Publications Since 2000

Publications in 2010

1. Langelaan, D.N. and Rainey, J.K. (2010) Membrane catalysis of peptide-receptor binding. Biochem Cell Biol 88:203-210
2. Reddy, T. and Rainey, J.K. (2010) Interpretation of biomolecular NMR spin relaxation parameters. Biochem Cell Biol 88:131-142
3. Reddy, T., Li, X., Fliegel, L., Sykes, B.D. and Rainey, J.K. (2010) Correlating structure, dynamics, and function in transmembrane segment VII of the Na⁺/H⁺ exchanger isoform 1. Biochim Biophys Acta Biomembranes 1798:94-104 [PubMed]
4. Tremblay, M-L., Banks, A.W. and Rainey, J.K. (2010) The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment. J Biomol NMR In press: [PubMed]
5. Bullerwell, C.E., Burger, G., Gott, J.M., Kourennaia, O., Schnare, M.N. and Gray, M.W. (2010) Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa. Eukaryot. Cell : in press
6. Curtis, B. A. and Archibald, J. M. (2010) Problems and progress in understanding the origins of mitochondria and plastids. Symbiosis and stress, J. Seckbach and M. Grube (eds.) Springer-Verlag, Germany:In Press
7. Doolittle, W.F. and Zhaxybayeva, O. (2010) Metagenomics and the units of biological organization. Bioscience 60:102-112
8. Gawryluk, R.M.R. and Gray, M.W. (2010) An ancient fission of mitochondrial cox1. Mol. Biol. Evol. 27: 7-10 [PubMed]
9. Gott, J.M., Somerlot, B.H. and Gray, M.W. (2010) Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA 16:482-488 [PubMed]
10. Gray, M.W. (2010) Ribonucleic acid (RNA). McGraw Hill Encyclopedia of Science & Technology : in press
11. Gray, M.W. (2010) Organelles. Brenner's Online Encyclopedia of Genetics 2E, S. Maloy and K. Hughes (eds.) Academic Press: in press
12. Hjort K., Goldberg, A. V., Tsaousis A. D., Hirt R. P., and Embley T. M. (2010) Diversity and reductive evolution of mitochondria among microbial eukaryotes Philos Trans R Soc Lond B Biol Sci 365(1541):713-727 [PubMed]
13. Hoef-Emden, K. & Archibald, J. M. (2010) Phylum Cryptophyta (Cryptomonads) In Handbook of Protoctista, Second Edition, L. Margulis (ed.) Jones and Bartlett:In Press
14. Hopkins, J. & Archibald, J. M. (2010) Plastid evolution and the nuclear genomic 'footprint' of red and green algal endosymbionts In: Red algae in the age of genomics, Seckbach, J. & Grube, M. (eds.) Springer-Verlag:In Press
15. Hug, L.A., Stechmann, A. and Roger, A.J. (2010) Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes. Mol. Biol. Evol. 27:311-324
16. Kim, E., Park, J. S., Simpson, A. G. B., Matsunaga, S. Watanabe, M., Murakami, A., Sommerfeld, K., Onodera, N. T. and Archibald, J. M. (2010) Complex array of endobionts in Petalomonas sphagnophila, a large heterotrophic euglenid protist from Sphagnum-dominated peatlands. ISME Journal Under Revision:
17. Lin, L.-J., Minard, L. V., Johnston, G. C., Singer, R. A. and Schultz, M. C. (2010) Asf1 can promote trimethylation of H3 K36 by Set2. Mol. Cell. Biol. 30: in press [PubMed]
18. Narmandakh, A., and Bearne, S.L.* (2010) Purification of recombinant mandelate racemase: Improved catalytic activity. Protein Expr. Purif. 69:39-46. [PubMed]
19. Ouazia, D., and Bearne, S.L.* (2010) A continuous assay for alpha-methylacyl-coenzyme A racemase using circular dichroism. Anal. Biochem. 398:45-51. [PubMed]
20. Roy, A.C., Lunn, F.A., and Bearne, S.L. (2010) Inhibition of CTP synthase from Escherichia coli by xanthines and uric acids Bioorg. Med. Chem. Lett. :20, 141-144. [PubMed]
21. Silver, T. D., Moore, C. E. and Archibald, J. M. (2010) Nucleomorph ribosomal DNA and telomere dynamics in chlorarachniophyte algae J. Euk. Microbiol. Under Revision:
22. Tanifuji, G. & Archibald, J. M. (2010) Actin gene family dynamics in cryptomonads and red algae J. Mol. Evol. Under review.:
23. Thirumalairajan, S., Mahaney, B., and Bearne, S.L.* (2010) Interrogation of the active site of OMP decarboxylase from Escherichia coli with a substrate analogue bearing an anionic group at C6 Chem. Comm., in press.:
24. Tsaousis, A. D., Stechmann A., Pérez-Brocal V., Hamblin K. A., van der Giezen M., and Clark C. G. (2010) The Blastocystis mitochondrion-like organelles Anaerobic Parasitic Protozoa: Genomics and Molecular Biology. Clark, C.G., Adam R.D., and Johnson P.J. (eds) Horizon Scientific Press:
25. Volkmann G, Murphy P.W., Rowland E.E., Cronan J.E. Jr, Liu X.Q., Blouin C, Byers D.M. (2010) Intein-mediated cyclization of bacterial acyl carrier protein stabilizes its folded conformation but does not abolish function. J Biol Chem. 2010 Jan 18. [Epub ahead of print]: [PubMed]
26. Volkmann, G., Murphy, P.W., Rowland, E.E., Cronan, J.E., Jr., Liu, X.Q., Blouin, C., and Byers, D.M. (2010) Intein-mediated cyclization of bacterial acyl carrier protein stabilizes its folded conformation but does not abolish function. J. Biol. Chem. 285:8605-8614 [PubMed]
27. Yoo B.H., Wu X., Li Y., Haniff M., Sasazuki T., Shirasawa S., Eskelinen E.-L. and Rosen K.V. (2010) Oncogenic ras-induced downregulation of autophagy mediator Beclin-1 is required for malignant transformation of intestinal epithelial cells. J. Biol. Chem. 285:5438-49 [PubMed]

Publications in 2009

28. Langelaan, D.N., Bebbington, E.M., Reddy, T. and Rainey, J.K. (2009) Structural insight into G-protein coupled receptor binding by apelin Biochemistry 48:537-548 [PubMed]
29. Langelaan, D.N. and Rainey, J.K. (2009) Headgroup-dependent membrane catalysis of apelin-receptor interactions is likely. J Phys Chem B 113:10465-10471 [PubMed]
30. Dellaire, G., Kepkay, R., Bazett-Jones, D.P. (2009) High resolution imaging of changes in the structure and spatial organization of chromatin, gamma-H2A.X and the MRN complex within etoposide-induced DNA repair foci. Cell Cycle 8(22):3750-3769 [PubMed]
31. Appleby, J.H., Zhou, K., Volkmann, G., and Liu, X.-Q. (2009) Novel split intein for trans-splicing synthetic peptide onto C-terminus of protein. J. Biol. Chem. 284:6194-6199 [PubMed]
32. Archibald, J. M. (2009) The origin and spread of eukaryotic photosynthesis—evolving views in light of genomics. Bot. Marina 52:95-103
33. Archibald, J. M. (2009) Secondary endosymbiosis. Encyclopedia of Microbiology, Third Edition, Schaechter, M. (ed.) Oxford: Elsevier:438-446
34. Archibald, J. M. (2009) The puzzle of plastid evolution. Curr. Biol. 19:R81-R88. [PubMed]
35. Archibald, J. M. (2009) Genomics: Green evolution, green revolution. Science 324:191-192 [PubMed]
36. Archibald, J. M., and Lane, C. E. (2009) Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. J. Heredity 100:582-590 [PubMed]
37. Blouin, C., Perry, S., Lavell, A., Susko, E. and Roger A.J. (2009) Reproducing the manual annotation of multiple sequence alignment with a SVM classifier. Bioinformatics 25:3093-3098
38. Burki, F., Inagaki, Y., Brate, J., Archibald, J. M., Keeling, P. J., Cavalier-Smith, T., Sakaguchi, M., Hashimoto, T., Horak, A., Kumar, S., Klaveness, D., Jakobsen, K. S., Pawkowski, J., & Shalchian-Tabrizi, K. (2009) Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol. Evol. 2009, 231-238 doi:10.1093/gbe/evp022:
39. Chappell, D.S., Patel, N.A., Jiang, K., Watson, J.E., Li, P., Byers, D.M., and Cooper, D.R. (2009) Functional involvement of protein kinase C-betaII and its substrate, MARCKS, in insulin-stimulated glucose transport in L6 rat skeletal muscle cells. Diabetologia 52:901-911 [PubMed]
40. Charette, J.M. and Gray, M.W. (2009) U3 snoRNA genes are multi-copy and frequently linked to U5 snRNA genes in Euglena gracilis. BMC Genomics 10:528 [PubMed]
41. Charman, M., Kennedy, B.E., Osborne, N. and Karten, B. (2009) MLN64 mediates egress of cholesterol from endosomes to mitochondria in the absence of functional Niemann-Pick Type C1 protein J. Lipid Res. in press:
42. Curwin, A.J., Fairn, G.D., and McMaster, C.R (2009) The Phospholipid Transfer Protein Sec14 is Required for Trafficking from Endosomes and Regulates Distinct trans-Golgi Export Pathways J. Biol. Chem. 284:7364-7375
43. DiPPo, J.L., Nesbo, C.L., Dahle, H., Doolittle, W.F., Birkland, N.-K. and Noll, K.M. (2009) Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid. Int J Syst Evol Microbiol. 59:2991-3000.
44. Donaher, N., Tanifuji, G., Onodera, N. T., Malfatti, S. A., Chain, P. S. G., Hara, Y., & Archibald, J. M. (2009) The complete plastid genome sequence of the secondarily non-photosynthetic alga Cryptomonas paramecium: reduction, compaction, and accellerated evolutionary rate. Genome Biol. Evol. 2009, 439-448. doi:10.1093/gbe/evp047:
45. Doolittle, W. F. (2009) The attempt on the life of the Tree of Life: science, philosophy and politics. Philosophy and Biology in press:
46. Doolittle, W. F. (2009) Eradicating typological thinking in prokaryotic systematics and evolution. Cold Spring Harbor Symposia, Quantitative Biology 74:[Aug. Epub ahead of print]
47. Doolittle, W. F. (2009) The practice of classification and the theory of evolution, and what the demise of Charles Darwin’s tree of life hypothesis means for both of them. Phil. Trans. Roy. Soc. Lond., Series B 364:2221-2228
48. Doolittle, W.F. and Zhaxybayeva, O. (2009) On the origin of prokaryotic species. Genome Research 19:744-756.
49. Elias, M. & Archibald, J. M. (2009) The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus. Gene. 442:63-72 [PubMed]
50. Elias, M. and Archibald, J. M. (2009) Sizing up the genomic footprint of endosymbiosis BioEssays 31:1273-1279 [PubMed]
51. Fernández-Murray, J.P., Gaspard, G.J., Jesch, S.A., and McMaster, C.R. (2009) Phosphatidylcholine Phospholipase B Neuropathy Target Esterase 1 (Nte1) Regulates Transcription of Phospholipid Biosynthetic Genes J. Biol. Chem. In press:
52. Gaston, D., Tsaousis, A.D. and Roger A.J. (2009) Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data. Methods Enzymol. 457:21-41 [PubMed]
53. Gawryluk, R.M.R. and Gray, M.W. (2009) A split and rearranged nuclear gene encoding the iron-sulfur subunit of mitochondrial succinate dehydrogenase in Euglenozoa. BMC Res. Notes 2:16 [PubMed]
54. Gehrig, K., Lagace, T.A., and Ridgway, N. D. (2009) Oxysterol activation of phosphatidylcholine synthesis involves CTP:phosphocholine cytidylyltransferase α translocation to the nuclear envelope Biochem. J. 418:209-217 [PubMed]
55. Gehrig, K., Morton, C.M. and Ridgway, N. D. (2009) Nuclear Export of CTP:phosphocholine cytidylyltransferase (CCT)α is Mediated by the Domain M Amphipathic Helix J. Lipid Res. 50:966-976 [PubMed]
56. Gray, M.W. (2009) RNA editing in plant mitochondria: 20 years later. IUBMB Life 61:1101-1104 [PubMed]
57. Gray, M.W. (2009) The path to RNA editing in plant mitochondria: the Halifax chapter. IUBMB Life 61:1114-1117 [PubMed]
58. Hampl, V., Hug, L.A., Leigh, J.W., Dacks, J.B., Lang, B.F., Simpson, A.G.B. and Roger, A.J. (2009) Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc. Natl. Acad. Sci. USA 106:3859-3864
59. Jezbera, J., Sharma, A.K., Brandt, U., Doolittle, W.F. and Hahn, M.W. (2009) Candidatus Planktophila limnetica’, an Actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton. IJSEM 59:2864-2869.
60. Joss MJ, Koenig JE, Labbate M, Polz MF, Gillings MR, Stokes HW, Doolittle WF, Boucher Y. (2009) ACID: annotation of cassette and integron data. BMC Bioinformatics 21:118
61. Kamikawa, R., Sanchez-Perez, G.F., Sako, Y., Roger, A.J. and Inagaki, Y. (2009) Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes. Mol. Phylogenet. Evol. 53:565-570
62. Koenig, J.E., Sharp, C., Dlutek, M., Curtis, B., Joss, M., Boucher, Y. and Doolittle, W.F. (2009) Integron Gene Cassettes and Degradation of Compounds Associated with Industrial Waste: The Case of the Sydney Tar Ponds. PLoS One 4:e5276
63. Lane, C. E. & Archibald, J. M. (2009) Reply to Bodyl, Stiller and Mackiewicz: Chromalveolate plastids Trends Ecol. Evol. 24:121-122
64. Lane, C. E. & Archibald, J. M. (2009) Reply to Bodyl, Stiller and Mackiewicz: "Chromalveolate plastids: direct descent or multiple endosymbioses?" Trends Ecol. Evol. 24:121-122 [PubMed]
65. LeBlanc, M.A., and McMaster, C.R. (2009) Surprising Roles for Phospholipid Binding Proteins Revealed by High Throughput Genetics Biochem. Cell Biol. In press:
66. Li H., Ray G., Yoo B.H., Erdogan M. and Rosen K.V. (2009) Downregulation of DAP kinase-2 is required for beta-catenin-induced anoikis resistance of malignant epithelial cells. J. Biol. Chem. 284:2012-2022 [PubMed]
67. MacKinnon, M.A., Curwin, A.J., Gaspard, G.J., Suraci, A.B., Fernández-Murray, J.P., McMaster, C.R. (2009) The Kap60/Kap95 Karyopherin Complex Directly Regulates Phosphatidylcholine Synthesis J. Biol. Chem. 284:7376-7384
68. Majdalawieh, A. and Ro, H.-S. (2009) LPS-induced suppression of macrophage cholesterol efflux is mediated by adipocyte enhancer-binding protein 1. Int. J. Biochem. Cell Biol. 41:1518-1525 [PubMed]
69. Moore, C. & Archibald, J. M. (2009) Nucleomorph genomes. Annu. Rev. Genet. 43:251-264
70. Nath-Sain, S and Marignani, P. A. (2009) LKB1 catalytic activity contributes to estrogen receptor alpha signaling. Molecular Biology of the Cell 20:2785-2795 [PubMed]
71. Nesbo¸ CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, and Doolittle WF (2009) The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol. 191:1974-78.
72. Nesbø CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, Doolittle WF. (2009) The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J. Bact E-pub, Jan 5: [PubMed]
73. Ngo, M. and Ridgway, N. D. (2009) Oxysterol Binding Protein (OSBP)-related Protein 9 (ORP9) Is a Cholesterol Transfer Protein that Regulates Golgi Structure and Function. Mol. Biol. Cell 20:1388-1399 [PubMed]
74. Ota, S., Silver, T. D., Archibald, J. M. & Ishida, K.-I. (2009) Lotharella oceanica sp. nov.—a new planktonic chlorarachniophyte studied by light and electron microscopy. Phycologia 48:317-325.
75. O’Donnell, A. F., Stevens, J. R., Kepkay, R., Barnes, C. A., Johnston, G. C. and Singer, R. A. (2009) New mutant versions of yeast FACT subunit Spt16 affect cell integrity. Mol. Genet. Genomics 282:487-502 [PubMed]
76. Potrykus, J., Flemming, J., and Bearne, S.L.* (2009) Kinetic Characterization and Quaternary Structure of Glutamate Racemase from the Periodontal Anaerobe Fusobacterium nucleatum Arch. Biochem. Biophys. 491:16-24. [PubMed]
77. Schindler, C., Rodriguez, F., Poon, P. P., Singer, R. A., Johnston, G. C. and Spang, A. (2009) The GAP domain and the SNARE, coatomer and cargo interaction region of the ArfGAP2/3 Glo3 are sufficient for Glo3 function. Traffic 10:1362-1375 [PubMed]
78. Sharma, A.K., Sommerfeld, K., Bullerjahn, G.S., Matteson, A.R., Wilhelm, S.W., Jezbera, J., Brandt, U., Doolittle, W.F. and Hahn, M.W. (2009) Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria. ISME J. 3:726-37
79. Soundararajan, R., Robertson, G., and Marignani, P. A. (2009) Triptolide: an inhibitor of a disintegrin and metalloproteinase 10 (ADAM10) in cancer cells. Cancer Biology and Therapy in press:
80. Susko, E. and Roger, A.J. (2009) Statistical analysis of expressed sequence tags. Expressed Sequence Tags (ESTs): Generation and Analysis, Vol. 533, Humana Press Inc.:277-287
81. Thomas, L.N., Douglas, R.C., Rittmaster, R.S. and Too, C.K.L. (2009) Overexpression of 5α-reductase Type 1 causes increased sensitivity to low concentrations of testosterone in LnGK9 prostate cancer cells. The Prostate 69 :595-602. [PubMed]
82. Volkmann, G. and Liu, P. X.-Q. (2009) Protein C-terminal labeling and biotinylation using synthetic peptide and split-intein. PLoS ONE 4(12):e8381 [PubMed]
83. Volkmann, G., Sun, W., and Liu, P. X.-Q. (2009) Controllable protein cleavages through intein fragment complementation. Protein Sci. 18:2393-2402 [PubMed]
84. Wang, H.-C., Susko, E. and Roger, A.J. (2009) PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specfic covarion pattern analysis. BMC Evol. Biol. 9:225-237
85. Wang, L., Martin, D. D. O., Genter, E., Wang, J., McLeod, R. S., and Small, D. M. (2009) Surface study of apoB1694-1880, a sequence which can anchor apoB to lipoproteins and makes it nonexchangeable. J. Lipid Res. in press.:
86. Yoo B.H., Wu X., Derouet M., Haniff M., Eskelinen E.-L. and Rosen K.V. (2009) Hypoxia-induced downregulation of autophagy mediator Beclin-1 reduces the susceptibility of malignant intestinal epithelial cells to hypoxia-dependent apoptosis. Autophagy 5:1166-79 [PubMed]
87. Zhaxybayeva, O., Doolittle, W.F., Papke, R.T. and Gogarten, J.P. (2009) Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biol. Evol. 2009:325-339
88. Zhaxybayeva, O., Swithers, K., Lapierre, P., Fournier, G., Bickhard, D., DeBoy, R.T., Nelson, K.E., Nesbø, C.L., Doolittle, W.F., Gogarten, J.P. and Noll, K.M. (2009) On the Chimeric Nature, Thermophilic Origin and Phylogenetic Placement of the Thermotogales. PNAS 106:5865-70

