlstra, J. M., G. Lindauer-van der Werf, O. S. Hoekstra, L. Hooft, I. I. Riphagen, and P. C. Huijgens. 2006. 18F-fluoro-deoxyglucose positron emission tomography for post- treatment evaluation of malignant lymphoma: A systematic review. Haematologica--The Hematology Journal 91(4):522-529.