Publications in 2008

89. Reddy, T., Ding, J., Li, X., Sykes, B.D., Rainey, J.K. and Fliegel, L. (2008) Structural and functional characterization of transmembrane segment IX of the NHE1 isoform of the Na⁺/H⁺ exchanger. J. Biol. Chem. 283:22018-22030 [PubMed]
90. Abdelmagid, S. A. Too, C. K. L. (2008) Prolactin and Estrogen Upregulate Carboxypeptidase-D to Promote Nitric Oxide Production and Survival of MCF-7 Breast Cancer Cells. Endocrinology 149:4821-4828 [PubMed]
91. Archibald, J. M. (2008) Plastid evolution: remant algal genes in ciliates. Curr. Biol. 18:663-665
92. Archibald, J. M. (2008) The eocyte hypothesis and the origin of eukaryotic cells. Proc. Natl. Acad. Sci. USA 51:20049-20050 [PubMed]
93. Arora P.D., Marignani, P. A.and McCulloch C. A. (2008) Collagen phagocytosis is regulated by the guanine nucleotide exchange factor Vav2. Am J Physiol Cell Physiol. in press April 23, 2008:
94. Arora, P.D, Marignani, P.A, and McCulloch, C.A. (2008) Collagen phagocytosis is regulated by the guanine nucleotide exchange factor Vav2. Am J Physiol Cell Physiol. 295(1):C130-7 [PubMed]
95. Bapteste, E., Susko, E., Leigh, J., Ruiz-Trillo, I., Bucknam, J. & Doolittle, W.F. (2008) Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol. Biol. Evol. 25:83-91
96. Beiko, R.G., Doolittle, W.F. and Charlebois, R.L. (2008) The impact of reticulate evolution on genome phylogeny. Systematic Biol. 57:844-56.
97. Bourque, J.R., and Bearne, S.L.* (2008) Mutational Analysis of the Active Site Flap (20s Loop) of Mandelate Racemase. Biochemistry 47:566-578 [PubMed]
98. Bowden, K. and Ridgway, N. D. (2008) Oxysterol binding protein (OSBP) negatively regulates ATP binding cassette transporter A1 (ABCA1) protein stability J. Biol. Chem. 283:18210-18217 [PubMed]
99. Cavalier-Smith, T., Chao, E.E., Stechmann, A., Oates, B., Nikolaev, S. (2008) Planomonadida ord. nov. (Apusozoa): Ultrastructural Affinity with Micronuclearia podoventralis and Deep Divergences within Planomonas gen. nov. Protist 159(4):535-562 [PubMed]
100. Clow, K.A., Ewart, K.V., Driedzic, W.R. (2008) Low temperature directly activates the initial glycerol antifreeze response in isolated rainbow smelt (Osmerus mordax) liver cells. Am. J. Physiol. 295:R961-R970 [PubMed]
101. Cooper, M.H., Miller, J.R., Mitchell, P.L., Currie, D. L. and McLeod, R.S. (2008) Conjugated linoleic acid isomers have no effect on atherosclerosis and adverse effects on lipoprotein and liver lipid metabolism in apoE-/- mice fed a high cholesterol diet. Atherosclerosis 200:294-302 [PubMed]
102. Curwin, A.J., and McMaster, C.R. (2008) Structure and Function of the Enigmatic Sec14 Domain Containing Proteins and the Etiology of Human Disease Future Lipidol. 3:399-410
103. Cuvelier, M. L., Ortiz, A., Kim, Eunsoo, Moehlig, H., Richardson, D. E., Heidelberg, J. F., Archibald, John M. & Worden, A. Z. (2008) Widespread distribution of a unique protistan lineage Env. Microbiol. doi: 10.1111/j.1462-2920.2008.01580.x: [PubMed]
104. Doolittle, W. F. (2008) Microbial evolution: stalking the wild bacterial species. Current Biology 18:R565-567
105. Doolittle, W. F., Nesbo, C.L., Bapteste, E. and Zhaxybayeva, O. (2008) Lateral gene transfer. Evolutionary Genomics and Proteonomics, M. Pagel and A. Pomiankowski (eds.) Sinauer:45-79
106. Elliot-Smith, E., Speak, A. O., Lloyd-Evans, E., Smith, D. A., van der Spoel, A. C., Jeyakumar, M., Butters, T. D., Dweka, R. A., d’Azzob, A., & Platt, F. M. (2008) Beneficial effects of substrate reduction therapy in a mouse model of GM1 gangliosidosis. Molecular Genetics and Metabolism 94(2):204-211 [PubMed]
107. Ewart, K.V., Williams, J., Richards, R.C., Gallant, J.W., Melville, K., Douglas, S.E. (2008) The early response of Atlantic salmon (Salmo salar) macrophages exposed in vitro to Aeromonas salmonicida cultured in broth and in fish. Dev. Comp. Immunol. 32 :380-390 [PubMed]
108. Fairn, G.D., and McMaster, C.R. (2008) Emerging Roles of the Oxysterol Binding Protein Family in Metabolism, Transport, and Signaling Cell Mol. Life Sci 65:228-236
109. Fisher, E.A., Lapierre, L.R., Junkins, R.D., & McLeod, R.S. (2008) The AAA-ATPase p97 is involved in the retrotranslocation of apolipoprotein B for proteasomal degradation. J.Lipid Res. 49:2149-2160 [PubMed]
110. Fong, A., & Archibald, J. M. (2008) Evolutionary dynamics of light-independent protochlorophyllide oxidoreductase (LIPOR) genes in the secondary plastids of cryptophyte algae. Euk. Cell. 7:550-553 [PubMed]
111. Furlong, S.F., Ridgway, N. D.and Hoskin, D.W. (2008) Modulation of ceramide metabolism in T-leukemia cell lines potentiates apoptosis induced by the cationic antimicrobial peptide bovine lactoferricin Int. J. Oncol. 32(3):537-544 [PubMed]
112. Gehrig, K., Cornell, R. B, and Ridgway N. D. (2008) Expansion of the Nucleoplasmic Reticulum Requires the Coordinated Activity of Lamins and CTP:Phosphocholine Cytidylyltransferase (CCT) {alpha} Mol. Biol. Cell 19(1):237-247 [PubMed]
113. Goldberg, A.V., Molik, S., Tsaousis, A.D., Kuhnke, G., Delbac, F., Vivares, C., Hirt, R.P., Lill, R. & Embley T.M. (2008) Localisation and functionality of microsporidian iron-sulphur cluster assembly proteins Nature 452:624-628 [PubMed]
114. Gong, H., Murphy, P.W., Langille, G.M., Minielly, S., Murphy, A., McMaster, C.R., and Byers, D. M. (2008) Tryptophan fluorescence reveals induced folding of Vibrio harveyi acyl carrier protein upon interaction with partner enzymes. BBA Proteins and Proteomics 1784:1835-1843 [PubMed]
115. Graham, L.A., Lougheed, S.C., Ewart, K.V., Davies P.L. (2008) Lateral transfer of a lectin-like antifreeze protein gene in fishes. PLoS ONE 3:e2616 [PubMed]
116. Hamblin, K., Standley, D.M., Rogers, M.B., Stechmann, A., Roger, A.J., Maytum, R., van der Giezen, M. (2008) Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Mol. Microbiol. 68(6):1395-1405 [PubMed]
117. Hampl, V., Silberman, J.D., Stechmann, A., Diaz-Triviño, S., Johnson, P.J. and Roger, A.J. (2008) Genetic evidence for a mitochondriate ancestry in the amitochondriate flagellate Trimastix pyriformis. PLoS ONE 3:e1383 [PubMed]
118. J Peter Gogarten, Gregory Fournier and Olga Zhaxybayeva (2008) Gene transfer and the reconstruction of life's early history from the molecular record Space Science Reviews 135:115-131
119. Keeling, P. J. and Archibald, J. M. (2008) Organelle evolution: what's in a name? Curr. Biol. 18:345-347 [PubMed]
120. Khan, H., & Archibald, J. M. (2008) Lateral transfer of introns in the cryptophyte plastid genome. Nucleic Acids Res. doi:10.1093/nar/gkn095: [PubMed]
121. Kim, E. and Archibald, J. M. (2008) Diversity and evolution of plastids and their genomes The chloroplast—interactions with the environment, Aronsson, H. &, Sandelius, A. S. (eds.) Springer-Verlag, Berlin:1-40
122. Kim, E., Lane, C. E., Curtis, B. A., Kozera, C., Bowman, S., & Archibald, J. M. (2008) Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). BMC Genomics 9:215 [PubMed]
123. Koenig, J.E., Boucher, Y., Charlebois, R.L., Nesbo, C., Zhaxybayeva, O., Bapteste, E., Spencer, M., Joss, M.J., Stokes, H.W. and Doolittle, W.F. (2008) Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environmental Microbiology 10:1024-1038.
124. Koenig, J.E., Boucher, Y., Charlebois, R.L., Nesbo, C., Zhaxybayeva, O., Bapteste, E., Spencer, M., Joss, M.J., Stokes, H.W. and Doolittle, W.F. (2008) Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Env. Microbiol. 10:1024-1038
125. Kolisko, M., Cepicka, I., Hampl, V., Leigh, J., Roger, A.J., Kulda, J., Simpson, A.G.B. and Flegr, J. (2008) Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, (alpha)-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evol.Biol. 8:205
126. Lane, C. E. & Archibald, J. M. (2008) New members of the genus Hemiselmis (Cryptomonadales, Cryptophyceae) J. Phycol. 44:339-350
127. Lane, C. E., & Archibald, J. M. (2008) The eukaryotic Tree of Life: endosymbiosis takes its TOL Trends Ecol. Evol. 23:268-275 [PubMed]
128. Leigh, J., Susko, E., Baumgartner, M. and Roger, A.J. (2008) Testing congruence in phylogenomic analysis. Syst. Biol. 57:104-115
129. Li, J., Sun, W., Wang, B., Xiao, X. and Liu, X.-Q. (2008) Protein trans-splicing as a means for viral vector-mediated in vivo gene therapy. Human Gene Therapy 19:958-964 [PubMed]
130. Lin, S., Zhang, H. and Gray, M.W. (2008) RNA editing in dinoflagellates and its implications for the evolutionary history of the editing machinery. In RNA and DNA Editing: Molecular Mechanisms and Their Integration into Biological Systems (Smith, H.C., ed.) Wiley Press:280-309
131. Lunn, F.A., MacDonnell, J.E., and Bearne, S.L.* (2008) Structural requirements for the activation of Escherichia coli CTP synthase by the allosteric effector GTP are stringent, but requirements for inhibition are lax. J. Biol. Chem. 283:2010-2020 [PubMed]
132. Lunn, F.A., MacLeod, T.J., Bearne, S.L.* (2008) Mutational analysis of conserved glycine residues 142, 143 and 146 reveals Gly-142 is critical for tetramerization of CTP synthase from Escherichia coli. Biochem. J. 412:113-121 [PubMed]
133. Lutz Hamel, Neha Nahar, Maria S. Poptsova, Olga Zhaxybayeva and J. Peter Gogarten (2008) Unsupervised Learning in Detection of Gene Transfer Journal of Biomedicine and Biotechnology 2008:472719
134. Miller, J.R., Siripurkpong, P., Hawes, J., Majdalawieh, A., Ro, H.-S. and McLeod, R.S. (2008) The trans-10, cis-12 isomer of conjugated linoleic acid decreases adiponectin assembly by PPARγ-dependent and PPARγ-independent mechanisms J. Lipid Res. 49:550-562 [PubMed]
135. Mitchell, P. L. and McLeod, R. S. (2008) Conjugated linoleic acid and atherosclerosis - Studies in animal models. (Review) Biochem. Cell Biol. 86:293-301 [PubMed]
136. Phipps, K., Donaher, N., Lane, C. E., & Archibald, J. M. (2008) Nucleomorph karyotype diversity in the freshwater cryptophyte genus Cryptomonas J. Phycol. 44:11-14
137. Potrykus, J., White, R.L.*, and Bearne, S. L.* (2008) Proteomic Investigation of Amino Acid Catabolism in the Indigenous Gut Anaerobe Fusobacterium varium. Proteomics 8:2691-2703 [PubMed]
138. Rabionet M, van der Spoel AC, Chuang CC, von Tümpling-Radosta B, Litjens M, Bouwmeester D, Hellbusch CC, Körner C, Wiegandt H, Gorgas K, Platt FM, Gröne HJ, and Sandhoff R. (2008) Male germ cells require polyenoic sphingolipids with complex glycosylation for completion of meiosis: A link to ceramide synthase-3. J Biol Chem 283:13357-13369 [PubMed]
139. Richards, R.C., Achenbach, J.C., Short, C.E., Kimball, J., Reith, M.E., Driedzic, W.R., Ewart, K.V. (2008) Seasonal expressed sequence tags of rainbow smelt (Osmerus mordax) revealed by subtractive hybridization and the identification of two genes up-regulated during winter. Gene 424:56-62 [PubMed]
140. Ruiz-Trillo, I., Roger, A.J., Burger, G., Gray, M.W. and Lang, B.F. (2008) A phylogenomic investigation into the origin of Metazoa. Mol. Biol. Evol. 25:664-672 [PubMed]
141. Ruiz-Trillo, I., Roger, A.J., Burger, G., Gray, M.W. and Lang, B.F. (2008) A phylogenomic investigation into the origin of Metazoa. Mol.Biol.Evol. 25:664-672
142. Salma A. Abdelmagid and Catherine K. L. Too (2008) Prolactin and Estrogen Up-Regulate Carboxypeptidase-D to Promote Nitric Oxide Production and Survival of MCF-7 Breast Cancer Cells Endocrinology 149:10 4821-4828
143. Sanchez-Perez, G., Hampl, V., Simpson, A.G.B. and Roger, A.J. (2008) A new divergent type of eukaryotic methionine adenosyltransferase that has spread by gene transfer between secondary algae. J. Euk. Microbiol. 55:374-381
144. Sharma, A.K., Zhaxybayeva, O., Papke, R.T. and Doolittle, W.F. (2008) Actinorhodopsins: Proteorhodopsin-like gene sequences found predominantly in non-marine environments. Env. Microbiol. 10:1039-1056
145. Soanes, K.H., Ewart, K.V., Mattatall, N.R. (2008) Recombinant production and characterization of the carbohydrate recognition domain from Atlantic salmon C-type lectin receptor C (SCLRC). Protein Expr. Purif. 59:38-46 [PubMed]
146. Stechmann, A., Hamblin, K., Perez-Brocal, V., Gaston, D., Richmond, G.S., van der Giezen, M., Clark, C.G. and Roger, A.J. (2008) Organelles in Blastocystis that blur the distinction between mitochondria and Hydrogenosomes. Curr. Biol. 18:580-585
147. Taylor, S.D.*, Lunn, F.A., and Bearne, S.L.* (2008) Ground State, Intermediate, and Multivalent Nucleotide Analogue Inhibitors of Cytidine 5’-Triphosphate Synthase ChemMedChem 3:1853-1857 [PubMed]
148. Taylor, S.D.*, Mirzaei, F., and Bearne, S.L. (2008) Bismethylene Triphosphate Nucleotides of Uridine 4-Phosphate Analogues: A New Class of Anionic Pyrimidine Nucleotide Analogues J. Org. Chem. 73:1403-1412 [PubMed]
149. Thomas, L.N., Douglas, R.C., Lazier, C.B., Gupta, R., Norman, R.W., Murphy, P.R., Rittmaster, R.S. and Too, C.K.L. (2008) Levels of 5α-reductase type 1 and type 2 are increased in malignant but not adjacent benign tissues from high grade as compared to low grade prostate cancer J. Urology 179:147-151 [PubMed]
150. Thomas, L.N., Douglas, R.C., Lazier, C.B., Too, C.K.L., Rittmaster, R.S. and Tindall, D.J. (2008) Type 1 and Type 2 5&alpha-reductase expression in the development and progression of prostate cancer. European Urology 53:244-252 (Review) [PubMed]
151. Tsaousis, A.D., Kunji E.R.S., Goldberg, A.V., Lucocq J.M., Hirt, R.P. and Embley T.M. (2008) A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi Nature 453:553-556 [PubMed]
152. van der Spoel, A. C., Mott, R., & Platt, F. M. (2008) Differential sensitivity of mouse strains to an N-alkylated imino sugar: glycosphingolipid metabolism and acrosome formation. Pharmacogenomics 9(6)717-31. Review.:717-731. Review. [PubMed]
153. von Schalburg, K.R., Leong, J., Cooper, G.A., Robb, A., Beetz-Sargent, M.R., Lieph, R., Holt, R.A., Moore, R., Ewart, K.V., Driedzic, W.R., Ten Hallers, B.F., Zhu, B., de Jong, P.J., Davidson, W.S., Koop, B.F. (2008) Rainbow smelt (Osmerus mordax) genomic library and EST resources. Mar. Biotechnol. 10:487-491 [PubMed]
154. Wang, H.-C., Li, K.M., Susko, E. and Roger A.J. (2008) A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol. Biol. 8:331
155. Wang, H.-C., Susko, E., Spencer, M. and Roger, A.J. (2008) Topological estimation biases with covarion evolution. J.Mol.Evol. 66:50-60
156. Watkins, R.F. and Gray, M.W. (2008) Sampling gene diversity across the supergroup Amoebozoa: large EST data sets from Acanthamoeba castellanii, Hartmannella vermiformis, Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp. Protist 159:269-281 [PubMed]
157. Wu, J. Susko, E. and Roger, A.J. (2008) An independent heterotachy model and its implications for phylogeny and divergence time estimation. Mol. Phylogenet. Evol. 46:801-806

Publications in 2007

158. Dellaire, G. and D.P. Bazett-Jones (2007) Beyond Repair Foci: Subnuclear Domains and the Cellular Response to DNA Damage Cell Cycle. 6(15):1864-1872 [PubMed]
159. Rainey, J.K., DeVries, J.S. and Sykes B.D. (2007) Estimation and measurement of flat or solenoidal coil inductance for radiofrequency NMR coil design J. Magn. Reson. 187:27-37 [PubMed]
160. Adl, S. M., Leander, B. S., Simpson, A. G. B., Archibald, J. M., Anderson, O. R., Bass, D., Bowser, S. S., Brugerolle, G., Farmer, M. A., Karpov, S., Kolisko, M., Lane, C. E., Lodge, D. J., Mann, D. G., Meisterfeld, R., Mendoza, L., Moestrup, O., Mozley-Standridge, S. E., Smirnov, A. V., & Spiegel, F. (2007) Diversity, nomenclature, and taxonomy of protists. Syst. Biol. 56:684-689 [PubMed]
161. Al-Hertani, W., Yan, S.R., Byers, D.M. and Bortolussi, R. (2007) Human newborn polymorphonuclear neutrophils exhibit decreased levels of MyD88 and attenuated p38 phosphorylation in response to lipopolysaccharide. Clin. Invest. Med. 30:E44-E53
162. Andersson, J.O., Sjogren, Å., Horner D.S., Murphy, C.A., Dyal, P., Svärd S., Logsdon J.M., Ragan, M.A., Hirt, R.P., and Roger, A.J. (2007) A genomic survey of the fish parasite Spironucleus salmonidia indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics 8:51
163. Archibald, J. M. (2007) Nucleomorph genomes: structure, function, origin and evolution. BioEssays. 4:392-402 [PubMed]
164. Archibald, J. M. (2007) Review of Genomics and Evolution of Microbial Eukaryotes Q. Rev. Biol. 82:275-276
165. Barberà, M. J., Ruiz-Trillo, I., Leigh, J. Hug, L.A. and Roger, A.J. (2007) The diversity of mitochondrion-related organelles amongst eukaryotic microbes. Origins of Mitochondria and Hydrogenosomes, W.Martin and M. Müller (Eds.) Springer-Verlag:239-268
166. Bhattacharya, D., Archibald, J. M., Weber, A. P. M. & Reyes-Prieto, A. (2007) How do endosymbionts become organelles? Understanding early events in plastid evolution. BioEssays 29:1239-1246 [PubMed]
167. Black, K.M. and Wallace, C.J.A. (2007) Probing the role of the conserved β-II turn, Pro76/Gly77 of mitochondrial cytochrome c. Biochem. Cell Biol 85:366-374 [PubMed]
168. Boucher, Y., Labbate, M., Koenig, J.E. & Stokes, H.W. (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol. 15:301-309
169. Bourque, J.R., Burley, R.K.M., and Bearne, S.L.* (2007) Intermediate analogue inhibitors of mandelate racemase: N-Hydroxyformanilide and cupferron. Bioorg. Med. Chem. Lett. 17:105-108 [PubMed]
170. Burnett, J.R., Zhong, S., Jiang, Z.G., Hooper, A., Fisher, E.A., McLeod, R.S., Zhao, Y., Barrett, P.H.R., Hegele, R.A., van Bockxmeer, F.M., Zhang, H., Vance, D.E., McKnight, C.J., and Yao, Z. (2007) Missense mutations in APOB within the βα1 domain of human apoB-100 result in impaired secretion of apoB and apoB-containing lipoproteins in familial hypobetalipoproteinemia. J. Biol. Chem. 282:24270-24283 [PubMed]
171. Case, R.J., Boucher, Y., Dahllof, I., Holmstrom, C., Doolittle, W. F. and Kjelleberg, S. (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Applied and Environmental Microbiology 73:278-288
172. Chen, L., Zhu, F., et al. (2007) The enhancing effects of the light chain on heavy chain secretion in split delivery of factor VIII gene. Mol. Therapy 15:1856-1862 [PubMed]
173. Cullen, J.J., Doolittle, W.F., Levin, S.A. and Li, W.K.W. (2007) Patterns and prediction in microbial oceanography. Oceanography 20:34-46
174. D'Angelo G, Polishchuk E, Di Tullio G, Santoro M, Di Campli A, Godi A, West G, Bielawski J, Chuang CC, van der Spoel AC, Platt FM, Hannun YA, Polishchuk R, Mattjus P, De Matteis MA. (2007) Non-vesicular transport of glucosylceramide via FAPP2 is required for glycosphingolipid synthesis and membrane transport to the plasma membrane. Nature 449:62-67 [PubMed]
175. Derouet M., Wu X., May L., Yoo BH, Sasazuki T., Shirasawa S., Rak J. and Rosen KV (2007) Acquisition of anoikis resistance promotes the emergence of oncogenic K-ras mutations in colorectal cancer cells and stimulates their tumorigenicity in vivo. Neoplasia 9(7):536-545 [PubMed]
176. Derry MC, Sutherland MR, Restall CM, Waisman DM, Pryzdial EL. (2007) Annexin 2-mediated enhancement of cytomegalovirus infection opposes inhibition by annexin 1 or annexin 5 J Gen Virol. 88:19-27 [PubMed]
177. Doolittle, W. F. and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. PNAS 104:2043-2049
178. Doolittle, W. F. and Zhaxybayeva, O. (2007) Evolution: reducible complexity -- the case for bacterial flagella. Current Biology 17:R510-512
179. Dragomir, I., Hagarman, A., Wallace, C. and Schweitzer-Stenner, R. (2007) Optical band splitting and electronic perturbations of the heme chromophore in cytochrome c at room temperature probed by visible electronic circular dichroism spectroscopy. Biophysical Journal 92:989-998 [PubMed]
180. E. Lessmann, M. Ngo, M. Leitges, S. Minguet, ND Ridgway, M. Huber (2007) Oxysterol-binding protein-related protein (ORP) 9 is a PDK-2 substrate and regulates Akt phosphorylation Cell. Signal. 19:384-392 [PubMed]
181. Fairn, G.D., and McMaster, C. R. (2007) Emerging Roles of the Oxysterol Binding Protein Family in Metabolism, Transport, and Signaling (Review) Cell Mol. Life Sci. in press:
182. Fairn, G.D., Curwin, A.J., Stefan, C., and McMaster, C. R. (2007) Regulation of Golgi Phosphatidylinositol 4-phosphate Function by the Oxysterol Binding Protein Kes1p Proc. Natl. Acad. Sci. U.S.A. 104:15352-15357
183. Fairn, G.D., MacDonald, K., and McMaster, C. R. (2007) A Chemogenomic Screen in Saccharomyces cerevisiae Uncovers a Primary Role for the Mitochondria in Farnesol Toxicity and its Regulation by the Pkc1 Pathway J. Biol. Chem. 282:4868-4874
184. Fernández-Murray, J.P., and McMaster, C.R. (2007) Phosphatidylcholine Synthesis and its Catabolism by Yeast Neuropathy Target Esterase 1 (Review) Biochim. Biophys. Acta 1771:331-336
185. Gill, E.E., Diaz-Triviño, S., Barberà, M.J., Silberman, J.D., Stechmann, A., Gaston, D., Tamas, I. and Roger, A.J. (2007) Novel mitochondrion-related organelles with a unique array of functions in the anaerobic amoeba Mastigamoeba balamuthi. Mol. Microbiol. 66:1306-1320 [PubMed]
186. Gong, H., Murphy, A., McMaster, C.R. and Byers, D.M. (2007) Neutralization of acidic residues in helix II stabilizes the folded conformation of acyl carrier protein and variably alters its function with different enzymes. J. Biol. Chem. 282:4494-4503 [PubMed]
187. Howe, A.L., Fairn, G.D., MacDonald, K., Bankaitis, V.A., and McMaster, C. R. (2007) Regulation of Phosphoinositide Levels by the Phospholipid Transfer Protein Sec14p Controls Cdc42p/PAK Mediated Cell Cycle Progression at Cytokinesis Euk. Cell 6:1814-1823
188. Hug, L.A. and Roger, A.J. (2007) The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol. Biol. Evol. 24:1889-1897
189. Hyo-Sung Ro, H.-S., Zhang, L., Majdalawieh, A., Kim, S-W, Wu, X., Lyons, P.J., Webber, C., Ma, H., Reidy, S.P., Boudreau, A., Miller, J.R., Mitchell, P.L., McLeod, R.S. (2007) AEBP1 modulates adiposity through effects on preadipocyte survival and differentiation. Obesity 15:288-302 [PubMed]
190. Jackson, C. J., Norman, J. E., Schnare, M. N., Gray, M. W., Keeling, P. J. and Waller, R. F. (2007) Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biol. 5: 41 [PubMed]
191. Kalanxhi, E. and Wallace, C.J.A. (2007) Cytochrome c impaled: investigation of the extended lipid anchorage of cytochrome c to mitochondrial membranes models Biochem. J. 407:179-187 [PubMed]
192. Khan, H., Kozera, C., Curtis, B. A., Tarrant Bussey, J., Theophilou, S., Bowman, S., & Archibald, J. M. (2007) Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae. J. Mol. Evol. 64:223-236 [PubMed]
193. Khan, H., Parks, N. Kozera, C., Curtis, B. A., Parsons, B., Bowman, S., & Archibald, J. M. (2007) Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny. Mol. Biol. Evol. 24:1832-1842 [PubMed]
194. Lane, C. E., van den Heuvel, K., Kozera, C., Curtis, B. A., Parsons, B., Bowman, S., & Archibald, J. M. (2007) Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc. Natl. Acad. Sci. U.S.A. 104:19908-19913 [PubMed]
195. Lapierre, L. R. and McLeod, R.S. (2007) Regulation of hepatic production of lipoproteins containing apolipoprotein B by ER-associated degradation. Future Lipidology 2:173-184
196. Lohan, A.J. and Gray, M.W. (2007) Analysis of 5'- or 3'-terminal tRNA editing: mitochondrial 5' editing in Acanthamoeba castellanii as the exemplar. Methods Enzymol. 424: 221-242 [PubMed]
197. Lutz Hamel, Neha Nahar, Maria S. Poptsova, J. Peter Gogarten and Olga Zhaxybayeva (2007) Unsupervised Learning in Spectral Genome Analysis Proceeding of the IEEE Conference Frontiers in the Convergence of Bioscience and Information Technologies :317 - 321
198. Majdalawieh, A., Zhang, L. and Ro, H.-S. (2007) Adipocyte enhancer-binding protein-1 promotes macrophage inflammatory responsiveness by up-regulating NF- &kappa B via I &kappa B &alpha negative regulation Mol. Biol. Cell 18:930-942 [PubMed]
199. Marignani, P. A., Scott, K.D., Bagnulo, R., Stella, A., Guanti, G., Simone, C., Resta, N. (2007) Novel splice isoforms of STRADa differentially affect LKB1 activity, complex assembly and sub-cellular localization. Cancer Biology and Therapy 6(9):1627-1631 [PubMed]
200. Meng, Q., Zhang Y., and Liu, X.-Q. (2007) Rare group I intron with insertion sequence element in a bacterial ribonucleotide reductase gene. J. Bacteriol. 189:2150-2154 [PubMed]
201. Murphy, P.W., Rowland, E.E., and Byers, D.M. (2007) Electrospray ionization mass spectra of acyl carrier protein are insensitive to its solution phase conformation. J. Amer. Soc. Mass Spectrom. 18(8):1525-1532 [PubMed]
202. Nien, W. L., Dauphinee, S. M., Moffat, L. D. and Too, C. K. L. (2007) Overexpression of mTOR alpha4 phosphoprotein activates PP2A and increases Stat1a binding to PIAS1 Mol. Cell. Endocrinol. 263:10-17
203. O'Brien, E.A., Koski, L.B., Zhang, Y., Yang, L., Wang, E., Gray, M.W., Burger, G. and Lang, B.F. (2007) TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). Nucleic Acids Res. 35:D445-D451 [PubMed]
204. Papke, R.T., Zhaxybayeva, O., Feil, E.J., Sommerfeld, K., Muise, D. and Doolittle, W.F. (2007) Searching for species in haloarchaea. PNAS 104:14092-14097
205. Pepke, S., Butt, D., Nadeau, I., Roger, A.J. and Blouin C. (2007) Using confidence set heuristics during topology search improves the robustness of phylogenetic inference. J.Mol.Evol. 64:80-89
206. Potrykus, J., Mahaney, B., White, R.L.*, and Bearne, S.L.* (2007) Proteomic investigation of glucose metabolism in the butyrate-producing gut anaerobe Fusobacterium varium. Proteomics 7:1839-1853 [PubMed]
207. Ro, H.-S., Zhang, L., Majdalawieh, A., Kim, S.-W., Wu, X., Lyons, P., Webber, C., Ma, H., Reidy, S., Boudreau, A., Miller, J., Mitchell, P. and McLeod, R. (2007) Adipocyte enhancer-binding protein 1 modulates adiposity and energy homeostasis. Obesity 15(2):288-302 [PubMed]
208. Rodríguez-Ezpeleta, N., Brinkmann, H., Burger, G., Roger, A. J., Gray, M.W., Philippe, H. and Lang, B.F. (2007) Towards resolving the eukaryotic tree: the phylogenetic positions of jakobiods and cercozoans. Curr. Biol. 17:1420-1425 [PubMed]
209. Rodriguez-Ezpeleta, N., Brinkmann, H., Burger, G., Roger, A.J., Gray M.W., Philippe H. and Lang, B.F. (2007) Toward resolving the eukaryotic tree: the phylogenetic position of jakobids and cercozoans. Curr. Biol. 17:1420-1425
210. Rogers, M.B., Watkins, R.F., Harper, J.T., Durnford, D.G., Gray, M.W. and Keeling, P.J. (2007) A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol. Biol. 7: 89 [PubMed]
211. Ruiz-Trillo, I., Burger, G., Holland, P., King, N., Lang, B.F., Roger, A.J. and Gray, M.W. (2007) The origins of multicellularity: a multi-taxon genome initiative. Trends Genet. 23:113-118
212. Ruiz-Trillo, I., Burger, G., Holland, P.W.H., King, N., Lang, B.F., Roger, A.J. and Gray, M.W. (2007) The origins of multicellularity: a multi-taxon genome initiative. Trends Genet. 23:113-118 [PubMed]
213. Sara Cuadros-Orellana, Ana-Belen Martin-Cuadrado, Boris Legault, Giuseppe D'Auria, Olga Zhaxybayeva, R. Thane Papke, Francisco Rodriguez-Valera (2007) Genomic Plasticity in Prokaryotes: the Case of the Square Haloarchaeon ISME Journal 1:235-245
214. Schweitzer-Stenner,R. Huang,Q., Hagasman,A.,Laberge,M. and Wallace, C. J. A. (2007) Static normal coordinate deformations of the heme group in mutants of ferrocytochrome c from Saccharomyces cerevisiae probed by resonance Raman spectroscopy. J.Phys.Chem.B III:6527-6533. [PubMed]
215. Scott KD, Nath-Sain S, Agnew MD and Marignani PA. (2007) LKB1 catalytic-deficient mutants enhance cyclin D1 expression. Cancer Research 67(12):5622-5627. [PubMed]
216. Sharma, A.K., Walsh, D.A., Bapteste, E., Rodriguez-Valera, F., Doolittle W.F., and Papke, R.T. (2007) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol. Biol. 7:79
217. Silver, T. D., Koike, S., Yabuki, A., Kofuji, R., Archibald, J. M., & Ishida, K.-I. (2007) Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algae. J. Ekaryot. Microbiol. 54:403-410 [PubMed]
218. Slepkov, E.R., Rainey, J.K., Sykes, B.D. and Fliegel, L. (2007) Structural and functional analysis of the Na⁺/H⁺ exchanger. Biochem. J. 401:623-631 [PubMed]
219. Smith, D. G. S., Gawryluk, R. M. R., Spencer, D. F., Pearlman, R. E., Siu, K. W. M. and Gray, M. W. (2007) Exploring the mitochondrial proteome of the ciliate protozoon, Tetrahymena thermophila: direct analysis by tandem mass spectrometry. J. Mol. Biol. 374: 837-863 [PubMed]
220. Susko, E. and Roger, A.J. (2007) On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24:2139-2150
221. Walden CM, Sandhoff R, Chuang CC, Yildiz Y, Butters TD, Dwek RA, Platt FM, van der Spoel AC (2007) Accumulation of Glucosylceramide in Murine Testis, Caused by Inhibition of beta-Glucosidase 2: IMPLICATIONS FOR SPERMATOGENESIS. J Biol Chem 282:32655-32664 [PubMed]
222. Walsh, D.A., Boudreau, M.E., Bapteste, E. and Doolittle, W.F. (2007) The root of the tree: lateral gene transfer and the nature of the domains. Archaea: Evolution, Physiology and Molecular Biology. Blackwell Publishing:29-37
223. Wyles, J.P., Perry, R.P. and Ridgway, N. D. (2007) Characterization of the sterol-binding domain of oxysterol-binding protein (OSBP)-related protein 4 reveals a novel role in vimentin organization Exp. Cell Res. 313:1426-1437 [PubMed]
224. Zhaxybayeva, O., Nesbo, C.L. and Doolittle, W. F. (2007) Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biology 8:402
225. Zhaxybayeva,O., Gogarten, J.P. and Doolittle, W.F. (2007) A hyperconserved protein in Prochlorococcus and marine Synechococcus. FEMS Microbiol. Lett. 274:30-34
226. Zheng, Q., Song, J., Doncaster, K., Rowland, E., and Byers, D. (2007) Qualitative and quantitative evaluation of protein extraction protocols for apple and strawberry fruit suitable for two-dimensional electrophoresis and mass spectrometry analysis. J. Agric. Food Chem, 55:1663-1673 [PubMed]

Publications in 2006

227. Reddy, T., Rot-Nikcevic, I., Downing, K.J., Belliveau, A.C., Hallgrímsson, B., Hall, B.K., and Kablar, B. (2006) Myf5-/-: MyoD-/- amyogenic fetuses reveal the importance of early contraction and static loading by striated muscle in mouse skeletogenesis. Development genes and evolution. 216:1-9 [PubMed]
228. Dellaire, G., R. Ching, H. Dehghani, Y. Ren and D.P. Bazett-Jones (2006) PML nuclear bodies increase in number in early S-phase by a fission mechanism J. Cell Sci. 119(6):1026-1033 [PubMed]
229. Dellaire, G., C. Eskiw, H. Dehghani, R. Ching, and D.P. Bazett-Jones (2006) Mitotic Accumulations of PML protein (MAPPs) contribute to the post-mitotic re-establishment of PML nuclear bodies. J. Cell Sci. 119(6):1034-1042 [PubMed]
230. Dellaire, G., R. Ching, K. Ahmed, K. Tse, F. Jalali, R.G. Bristow, and D.P. Bazett-Jones (2006) PML nuclear bodies are DNA damage sensors whose response to DNA double-strand breaks is regulated by NBS1, Chk2 and ATR J. Cell Biol. 175(1):55-66 [PubMed]
231. Rainey, J.K.*, Ding, J.*, Xu, C., Sykes, B.D. and Fliegel, L. (* contributed equally) (2006) Structural and functional characterization of TM VII of the NHE1 isoform of the Na⁺/H⁺ exchanger. J. Biol. Chem. 281:29817-29829 [PubMed]
232. Rainey, J.K., Fliegel, L. and Sykes, B.D. (2006) Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides. Biochem. Cell Biol. 84:918-929 [PubMed]
233. Andersson, J.O., Hirt, R.P., Foster, P.G. and Roger, A.J. (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol. Biol. 6:27
234. Archibald, J. M. (2006) Endosymbiosis: double-take on plastid origins. Curr. Biol. 16:R690-R692 [PubMed]
235. Archibald, J. M. (2006) Genome complexity in a lean, mean photosynthetic machine. Proc. Natl. Acad. Sci. USA 103:11433-11434 [PubMed]
236. Archibald, J. M. (2006) Algal genomics: exploring the imprint of endosymbiosis. Curr. Biol. 16:R1033-1035 [PubMed]
237. Baguma-Nibasheka, M., Reddy, T., Abbas-Butt, A., and Kablar, B. (2006) Fetal ocular movements and retinal cell differentiation: analysis employing DNA microarrays. Histology and histopathology 21:1331-1337 [PubMed]
238. Bhattacharya, D. & Archibald, J. M. (2006) Response to: "The difference between endosybmionts and organelles". Curr. Biol. 16:R1017-1018
239. Bishop, J.D., Nien, W.L., Dauphinee, S.M. and Too, C.K.L. (2006) Prolactin activates mTOR through phosphatidylinositol 3-kinase and stimulates phosphorylation of p70S6K and 4E-BP1 in lymphoma cells. J. Endocrinology 190:307–312 [PubMed]
240. Block, G., C.H. Eskiw, G. Dellaire, and D.P. Bazett-Jones (2006) Transcriptional regulation is affected by subnuclear targeting of reporter plasmids to PML nuclear bodies Mol. Cell. Biol. 26(23):8814-8825 [PubMed]
241. Boucher, Y., Nesbo, C.L., Joss, M.J., Robinson, A., Mabbutt, B.C., Gilllings, M.R., Doolittle, W. F. and Stokes, H.W. (2006) Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio. BMC Evol. Biol. 6:3
242. Doolittle, W.F. (2006) Species. Microbiology Today 33:148-151
243. Doolittle, W.F. and Papke, R.T. (2006) Genomics and the bacterial species problem. Genome Biology 7:116.1-116.7
244. Driedzic W.R., Clow, K.A., Short C.E. and Ewart, K.V. (2006) Glycerol production in rainbow smelt (Osmerus mordax) may be triggered by low temperature alone and is associated with the activation of GPDH and G3Pase. J. Exp. Biol. 209:1016-1023 [PubMed]
245. Durnford, D.G. and Gray, M.W. (2006) Analysis of Euglena gracilis plastid-targeted proteins reveals different classes of transit sequences. Eukaryot. Cell 5:2079-2091 [PubMed]
246. Fernández-Murray, J.P., and McMaster, C.R. (2006) Identification of Novel Phospholipid Binding Proteins in Saccharomyces cerevisiae Febs Lett. 580:82-86
247. Gleave, M. et al. (on behalf of the ARI40010 study team) (2006) The effects of the dual 5alpha-reductase inhibitor dutastaride on localized prostate cancer : results from a 4-month pre-radical prostatectomy study. The Prostate 66:1674-1685. [PubMed]
248. Goddard, M., Leigh, J., Roger, A.J. and Pemberton, A.J. (2006) Invasion and persistence of a selfish gene in the Cnidaria. PLoS ONE 1:e3
249. Gophna, U., Charlebois, R.L. and Doolittle, W. F. (2006) Lateral gene transfer in the evolution of Bdellovibrio bacteriovorus. Trends in Microbiology 14:64-69
250. Gophna, U., Sommerfeld, K., Gophna, S., Doolittle, W. F. and van Zanten, S.J.O.V. (2006) Differences between Crohn's disease and ulcerative colitis patients in tissue-associated intestinal microflora. J. Clin. Microbiol. 44:4136-4141
251. Gophna, U., Thompson, J.R., Boucher, Y. and Doolittle, W.F. (2006) Complex historiesof genes encoding 3-hydroxy-3-methylglutaryl-CoenymeA reductase. Mol. Biol. Evol. 23:168-178
252. Howe, A.G., and McMaster, C.R. (2006) Regulation of Phosphatidylcholine Homeostasis by Sec14 (Review) Can. J. Physiol. Pharmacol 84:29-38
253. Inagaki, Y. and Roger, A.J. (2006) Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. Mol. Phylogenet. Evol. 40:428-434
254. Inagaki, Y., Susko, E. and Roger, A.J. (2006) Recombination between elongation factor 1(alpha) genes from distantly-related archaeal linages. Proc. Natl. Acad. Sci. USA 103:4528-4533
255. Karten, B., Campenot R. B., Vance, D. E., and Vance, J. E. (2006) Expression of ABCG1, but not ABCA1, correlates with cholesterol release from cerebellar astroglia J. Biol. Chem. 281:4049-4057 [PubMed]
256. Karten, B., Campenot R. B., Vance, D. E., and Vance, J. E. (2006) The Niemann-Pick Type C1 protein in recycling endosomes of pre-synaptic nerve terminals. J. Lipid Res. 47:504-514 [PubMed]
257. Kruhlak, M.J., A. Celeste, G. Dellaire, O. Fernandez-Capetillo,W.G. Müller, J.G. McNally, D.P. Bazett-Jones, and A. Nussenzweig (2006) Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks J. Cell Biol. 172(6):823-834 [PubMed]
258. L.J. Mix, J.C. Armstrong, A.M. Mandell, A.C. Mosier, J. Raymond, S.N. Raymond, F.J. Stewart, K. von Braun, and O. Zhaxybayeva, L. Billings, V. Cameron, M. Claire, G.J. Dick, S.D. Domagal-Goldman, E.J. Javaux, O.J. Johnson, C. Laws, M.S. Race, J. Rask, J.D. Rummel, R.T. Schelble, and S. Vance (2006) The Astrobiology Primer: An Outline of General Knowledge. Version 1, 2006 Astrobiology 6:735-813
259. Lane, C. E. & Archibald, J. M. (2006) Novel nucleomorph genome architecture in the cryptomonad genus Hemiselmis. J. Euk. Microbiol. 53:515-521 [PubMed]
260. Lane, C.E., Khan, H., MacKinnon, M., Fong, A., Theophilou, S., and Archibald, J.M. (2006) Insight into the diversity and evolution of the cryptomonad nucleomorph genome Mol. Biol. Evol. 23:856-865 [PubMed]
261. Legault, B.A., Lopez-Lopez, A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodriguez-Valera, F. and Papke, T.R. (2006) Environmental genomics of Haloquadratum walsbyi in a saltern crystallizer indicates a large pool of accessory genes in an outside coherent species. BMC Genomics 7:171
262. Liebscher, R.S., Richards, R.C., Lewis, J.M, Short, C.E., Muise, D.E., Driedzic, W.R. and Ewart, K.V. (2006) Seasonal freeze resistance of rainbow smelt (Osmerus mordax) is generated by differential expression of glycerol-3-phosphate dehydrogenase, phosphoenolpyruvate carboxykinase and antifreeze protein genes. Physiol. Zool. 79:411-423 [PubMed]
263. Liu, Z., Li, H., Wu, X., Yoo, B., Yan, S., Stadnyk, A., Sasazuki, T., Shirasawa, S., LaCasse, E., Korneluk, RG. and Rosen KV (2006) Detachment-induced upregulation of XIAP and cIAP2 delays anoikis of intestinal epithelial cells. Oncogene 25:7680-90 [PubMed]
264. Liu, Z., Li, H., Derouet, M., Berezkin, A., Sasazuki, T., Shirasawa, S., and Rosen, K. (2006) Oncogenic Ras inhibits anoikis of intestinal epithelial cells by preventing the release of a mitochondrial pro-apoptotic protein Omi/HtrA2 into the cytoplasm. J. Biol. Chem. 281:14738-47 [PubMed]
265. Lyons, P.J., Mattatall, N.R. and Ro, H.-S. (2006) Modeling and functional analysis of AEBP1, a transcriptional repressor. Proteins 63:1069-1083 [PubMed]
266. MacLeod, T.J., Lunn, F.A., and Bearne, S.L.* (2006) The role of lysine residues 297 and 306 in nucleoside triphosphate regulation of E. coli CTP synthase. Inactivation by 2',3'-dialdehyde ATP and mutational analyses. Biochim. Biophys. Acta 1764:199-210 [PubMed]
267. Majdalawieh, A.F., Zhang, L., Fuki, I.V., Rader, D.J. and Ro, H.-S. (2006) Adipocyte Enhancer-Binding Protein-1 is a potential novel atherogenic factor involved in macrophage cholesterol homeostasis and inflammation. Proc. Natl. Acad. Sci. USA 103 (7):2346-2351 [PubMed]
268. Moffatt, B., Ewart, V. and Eastman, A. (2006) Cold comfort: antifreeze proteins. Phyisol. Plant. 126:5-16
269. Murphy, P.W., Rowland, E.E., and Byers, D.M. (2006) pH-Dependent conformation of acyl carrier protein: difference between solution and gas phases 89th Annual Canadian Society of Chemistry Conference (Halifax, N.S., Canada; May 27 – 31, 2006) :
270. Nesbo, C.L., Dlutek, M., Zhaxybayeva, O. and Doolittle, W.F. (2006) Evidence for existence of "Mesotogas", members of the order Thermotogales adapted to low-temperature environments. Applied and Env. Microbiol. 72:5061-5068
271. Nesbo, C.L., Doolittle, W.F., Mongodin, E.F. and Nelson, K.E. (2006) Outside forces helped shape the Thermotoga metagenome. Microbe 1:235-241
272. Nesbo,C.L., Dlutek, M. and Doolittle, W.F. (2006) Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172:759-769
273. Olga Zhaxybayeva, Pascal Lapierre and J. Peter Gogarten (2006) Ancient Gene Duplications and the Root(s) of the Tree of Life Protoplasma 227:53-64
274. Perry, R.J and Ridgway, N. D. (2006) OSBP and VAP are required for sterol dependent regulation of ceramide transprot protein (CERT) Mol. Biol. Cell 17:2604-1616 [PubMed]
275. Richard, K.C., Bertolesi, G.E., Dunfield, L.D., McMaster, C.R., and Nachtigal, M. W. (2006) TSAd interacts with Smad2 and Smad3 Biochem. Biophys. Res. Comm. 347:266-272
276. Rise, M.S., Douglas, S.E., Sakhrani, D., Williams, J., Ewart, K.V., Rise, M., Davidson, W.S., Koop, B.F. and Devlin, R.H. (2006) Multiple microarray platforms utilized for hepatic gene expression profiling of growth hormone transgenic coho salmon with and without ration restriction J. Mol. Endocrinol. 37:259-282 [PubMed]
277. Robinson, M., Poon, P.P., Schindler, C., Murray, L.E., Kama, R., Gabriely, G., Singer, R.A., Spang, A., Johnston, G.C. and Gerst, J.E. (2006) The Gcs1 Arf-GAP mediates Snc1,2 v-SNARE retrieval to the Golgi in yeast. Mol. Biol. Cell 17:1845-1858 [PubMed]
278. Roger, A. J. (2006) Telling evolutionary tales (book review). Nat.Rev.Genet. 38:1357
279. Roger, A.J. and Hug, L.A. (2006) The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Phil. Trans. R. Soc. B 361:1039-1054
280. Ruiz-Trillo, I., Lane C., Archibald, J.M. and Roger, A.J. (2006) Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J. Euk. Microbiol. 53:379-384
281. Ruiz-Trillo, I., Lane, C. E., Archibald, J. M. and Roger, A. J. (2006) Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J. Euk. Microbiol. 53:379-384. [PubMed]
282. Russell, A.G., Charette, J.M., Spencer, D.F. and Gray, M.W. (2006) An early evolutionary origin for the minor spliceosome. Nature 443:863-866 [PubMed]
283. Russell, A.G., Schnare, M.N. and Gray, M.W. (2006) A large collection of compact box C/D snoRNAs and their isoforms in Euglena gracilis: structural, functional and evolutionary insights. J. Mol. Biol. 357: 1548-1565 [PubMed]
284. Schweitzer-Stenner, R., Levantino, M., Cupane, A., Wallace, C., Leberge, M. and Huang, Q. (2006) Functionally relevant electric field-induced perturbations of the prosthetic group of yeast ferro-cytochrome c mutants obtained from a vibronic analysis of low-temperature absorption spectra. J. Phys. Chem. B. 110:12155-12161. [PubMed]
285. Shao C, Zhang F, Kemp MM, Linhardt RJ, Waisman DM, Head JF, Seaton BA. (2006) Crystallographic analysis of calcium-dependent heparin binding to annexin A2 J Biol Chem. 20:31689-31695 [PubMed]
286. Sharma, A.K., Spudich, J.L. and Doolittle, W. F. (2006) Microbial rhodopsins: functional versatility and genetic mobility. Trends Microbiol. 14:463-469
287. Shutt, T.E. and Gray, M.W. (2006) Twinkle, the mitochondrial replicative DNA helicase, is widespread in the eukaryotic radiation and may also be the mitochondrial DNA primase in most eukaryotes J. Mol. Evol. 62:588-599 [PubMed]
288. Shutt, T.E. and Gray, M.W. (2006) Bacteriophage origins of mitochondrial replication and transcription proteins. Trends Genet. 22:90-95 [PubMed]
289. Shutt, T.E. and Gray, M.W. (2006) Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont. Mol. Biol. Evol. 23:1169-1179 [PubMed]
290. Simpson, A.G.B., Inagaki, Y. and Roger, A.J. (2006) Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of 'primitive' eukaryotes. Mol. Biol. Evol. 23:615-625
291. Spencer, M., Susko, E. and Roger, A.J. (2006) Modeling prokaryote gene content. Evol. Bioinf. Online 2:165-186
292. Stechmann, A., Baumgartner, M., Silberman, J.D. and Roger, A.J. (2006) The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic. BMC Evol. Biol 6:101
293. Susko, E., Leigh, J., Doolittle, W.F. and Bapteste, E. (2006) Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the (gamma)-proteobacteria. Mol. Biol. Evol. 23:1019-1030
294. Taylor, S.D.*, Mirzaei, F., and Bearne, S.L. (2006) An unsymmetrical approach to the synthesis of bismethylene triphosphate analogues. Org. Lett. 8:4243-4246 [PubMed]
295. Taylor, S.D.*, Mirzaei, F., Sharifi, S., and Bearne, S.L. (2006) Synthesis of Methylene- and Difluoromethylenephosphonate Analogs of Uridine-4-Phosphate and 3-Deazauridine-4-Phosphate. J. Org. Chem. 71:9420-9430 [PubMed]
296. Tran, K., Sun, F., Cui, Z., Thorne-Tjomsland, G., Lapierre, L.R., McLeod, R.S., Jamieson, J.C. and Yao, Z. (2006) Attenuated secretion of very low density lipoproteins from McA-RH7777 cells treated with eicosapentaenoic acid is associated with impaired utilization of triacylglycerol synthesized via phospholipid remodeling. Biochim. et Biophys. Acta 1761:463-473 [PubMed]
297. Vance, JE., Karten, B. and Hayashi, H. (2006) Lipid dynamics in neurons Biochem. Soc. Trans. 34:399-403 [PubMed]
298. Walter, J.A., Ewart, K.V., Short, C.E., Burton, I.W. and Driedzic W.R. (2006) Accelerated hepatic glycerol synthesis in rainbow smelt (Osmerus mordax) is fuelled directly by glucose and alanine: a 1H and 13C nuclear magnetic resonance study. J. Exp. Zool. 305:480-488 [PubMed]
299. Wang, H.C., Spencer, M., Susko, E. and Roger, A.J. (2006) Testing for covarion-like evolution in protein sequences. Mol.Biol.Evol. 24:294-305
300. Wang, H.C., Susko, E. and Roger, A.J. (2006) On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors. Biochem. Biophys. Res. Commun. 342:681-684
301. Watkins, R.F. and Gray, M.W. (2006) The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation in the phylum Amoebozoa J. Mol. Evol. 63:801-814 [PubMed]
302. Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F. and Papke, R.T. (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Research 16:1099-1108

Publications in 2005

303. Rainey, J.K. and Sykes, B.D. (2005) Optimizing oriented planar-supported lipid samples for solid-state protein NMR. Biophys. J. 89:2792-2805 [PubMed]
304. Rainey, J.K., DeVries, J.S. and Sykes, B.D. (2005) A rotatable flat-coil for static solid-state nuclear magnetic resonance spectroscopy. Rev. Sci. Instrum. 76:086102
305. Alessia Morandi, Olga Zhaxybayeva, J. Peter Gogarten and Joerg Graf (2005) Evolutionary and Diagnostic Implications of Intragenomic Heterogeneity in the 16S rRNA Gene in Aeromonas Strains J. Bact. 187:6561-6564
306. Anderson, I.J., Watkins, R.F., Samuelson, J., Spencer, D.F., Majoros, W.H., Gray, M.W. and Loftus, B.J. (2005) Gene discovery in the Acanthamoeba castellanii genome. Protist 156:203-214 [PubMed]
307. Andersson, J.O., Sarchfield, S. and Roger, A.J. (2005) Gene transfers from Nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol. Biol. Evol. 22:85-90
308. Andriole G.L., Humphrey P., Ray P., Gleave M.E., Trachtenberg J., Thomas L.N., Lazier C.B., Rittmaster R.S. (2005) RE: EFFECT OF THE DUAL 5alpha-REDUCTASE INHIBITOR DUTASTERIDE ON MARKERS OF TUMOR REGRESSION IN PROSTATE CANCER. J. Urol. 173(4):1433-1434 [PubMed]
309. Archibald, J. M. (2005) Jumping genes and shrinking genomes—probing the evolution of eukaryotic photosynthesis using genomics IUBMB Life 57:539-547 [PubMed]
310. Archibald, J. M. & Keeling, P. J. (2005) On the origin and evolution of plastids. Microbial phylogeny and evolution, J. Saap (ed.) Oxford University Press, New York:238-260
311. Baguma-Nibasheka, M., Li, A.W., Osman, M.S., Geldenhuys, L., Casson, A.G., Too C.K.L. and Murphy, P.R. (2005) Co-expression and regulation of the FGF-2 and FGF antisense genes in leukemic cells. Leukemia Res. 29:423-433 [PubMed]
312. Bailey, K., Cook, H.W., and McMaster, C.R. (2005) The Phospholipid Scramblase PLSCR1 Increases UV Induced Apoptosis in Chinese Hamster Ovary Cells by Primarily Augmenting the Intrinsic Apoptotic Pathway Biochim. Biophys. Acta 1733:199-209
313. Bapteste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R.L. and Doolittle, W.F. (2005) Do orthologous gene phylogenies really support tree-thining? BMC Evol. Biol. 5:33
314. Baryshnikova, O.K., Rainey, J.K. and Sykes, B.D. (2005) Nuclear magnetic resonance studies of CXC chemokine receptor 4 allosteric peptide agonists in solution. J. Pept. Res. 66(s1):12-21 [PubMed]
315. Bearne, S.L.*, and Spiteri, R.J. (2005) Reduction of intrinsic kinetic and thermodynamic barriers for enzyme-catalysed proton transfers from carbon acid substrates. J. Theor. Biol. 233:563-571 [PubMed]
316. Blouin, C., Butt, D., Roger, A.J. (2005) The impact of taxon sampling on the estimatio nof rate of evolution at sites. Mol. Biol. Evol. 22(3):784-791 [PubMed]
317. Blouin, C., Butt, D., Roger, A.J. (2005) libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny. BMC Bioinformatics 22(3):784-791 [PubMed]
318. Brianna L. Sollod, David Wilson, Olga Zhaxybayeva, J. Peter Gogarten, Roger Drinkwater, and Glenn F. King (2005) Were arachnids the first to use combinatorial peptide libraries? Peptides 26:131-139
319. Brosseau, C.L., St. Maurice, M., Bearne, S.L., and Roscoe, S.G.* (2005) Electrochemical quartz crystal nanobalance (EQCN) studies of the adsorption behaviour of an enzyme, mandelate racemase, and its substrate, mandelic acid, on Pt. Electrochim. Acta 50:1289-1297
320. Bullerwell, C.E. and Gray, M.W. (2005) In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a chytridiomycete fungus. J. Biol. Chem. 280:2463-2470 [PubMed]
321. Burley, R.K.M., and Bearne, S.L.* (2005) Inhibition of mandelate racemase by the substrate-intermediate-product analogue 1,1-diphenyl-1-hydroxymethylphosphonate. Bioorg. Med. Chem. Lett. 15:4342-4344 [PubMed]
322. Butt, D., Roger, A.J. and Blouin, C. (2005) A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny. BMC Bioinformatics 6:138
323. Dauphinee S.M., Ma M. and Too C.K.L. (2005) Role of O-linked beta-N-acetylglucosamine modification in the subcellular distribution of alpha4 phosphoprotein and Sp1 in rat lymphoma cells. J. Cell. Biochem. 96:579-588 [PubMed]
324. Dobson, M.J., Pickett, A.J., Velmurugan, S., Pinder, J.B., Barrett, L.A., Jayaram, M., and Chew, J.S.K. (2005) The 2µm plasmid causes cell death in yeast with a mutation in Ulp1 protease. Mol. Cell Biol. 25:4299-4310 [PubMed]
325. Doolittle, W. F. (2005) The origin and early evolution of life. Evolutionary Science and Society: Educating a New Generation, J. Cracraft and R.W. Bybee (eds.) American Institute of Biological Sciences, Washington:35-42
326. Doolittle, W.F. (2005) Some thoughts on the Tree of Life. The Harvey Lectures 2003-2004:99:111-128
327. Doolittle, W.F. (+17 authors) (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. USA 102:18147-18152
328. Ewart, K.V., Belanger, J.C., Williams, J., Karakach, T., Penny, S., Tsoi, S.C.M., Richards, R.C. and Douglas, S.E. (2005) Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromononas salmonicida using cDNA microarray technology. Dev. Comp. Immunol. 29:333-347 [PubMed]
329. Fairn, G.D. and McMaster, C.R. (2005) Identification and Assessment of the Role of a Nominal Phospholipid Binding Region of Oxysterol Binding Protein Related Protein ORP1S in the Regulation of Vesicular Transport Biochem. J. 387:889-896
330. Fairn, G.D. and McMaster, C.R. (2005) Studying Phospholipid Metabolism Using Yeast Systematic and Chemical Genetics Methods 36:102-108
331. Fairn, G.D., and McMaster, C.R. (2005) The Roles of the Human Lipid Binding Proteins ORP9S and ORP10S in Vesicular Transport Biochem. Cell Biol. 83:631-636
332. Fernandez-Murray, J.P. and McMaster, C.R. (2005) Nte1p Mediated Deacylation of Phosphatidylcholine Functionally Interacts with Sec14p J. Biol. Chem. 280:8544-8552
333. Fernandez-Murray, J.P., and McMaster, C. R. (2005) Glycerophosphocholine Catabolism as a New Route for Choline Formation by the Kennedy Pathway J. Biol. Chem. 280:38290-38296
334. Fernández-Murray, J.P., and McMaster, C.R (2005) Glycerophosphocholine Catabolism as a New Route for Choline Formation for Phosphatidylcholine Synthesis by the Kennedy Pathway J. Biol. Chem. 280:38290-38296
335. Gophna, U., Bapteste, E., Doolittle, W.F., Biran, D. and Ron, E.Z. (2005) Evolutionary plasticity of methionine biosynthesis. Gene 355:48-57
336. Gophna, U., Doolittle, W.F. and Charlebois, R.L. (2005) Weighted genome trees: refinements and applications. Journal of Bacteriology 187:1305-1316
337. Gray, M. W. (2005) The hydrogenosome's murky past. Nature 434:29-31 [PubMed]
338. Gray, M.W. (2005) Contemporary issues in mitochondrial origins and evolution. Microbial Phylogeny and Evolution (J. Sapp, ed.) Oxford University Press, New York:224-237
339. Hall, J.R., Richards, R.C., Maccormack, T.J., Ewart, K.V., Driedzic, W.R. (2005) Cloning of GLUT3 cDNA from Atlantic cod (Gadus morhua) and expression of GLUT1 and GLUT3 in response to hypoxia. Biochim. Biophys. Acta 1730:245-252 [PubMed]
340. Hopkins, J. (2005) Molecular Beacons as probes of RNA unfolding under native conditions. Nucleic Acids Research 33:5763-5770
341. Jiang, H., Blouin, C. (2005) Ab Initio Construction of All-atom Loop Conformations. J. Mol. Modeling. J. Mol. Modeling in press:
342. Karten B., Hayashi H., Campenot R.B., Vance D.E., and Vance J.E. (2005) Neuronal Models for Studying Lipid Metabolism and Transport. Methods 36:117-128 [PubMed]
343. Karten B., Hayashi H., Francis G.A., Campenot R.B., Vance D.E., and Vance J.E. (2005) Generation and Function of Astroglial Lipoproteins from Niemann-Pick Type C1-deficient Mice. Biochem. J. 387:779-788 [PubMed]
344. Keeling, P.J., Burger, G., Durford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. and Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676
345. Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A. J. and Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20: 670-676 [PubMed]
346. Kim, J. C., Ou, Y. Y., Badano, J., Esmail, M. A., Leitch, C. C., Fiedrich, E., Beales, P. L., Archibald, J. M., Katsanis, N., Rattner, J. B., Leroux, M. R. (2005) MKKS/BBS6, a divergent chaperonin-like protein linked to the obesity disorder Bardet-Biedl syndrome, is a novel centrosomal component required for cytokinesis. J. Cell Sci. 118:1007-1020 [PubMed]
347. Koski, L.B., Gray, M.W., Lang, B.F. and Burger, G. (2005) AutoFACT: an Automatic Functional Annotation and Classification Tool. BMC Bioinfomatics 6:151 [PubMed]
348. Kwon, M. C. S. Yoon W. Jeong S. G. Rhee & D. M. Waisman. (2005) Annexin A2-S100A10 heterotetramer, a novel substrate of thioredoxin. J.Biol.Chem. 280:23584-23592 [PubMed]
349. Kwon, M. T. J. MacLeod Y. Zhang & D. M. Waisman. (2005) S100A10, annexin A2, and annexin a2 heterotetramer as candidate plasminogen receptors. Front Biosci. 10:300-325 [PubMed]
350. Lagace, T.A. and Ridgway, N. D. (2005) The rate-limiting enzyme in phosphatidylcholine synthesis regulates proliferation of the nucleoplasmic reticulum Mol. Biol. Cell 16:1120-1130 [PubMed]
351. Lagace, T.L. and Ridgway, N. D. (2005) Induction of apoptosis by lipophilic activators of CTP:phosphcholine cytidylyltransferase (CCT) alpha Biochem. J. 392:449-56 [PubMed]
352. Liu Z, Li H, Derouet M, Filmus J, LaCasse EC, Korneluk RG, Kerbel RS, and Rosen KV (2005) ras oncogene triggers upregulation of cIAP2 and XIAP in intestinal epithelial cells: EGF receptor-dependent and -independent mechanisms of ras-induced transformation. J. Biol. Chem. 280:37383-37392 [PubMed]
353. Lutz Hamel, Olga Zhaxybayeva and J. Peter Gogarten: (2005) PentaPlot: A software tool for the illustration of genome mosaicism BMC Bioinformatics 6:13
354. Lyons, P.J., Muise, A.M. and Ro, H.-S. (2005) MAPK modulates the DNA binding of adipocyte enhancer-binding protein 1. Biochemistry 44:926-931 [PubMed]
355. MacLeod, D., Charlebois, R.L., Doolittle, W.F. and Bapteste, E. (2005) Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol. Biol. 5:27
356. MacLeod, T. J. N. R. Filipenko & D. M. Waisman. (2005) Characterization of the RNA-Binding Properties of Annexin A2 Heterotetramer. Annexins 1:191-199
357. Marignani, P. A. (2005) LKB1, the multi-tasking tumour suppressor kinase. Journal of Clinical Pathology 58:15-19 [PubMed]
358. Matte, G., Sangster, S.M., Acker, M., Hudgins, M. and Too, C.K.L. (2005) Characterization of 123I-iodo-alpha-methyltyrosine transport in rat lymphoma cells. Nuclear Medicine and Biology 32:67-73 [PubMed]
359. Meng, Q. Wang, Y. Liu, P. X.-Q. (2005) An intron-encoded protein assists RNA splicing of multiple similar introns of different genes. J Biol Chem. 280:35085-35088 [PubMed]
360. Mitchell, P. L., Langille, M., Currie, D.L., and McLeod, R.S. (2005) Effect of conjugated linoleic acid isomers on lipoproteins and atherosclerosis in the Syrian golden hamster. Biochimica et Biophysica Acta 1734:269-276 [PubMed]
361. Mohan, K., Cordeiro, E., Vaci, M., McMaster, C.R., and Issekutz, T.B. (2005) CXCR3 is Required for Migration to Dermal Inflammation by Normal and In Vivo Activated T Cells: Differential Requirements by CD4 and CD8 Memory Subsets Eur. J. of Immunol. 35:1702-1711
362. Morash, S.M., Douglas, D., Cook, H.W., McMaster, C.R., and Byers, D.M. (2005) Expression of MARCKS Effector Domain Mutants Alters Phospholipase D Activity and Cytoskeletal Morphology of SK-N-MC Neuroblastoma Cells Neurochem. Res. 11:1353-1364 [PubMed]
363. Nesbo, C.L., Boucher, Y., Dlutek, M. and Doolittle, W.F. (2005) Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environmental Microbiology 7:2011-2026
364. Olga Zhaxybayeva and J. Peter Gogarten (2005) Review of "Cladistics: a practical primer on CD-ROM" by Peter Skelton and Andrew Smith. Origin of Life and Evolution of Biospheres 35:69-71
365. O’Malley, P.G.P., Sangster, S.M., Abdelmagid, S.A., Bearne, S.L. and Too, C.K.L.* (2005) Characterizaion of a novel, cytokine-inducible carboxypeptidase-D isoform in hematopoietic tumor cells. Biochem J. 390:665-673 [PubMed]
366. Padraic G. P. O'Malley, Shirley M. Sangster, Salma A. Abdelmagid, Stephen L. Bearne, and Catherine K. L. Too (2005) Characterization of a novel, cytokine-inducible carboxypeptidase D isoform in haematopoietic tumour cells Biochem J 390(Pt 3):665–673
367. Patron, N. J., Waller, R. F., Archibald, J. M. & Keeling, P. J. (2005) Complex protein targeting to dinoflagellate plastids. J. Mol. Biol. 348:1015-1024 [PubMed]
368. Paul C.A., Reid P.C., Boegle A.K., Karten B., Zhang M., Jiang Z.G, Franz D., Lin L., Chang T.Y., Vance J.E., Blanchette-Mackie J., and Maue R.A. (2005) Adenovirus expressing an NPC1-GFP fusion gene corrects neuronal and nonneuronal defects associated with Niemann pick type C disease. J Neurosci Res. 86:706-719 [PubMed]
369. Perry, R. J. and Ridgway, N. D. (2005) Molecular mechanisms and regulation of ceramide transport Biochem. Biophys. Acta 1734:220-234 [PubMed]
370. Russell, A.G., Shutt, T.E., Watkins, R.F. and Gray, M.W. (2005) An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia. BMC Evol. Biol. 5:45 [PubMed]
371. Russell, A.G., Watanabe, Y-i., Charette, J.M. and Gray, M.W. (2005) Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins in methylation-guide box C/D snoRNPs throughout the domain Eucarya. Nucleic Acids Res. 33:2781-2791 [PubMed]
372. Siddiqi, F., Bourque, J.R., Jiang, H., Gardner, M., St. Maurice, M., Blouin, C., and Bearne, S.L.* (2005) Perturbing the Hydrophobic Pocket of Mandelate Racemase To Probe Phenyl Motion during Catalysis. Biochemistry 44:9013-9021 [PubMed]
373. Slepkov, E.R., Rainey, J.K., Li, X., Liu, Y., Cheng, F.J., Lindhout, D.A., Sykes, B.D. and Fliegel, L. (2005) Structural and functional characterization of transmembrane segment IV of the NHE1 isoform of the Na⁺/H⁺ exchanger. J. Biol. Chem. 280:17863-17872 [PubMed]
374. Spencer, M., Susko, E. and Roger, A.J. (2005) Likelihood, parsimony and heterogeneous evolution. Mol. Biol. Evol. 22:1161-1164
375. Susko, E., Spencer, M. and Roger, A.J. (2005) Biases in phylogenetic estimation can be caused by random sequence segments. J. Mol. Evol. 61:351-359
376. Taylor, M.M., MacDonald, K., Morris, A.J., and McMaster, C.R. (2005) Enhanced Apoptosis Through Farnesol Inhibition of Phospholipase D Signal Transduction FEBS J. 272:5056-5063
377. Thomas L.N., Lazier C.B., Gupta R., Norman R.W., Troyer D.A., O'Brien S.P., Rittmaster R.S. (2005) Differential alterations in 5alpha-reductase type 1 and type 2 levels during development and progression of prostate cancer. Prostate 63(3):231-239 [PubMed]
378. Tsaousis, A.D., Martin, D.P., Ladoukakis, E.D., Posada, D. & Zouros, E. (2005) Widespread Recombination in Published Animal mtDNA Sequences Mol Biol Evol 22:925-933 [PubMed]
379. Vance J.E., Hayashi H., and Karten B. (2005) Cholesterol Homeostasis in Neurons and Glial Cells. Semin. Cell Dev. Biol. 16:193-212 [PubMed]
380. Waisman, D. M. (2005) Annexin A2 may not play a role as a plasminogen receptor. Br.J.Haematol. 131:553-554 [PubMed]
381. Waisman, D. M. (2005) Characterization of the RNA-Binding Properties of Annexin A2 Heterotetramer. Annexins 1:191-199
382. Walsh, D.A. and Doolittle, W.F. (2005) The real domains of life. Current Biology 15:R237-R240
383. Walsh, D.A., Papke, R.T. and Doolittle, W.F. (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environmental Microbiology 7:1655-1666
384. Wong, T., Fairn, G.D., Poon, P.P., McMaster, C.R., Singer, R.A., and Johnston, G.C. (2005) Membrane Metabolism Mediated by Sec14p Family Members Influences ArfGAP Activity for Transport from the trans-Golgi Proc. Natl. Acad. Sci. U.S.A 102:12777-12802
385. Wong, T., Fairn, G.D., Poon, P.P., Shmulevitz, M., McMaster, C.R., Singer, R.A. and Johnston, G.C. (2005) Membrane metabolism mediated by Sec14 family members influences Arf GTPase activating protein activity for transport from the trans-Golgi. Proc. Natl. Acad. Sci. USA 102:12777-12782 [PubMed]
386. Yan SR, Joseph RR, Rosen K, Reginato MJ, Jackson A, Allaire N, Brugge JS, Jobin C, Stadnyk AW (2005) Activation of NF-kappaB following detachment delays apoptosis in intestinal epithelial cells. Oncogene 24:6482-91 [PubMed]
387. Zaremberg, V., Gajate, G., Cacharro, L.M., Mollinedo, F., and McMaster, C.R. (2005) Cytotoxicity of the Anti-cancer Lipid Edelfosine is Through Selective Modification of Lipid Raft Composition J. Biol. Chem. 280:38047-38058
388. Zhang, L., Reidy, S.P., Nicholson, T.E., Lee, H.-J., Majdalawieh, A., Webber, C., Stewart, B.R., Dolphin, P. and Ro, H.-S. (2005) The role of AEBP1 in sex-specific diet-induced obesity. Mol. Med. 11:39-47 [PubMed]

Publications in 2004

389. Hunt, A.N., Fenn, H.C., Clark, G.T., Wright, M.M., Postle, A.D., and McMaster, C.R. (2004) Lipidomic Analysis of the Molecular Specificity of a Cholinephosphotransferase In Situ. Biochem. Soc. Trans 32:1060-1062
390. Reddy, T. and Kablar, B. (2004) Evidence for the involvement of neurotrophins in muscle transdifferentiation and acetylcholine receptor transformation in the esophagus of Myf5-/-:MyoD-/- and NT-3-/- embryos. Developmental Dynamics. 231:683-692 [PubMed]
391. Dellaire, G. and D.P. Bazett-Jones (2004) PML nuclear bodies: Dynamic sensors of DNA damage and cellular stress. Bioessays 26(9):963-977 [PubMed]
392. Rainey, J.K. and Goh, M.C. (2004) An interactive triple-helical collagen builder. Bioinformatics 20:2458-2459 [PubMed]
393. Rainey, J.K. and Goh, M.C. (2004) Statistically based reduced representation of amino acid side chains. J. Chem. Inf. Comput. Sci. 44:817-830 [PubMed]
394. Andriole G.L., Humphrey P., Ray P., Gleave M.E., Trachtenberg J., Thomas L.N., Lazier C.B., Rittmaster R.S. (2004) Effect of the dual 5alpha-reductase inhibitor dutasteride on markers of tumor regression in prostate cancer. J. Urol. 172(3):915-919 [PubMed]
395. Archibald, J. M. & Keeling, P. J. (2004) The evolutionary history of plastids: a molecular phylogenetic perspective. Organelles, genomes and eukaryote phylogeny: an evolutionary synthesis in the age of genomics, R. P. Hirt and D. S. Horner (eds.) Taylor and Francis Books, London:55-74
396. Archibald, J. M. and Keeling, P. J. (2004) Ubiquitin and actin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens. J. Euk. Microbiol. 51:1-6 [PubMed]
397. Bapteste, E., Boucher, Y., Leigh, J. and Doolittle, W.F. (2004) Phylogenetic reconstruction and lateral gene transfer. Trends in Microbiology 12:406-411
398. Barabas, A. Z. C. D. Cole A. D. Barabas J. M. Cowan C. S. Yoon D. M. Waisman & R. Lafreniere. (2004) Presence of immunoglobulin M antibodies around the glomerular capillaries and in the mesangium of normal and passive Heymann nephritis rats. Int.J.Exp.Pathol. 85:201-212 [PubMed]
399. Blouin, C. Butt, D. and Roger, A.J. (2004) Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain. Prot. Sci. 13(3):608-616 [PubMed]
400. Boucher, Y., Douady, C.J., Sharma, A.K., Kamekura, M. and Doolittle, W.F. (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J. Bacteriol. 186:3980-3990
401. Boucher, Y., Kamekura, M. and Doolittle, W.F. (2004) Origins and evolution of isoprenoid lipid biosynthesis in archaea. Molecular Microbiology 52:515-527
402. Caplan, J. F. N. R. Filipenko S. L. Fitzpatrick & D. M. Waisman. (2004) Regulation of annexin A2 by reversible glutathionylation. J.Biol.Chem. 279:7740-7750 [PubMed]
403. Charlebois, R.L. and Doolittle, W.F. (2004) Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Research 14:2469-2477
404. Dacks, J.B. and Doolittle, W.F. (2004) Molecular and phylogenetic characterization of syntaxin genes from parasitic protozoa. Molecular & Biochemical Parasitology 136:123-136
405. Doolittle, W.F. (2004) Q & A Current Biology 14(5):R176-177
406. Doolittle, W.F. (2004) Bacteria and archaea. In Assembling the Tree of Life J. Cracraft & M.J. Donoghue, eds. (from Tree of Life Symposium, American Museum of Natural History, June 2002) Oxford University Press, New York:
407. Doolittle, W.F. (2004) If the Tree of Life fell, would we recognize the sound? In J. Sapp (Ed.), Microbial Evolution: Concepts and controversies Oxford University Press, USA:119-133
408. Driedzic, W.R. and Ewart, K.V. (2004) Control of glycerol production by rainbow smelt (Osmerus mordax) to provide freeze resistance and allow foraging at low winter temperatures. Comp. Biochem. Physiol. 139:347-357 [PubMed]
409. Ewart, K.V. and Tsoi, S.C.M. (2004) Innate immune recognition of pathogens in teleost fish. pp. 82-116 In: Molecular aspects of fish and marine biology Volume III: Trends in the study of bacterial and viral fish diseases. K.Y. Leung and C.L. Hew (eds.), World Scientific Publishing: Singapore
410. Filipenko, N. R. T. J. MacLeod C. S. Yoon & D. M. Waisman. (2004) Annexin A2 is a novel RNA-binding protein. J. Biol. Chem. 279:8723-8731 [PubMed]
411. Gophna, U., Charlebois, R.L. and Doolittle, W.F. (2004) Have archaeal genes contributed to bacterial virulence? Trends in Microbiology 12:213-219
412. Gray, J.V., Petsko, G.A., Johnston, G.C., Ringe, D., Singer, R.A. and Werner-Washburne, M. (2004) 'Sleeping beauty' quiescence in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 68:187-206 [PubMed]
413. Hayashi H., Karten B., Vance D.E., Campenot R.B., Maue R.A., Vance J.E. (2004) Methods for the study of lipid metabolism in neurons. Anal. Biochem. 331:1-16 [PubMed]
414. Inagaki, Y., Simpson, A.G.B., Dacks, J. and Roger, A.J. (2004) Phylogenetic artifacts can be caused by leucine, serine and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Syst. Biol. 53:582-593
415. Inagaki, Y., Susko, E. Fast, N.M. and Roger, A.J. (2004) Covarion shifts cause a long-branch attraction artifact that unites Microsporidia and Archaebacteria in EF-1alpha phylogenies. Mol. Biol. Evol. 21:1340-1349
416. J.P. Wyles and N.D. Ridgway (2004) VAMP-associated protein regulates partitioning of oxysterol-binding protein-related protein -9 between the endoplasmic reticulum and Golgi apparatus. Exp. Cell Res. 297:533-547 [PubMed]
417. Keeling, P. J., Archibald, J. M., Fast, N. M., Palmer, J. D. (2004) Comment on “The evolution of modern eukaryotic phytoplankton”. Science 306:2191b [PubMed]
418. Lagace, D.C., McLeod, R.S., and Nachtigal, M.W. (2004) Valproic acid inhibits leptin secretion and reduces leptin mRNA levels in adipocytes. Endocrinology 145:5493-5503 [PubMed]
419. Lapierre, L.R., Currie, D.L., Yao, Z., Wang, J. and McLeod, R.S. (2004) Amino acid sequences within the β-1 domain of human apolipoprotein B can mediate rapid intracellular degradation. J. Lipid Res. 45:366-377 [PubMed]
420. Lazier C.B., Thomas L.N., Douglas R.C., Vessey J.P., Rittmaster R.S. (2004) Dutasteride, the dual 5alpha-reductase inhibitor, inhibits androgen action and promotes cell death in the LNCaP prostate cancer cell line. Prostate 58(2):130-144 [PubMed]
421. Lewis, S.L., Poon, P.P., Singer, R.A., Johnston, G.C. and Spang, A. (2004) The ArfGAP Glo3 is required for the generation of COPI vesicles. Mol. Biol. Cell 15:4064-4072 [PubMed]
422. Li, Z., Lin Q., Yang, D.S.C. Ewart, K.V. and Hew, C.L. (2004) The role of Ca2+-coordinating residues of herring antifreeze protein in ice binding. Biochemistry 43:14547-14554 [PubMed]
423. Liu, X.-Q. and Yang, J. (2004) Prp8 intein in fungal pathogens: target for potential antifungal drugs. FEBS Lett. 572:46-50 [PubMed]
424. Liu, X.-Q. and Yang, J. (2004) Bacterial thymidylate synthase with intein, group II intron, and distinctive ThyX motifs. J. Bacteriol. 186:6316-6319 [PubMed]
425. Lunn, F.A., and Bearne, S.L.* (2004) Alternative Substrates for Wild-type and L109A E. coli CTP Synthases. Kinetic Evidence for a Constricted Ammonia Tunnel. Eur. J. Biochem. 271:4204-4212 [PubMed]
426. MacDonnell, J.E., Lunn, F.A., and Bearne, S.L.* (2004) Inhibition of E. coli CTP synthase by the positive allosteric effector GTP. Biochim. Biophys. Acta 1699:213-220 [PubMed]
427. McLeod, R. S., LeBlanc, A. M., Langille, M. A., Mitchell, P. L. and Currie, D. L. (2004) Conjugated linoleic acids, atherosclerosis and hepatic very low density lipoprotein metabolism. Amer. J. Clin. Nutr. 79:1169S-1174S [PubMed]
428. O'Donnell, A.F., Brewster, N.K., Kurniawan, J., Minard, L.V., Johnston, G.C. and Singer, R.A. (2004) Domain organization of the yeast histone chaperone FACT: the conserved N-terminal domain of FACT subunit Spt16 mediates recovery from replication stress. Nucl. Acids Res. 32:5894-5906 [PubMed]
429. O. Zhaxybayeva and J. Peter Gogarten (2004) Cladogenesis, Coalescence and the Evolution of the Three Domains of Life Trends in Genetics 20(4):182-187
430. Olga Zhaxybayeva, Lutz Hamel, Jason Raymond, and J. Peter Gogarten (2004) Visualization of Phylogenetic content of Five Genomes with Dekapentagonal Maps. Genome Biology 5:R20
431. Papke, R.T., Koenig, J.E., Rodriguez-Valera, F. and Doolittle, W.F. (2004) Frequent recombination in a saltern populationof Halorubrum. Science 306:1928-1929
432. Perry, R.J. and Ridgway N.D. (2004) The role of de novo ceramide synthesis in the mechanism of action of the tricyclic xanthate D609 J. Lipid Res. 45:164-173 [PubMed]
433. Ro, H.-S. (2004) Adipocyte-enhancer binding unit 1 Handbook of Proteolytic Enzymes 2nd Edn, A.J. Barrett, N.D. Rawlings and J.F. Woessner (eds.) Academic Press Limited:846-848
434. Rogers, M.B., Archibald, J.M., Field, M.A., Li, C., Striepen, B. and Keeling, P. J. (2004) Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natans. J. Eukaryot. Microbiol. 51:529-535 [PubMed]
435. Ruiz-Trillo, I., Inagaki, Y., Davis, L.A., Sperstad, S., Landfald, B. and Roger, A.J. (2004) Capsaspora owczarzaki is an independent opisthokont lineage. Curr. Biol. 14:R946-R947
436. Silberman, J.D., Collins, A.G., Gershwin, L.-A., Johnson, P.J. and Roger, A.J. (2004) Ellobiopsidae of the genus Thallasomyces are alveolates. J. Euk. Microbiol. 51:246-252
437. Simpson, A.G.B. and Roger, A. J. (2004) The real 'kingdoms' of eukaryotes. Curr. Biol. 14:R693-R696
438. Simpson, A.G.B. and Roger, A.J. (2004) Excavata and the origin of amitochondriate eukaryotes. Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics, R.P. Hirt and D.S. Horner (eds.) CRC Press, Boca Raton, Florida:27-53
439. Simpson, A.G.B., Gill, E.E., Callahan, H.A., Litaker, R.W. and Roger, A.J. (2004) Early evolutin within kinetoplastids (euglenozoa), and the late emergence of trypanosomatids. Protist 155:407-422
440. Singer, R.A. and Johnston, G.C. (2004) The FACT of chromatin modulator: genetic and structure/function relationships. Biochem. Cell Biol. 82:419-427 [PubMed]
441. Soanes, K.H., Figuereido, K., Richards, R.C., Mattatall, N.R. and Ewart, K.V. (2004) Sequence and expression of C-type lectin receptors in Atlantic salmon (Salmo salar). Immunogenetics 56:572-584 [PubMed]
442. St. Maurice, M., and Bearne, S.L.* (2004) Hydrophobic Nature of the Active Site of Mandelate Racemase. Biochemistry 43:2524-2532 [PubMed]
443. Stechmann, A. (2004) Genome Biology: the dynamics of static genomes. Curr. Biol. 14(12):R473-R474 [PubMed]
444. Stechmann, A. and Cavalier-Smith, T. (2004) Evolutionary origins of Hsp90 chaperones and a deep paralogy in their bacterial ancestors. 51(3):364-373 [PubMed]
445. Stratton, L., Wu, S., Richards, R.C. and Ewart, K.V. (2004) Oligomerisation and carbohydrate binding in a salmon serum C-type lectin consistent with non-self recognition. Fish Shellfish Immunol. 17:315-323 [PubMed]
446. Sun, W. Yang, J. Liu, X.-Q. (2004) Synthetic two-piece and three-piece split inteins for protein trans-splicing. J. Biol. Chem. 279:35281-35286 [PubMed]
447. Sundaram, M., Cook, H.W., and Byers, D.M. (2004) The MARCKS family of phospholipid binding proteins: regulation of phospholipase D and other cellular components. Biochem. Cell Biol. 82:191-200 [PubMed]
448. Susko, E. and Roger, A. J. (2004) Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies from EST surveys. Bioinformatics 20:2279-2287
449. Susko, E., Inagaki, Y. and Roger, A.J. (2004) On inconsistency of the neighbor-joining method, least squares and minimum evolution estimation when distances are incorrectly specified. Mol. Biol. Evol. 21:1629-1642
450. Tsoi, S.C.M., Ewart, K.V., Penny, S., Melville, K., Liebscher, R.S., Brown, L.L. and Douglas, S.E. (2004) Identification of immune-relevant genes from Atlantic salmon using suppression subtractive hybridization. Mar. Biotechnol. 6:199-214 [PubMed]
451. Walsh, D.A., Bapteste, E., Kamekura, M. and Doolittle, W.F. (2004) Evolution of RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol. Biol. Evol. 21:2340-2351
452. Yan, S. R., Byers, D. M., and Bortolussi, R. (2004) Role of protein tyrosine kinase p53/p56lyn in diminished lipopolysaccharide priming of fMLP-induced superoxide production in human newborn neutrophils Infect. Immun. 72:6455-6462 [PubMed]
453. Yan, S.R., Qing, G., Byers, D.M., Stadnyk, A.W., Al-Hertani, W., and Bortolussi, R. (2004) Role of MyD88 in diminished TNF-a production by newborn mononuclear cells in response to lipopolysaccharide. Infect. Immun. 72:1223-1229 [PubMed]
454. Yang, J., Meng, Q., and Liu, X.-Q. (2004) Intein harboring large tandem repeats in replicative DNA helicase of Trichodesmium erythraeum. Mol. Microbiol. 51:1185-1192 [PubMed]
455. Yu, A., McMaster, C.R., Byers, D.M., Ridgway, N.D., and Cook, H.W. (2004) Resistance to UV-induced apoptosis in Chinese hamster ovary cells overexpressing phosphatidylserine synthases. Biochem. J. 381:609-618 [PubMed]
456. Zhang, L. D. K. Fogg & D. M. Waisman. (2004) RNA interference-mediated silencing of the S100A10 gene attenuates plasmin generation and invasiveness of Colo 222 colorectal cancer cells. J.Biol.Chem. 279:2053-2062 [PubMed]
457. Zhao, W. Q. D. M. Waisman & M. Grimaldi. (2004) Specific localization of the annexin II heterotetramer in brain lipid raft fractions and its changes in spatial learning. J. Neurochem. 90:609-620 [PubMed]
458. Zhaxybayeva, O., Lapierre, P. and Gogarten J.P. (2004) Genome Mosaicism and Organismal Lineages Trends in Genetics 20(5):254-260

Publications in 2003

459. Ridgway, N.D. and Lagace, T.L. (2003) Regulation of he CDP-choline pathway by sterol-regulatory element binding proteins involves transcriptional and post-transcriptional mechanisms Biochem. J. 372:811-819 [PubMed]
460. Andersson, J.O. and Roger, A.J. (2003) Evolution of glutamate dehydrogenase genes: lateral gene transfer within and between prokaryotes and eukaryotes. BMC Evolutionary Biology 3:14
461. Andersson, J.O., Sjogren M., Davis, L.A.M., Embley, T.M. and Roger, A.J. (2003) Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr. Biol. 13:94-104
462. Archibald, J. M., Longet, D., Pawlowski, J. and Keeling, P. J. (2003) A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol. 20:62-66 [PubMed]
463. Archibald, J. M., Rogers, M., Toop, M. Ishida, K., and Keeling, P. J. (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc. Natl. Acad. Sci. U.S.A. 100:7678-7683 [PubMed]
464. Archibald, J. M., Teh, E. M. and Keeling, P. J. (2003) Novel ubiquitin fusion proteins: ribosomal protein P1 and actin. J. Mol. Biol. 328:771-778 [PubMed]
465. Archibald, J.M. and Keeling, P.J. (2003) Plant genomes: cyanobacterial genes revealed. Heredity 90:2-3 [PubMed]
466. Blouin, C., Boucher, Y., and Roger, A.J. (2003) Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res. 31:790-797 [PubMed]
467. Choi H.Y., Karten B., Chan T., Vance J.E., Greer W.L., Heidenreich R.A., Garver W.S., Francis G.A. (2003) Impaired ABCA1-dependent lipid efflux and hypoalphalipoproteinemia in human Niemann-Pick type C disease. J. Biol. Chem. 278:32569-32577 [PubMed]
468. Choi, K. S. D. K. Fogg C. S. Yoon & D. M. Waisman. (2003) P11 regulates extracellular plasmin production and invasiveness of HT1080 fibrosarcoma cells. FASEB J 17:235-246
469. Choi, K.S., D.K. Fogg, S.L. Fitzpatrick & D.M. Waisman (2003) Role of annexin II tetramer in the regulation of plasmin activity. Annexins: Biological importance and annexin-related pathologies. Eds. Joanna Bandorowicz-Pikula Ed Landes Bioscience:218-233
470. Dacks, J.B., Davis, L.A.M., Sjogren, A.M., Andersson, J.O., Roger, A.J. and Doolittle, W.F. (2003) Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages. Proc. R. Soc. Lond. B. Suppl. 2:S168-S171
471. Doolittle, W.F., Boucher, Y., Nesbo, C.L., Douady, C.J., Andersson, J.O. and Roger, A.J. (2003) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Proc. Roy. Soc. Lond. Series B 358:39-58
472. Filipenko, N.R. & D.M. Waisman (2003) Annexin II- Analysis of a pleiotropic protein. In Annexins: Biological importance and annexin-related pathologies. Bioscience:127-156
473. Gong, H. and Byers, D.M. (2003) Glutamate-41 of Vibrio harveyi acyl carrier protein is essential for fatty acid synthase but not acyl-ACP synthetase activity. Biochem. Biophys. Res. Commun. 302:35-40 [PubMed]
474. Inagaki, Y., Blouin, C., Susko, E., and Roger, A.J. (2003) Assessing functional divergence in EF-1alpha and its paralogues in eukaryotes and archaebacteria. Nucleic Acids Res. 31:4227-4237 [PubMed]
475. Iyengar, A., and Bearne, S.L.* (2003) Aspartate-107 and leucine-109 facilitate efficient coupling of glutamine hydrolysis to CTP synthesis by Escherichia coli CTP synthase. Biochem. J. 369:497-507 [PubMed]
476. Jason Raymond, Olga Zhaxybayeva, J. Peter Gogarten and Robert E. Blankenship (2003) Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Phil. Trans. R. Soc. Lond. B 358:223-230
477. Jeyakumar, M., R. Thomas, E. Elliot-Smith, D.A. Smith, A.C. Van Der Spoel, A. D'Azzo, V. Hugh Perry, T.D. Butters, R.A. Dwek and F.M. Platt. (2003) Central nervous system inflammation is a hallmark of pathogenesis in mouse models of GM1 and GM2 gangliosidosis. Brain 126:974-987 [PubMed]
478. Johnston, G.C. and Singer, R.A. (2003) Resumption of cell proliferation from stationary phase. Dormancy and Low-Growth States in Microbial Disease, A.R.M. Coates (ed.) Adv. Mol. Cell. Microbiol., vol. 3, Cambridge Univ. Press:223-233
479. Karten B., Vance D.E., Campenot R.B., and Vance J.E. (2003) Trafficking of cholesterol from cell bodies to distal axons in Niemann Pick C1-deficient neurons. J. Biol. Chem. 278:4168-4175 [PubMed]
480. Kwon, M. & D.M. Waisman (2003) Mechanism of angiostatin formation from plasminogen. Plasminogen: Structure, Activation, and Regulation Eds. Waisman, D. M. Kluwer academic/plenum publishers New York 8,:135-156
481. Le, D. M. A. Besson D. K. Fogg K. S. Choi D. M. Waisman C. G. Goodyer B. Rewcastle & V. W. Yong. (2003) Exploitation of astrocytes by glioma cells to facilitate invasiveness: a mechanism involving matrix metalloproteinase-2 and the urokinase-type plasminogen activator-plasmin cascade. J. Neurosci. 23:4034-4043 [PubMed]
482. Liu, X.-Q. and Yang, J. (2003) Split dnaE genes encoding multiple novel inteins in Trichodesmium erythraeum. J. Biol. Chem. 278:26315-26318 [PubMed]
483. Liu, X.-Q., Yang, J., and Meng, Q. (2003) Four inteins and three group II introns encoded in a bacterial ribonucleotide reductase gene. J. Biol. Chem. 278:46826-46831 [PubMed]
484. Longet, D., Archibald, J.M., Keeling, P.J., and Pawlowski, J. (2003) Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int. J. Syst. Evol. Microbiol. 53:1735-1739 [PubMed]
485. Olga Zhaxybayeva and J. Peter Gogarten (2003) Spliceosomal Introns: New Insights into Their Evolution. Current Biology 13:R764-766
486. Olga Zhaxybayeva and J. Peter Gogarten (2003) An Improved Probability Mapping Approach to Assess Genome Mosaicism BMC Genomics 4:37
487. Shan, Y., Milios, E., Roger, A., Blouin, C. and Susko, E. (2003) Automatic recognition of regions of intrinsically poor multiple alignment. Proceedings of the 2003 IEEE Bioinformatics Conference (CSB2003):483-483
488. Simard. D., Hewitt, K.A., Lunn, F., Iyengar, A., and Bearne, S.L.* (2003) Limited proteolysis of Escherichia coli cytidine 5'-triphosphate synthase. Identification of residues required for CTP formation and GTP-dependent activation of glutamine hydrolysis. Eur. J. Biochem. 270:2195-2206 [PubMed]
489. Simpson, A.G.B. and Roger, A.J. (2003) Protein phylogenies robustly resolve the deep-level evolutionary relationships amongst Euglenozoa. Mol. Phylogenet. Evol. 30:201-212
490. St. Maurice, M., Bearne, S.L.*, Lu, W., and Taylor, S.D. (2003) Inhibition of mandelate racemase by alpha-fluorobenzylphosphonates. Bioorg. Med. Chem. Lett. 13:2041-2044 [PubMed]
491. Stechmann, A. , Cavalier-Smith, T. (2003) The root of the eukaryote tree pinpointed. Curr. Biol. 13(17):R665-R666 [PubMed]
492. Stechmann, A. , Cavalier-Smith, T. (2003) Eukaryote phylogeny using heat-shock protein Hsp90. J. Mol. Evol. 57(4):408-419 [PubMed]
493. Susko, E., Field, C., Blouin, C. and Roger, A.J. (2003) Estimation of rates-across-sites distributions in phylogenetic substitution models. Syst. Biol. 52(5):594-603 [PubMed]
494. Thomas L.N., Douglas R.C., Vessey J.P., Gupta R., Fontaine D., Norman R.W., Thompson I.M., Troyer D.A., Rittmaster R.S., Lazier C.B. (2003) 5alpha-reductase type 1 immunostaining is enhanced in some prostate cancers compared with benign prostatic hyperplasia epithelium. J. Urol. 170(5):2019-2025 [PubMed]
495. Vickaryous, N., Teh, E., Stewart, B., Dolphin, P.J., Too, C.K.L., and McLeod, R.S. (2003) Deletion of N-terminal amino acids from human lecithin:cholesterol acyltransferase differentially affects enzyme activity toward alpha- and beta-substrate lipoproteins. Biochim et Biophys Acta 1646:164-172 [PubMed]
496. Waisman, D. M. (2003) Phospholipid-associated annexin A2-S100A10 heterotetramer and its subunits: characterization of the interaction with tissue plasminogen activator, plasminogen, and plasmin. J.Biol.Chem. 278:25577-25584 [PubMed]
497. Waisman, D. M. (2003) Plasminogen Receptors Plasminogen:Structure, Activation and Regulation/. Eds. Waisman, D. M. luwer Academic/Plenum publishers 5:81-101

Publications in 2002

498. Rainey, J.K. and Goh, M.C. (2002) A statistically derived parameterization for the collagen triple-helix. Protein Sci. 11:2748-2754 [PubMed]
499. Rainey, J.K. and Goh, M.C. (2002) Parallel atomic force microscopy and NMR spectroscopy to investigate self-assembled protein-nucleotide aggregates. J. Phys. Chem. B 106:5553-5560
500. Rainey, J.K., Wen, C.K. and Goh, M.C. (2002) Hierarchical assembly and the onset of banding in fibrous long spacing collagen revealed by atomic force microscopy. Matrix Biol. 21:647-660. [PubMed]
501. Andersson, J. and Roger, A.J. (2002) Evolutionary analysis of the small subunit of glutamate synthase: Gene order conservation, gene fusions and prokaryote-to-eukaryote lateral gene transfers. Euk. Cell. 1:304-310
502. Andersson, J.A. and Roger, A.J. (2002) A cyanobacterial gene in non-photosynthetic protists - an early chloroplast acquisition in eukaryotes? Curr. Biol. 12:115-119
503. Archibald, J. M. and Keeling, P. J. (2002) Recycled plastids: a green movement in eukaryotic evolution. Trends Genet. 18:577-584 [PubMed]
504. Archibald, J. M. and Roger, A. J. (2002) Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signal. J. Mol. Evol. 55:232-245 [PubMed]
505. Archibald, J. M. and Roger, A. J. (2002) Gene duplication and gene conversion shape the evolution of archaeal chaperonins. J. Mol. Biol. 316:1041-1050 [PubMed]
506. Blouin C, Guillemette JG, Wallace CJ. (2002) Probing electrostatic interactions in cytochrome c using site-directed chemical modification. Biochem. Cell. Biol. 80(2):197-203 [PubMed]
507. Boudreau, R.T.M., Sangster, S.M., Johnson, L.M., Dauphinee, S., Li, A.W. and Too, C.K.L. (2002) Implication of alpha4 phosphoprotein and rapamycin-sensitive mTOR pathway in prolactin receptor signalling. J. Endocrinology 173:493-506 [PubMed]
508. Brooks, N. D. J. E. Grundy N. Lavigne M. C. Derry C. M. Restall C. R. MacKenzie D. M. Waisman & E. L. Pryzdial. (2002) Ca2+-dependent, phospholipid-independent binding of annexin 2 to annexin 5. Biochem.J. 367:895-900 [PubMed]
509. Byers D. M. and Shen, Z. (2002) Biochemical evidence against protein-mediated uptake of myristic acid in the bioluminescent marine bacterium Vibrio harveyi. Can. J. Microbiol. 48:933-939 [PubMed]
510. C. Wang, L. JeBailey and N.D. Ridgway (2002) Oxysterol-binding protein (OSBP)-related protein 4 binds 25-hydroxycholesterol and interacts with vimentin intermediate filaments. Biochem. J. 361:461-472 [PubMed]
511. Coll ML, Rosen K, Ladeda V, Filmus J. (2002) Increased Bcl-xL expression mediates v-Src-induced resistance to anoikis in intestinal epithelial cells. Oncogene 21(18):2908-13 [PubMed]
512. Fogg, D. K. D. E. Bridges K. T. Cheung G. Kassam N. R. Filipenko K. S. Choi S. L. Fitzpatrick M. Nesheim & D. M. Waisman. (2002) The p11 subunit of annexin II heterotetramer is regulated by basic carboxypeptidase. Biochemistry 41:4953-4961
513. Henneberry, A.L., Wright, M.M., and McMaster, C.R. (2002) The Major Sites of Cellular Phospholipid Synthesis and Molecular Determinants of Fatty Acid and Lipid Head Group Specificity. Mol. Biol. Cell 13:3148-3161
514. Howe, A.G., Zaremberg, V., and McMaster, C.R. (2002) Cessation of Growth to Prevent Cell Death Due to Inhibition of Phosphatidylcholine Synthesis is Impaired at 37C in Saccharomyces cerevisiae. J. Biol. Chem. 277:44100-44107
515. Inagaki, Y., Blouin, C., Doolittle, W.F. and Roger, A.J. (2002) Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity. Nucleic Acids Res. 30:532-544
516. Inagaki, Y., Doolittle, W.F., Baldauf, S.L. and Roger, A.J. (2002) Lateral transfer of an EF-1(alpha) gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria. Curr. Biol. 12:1-20
517. Iyengar, A., and Bearne, S.L.* (2002) An assay for cytidine 5'-triphosphate synthetase glutaminase activity using high performance liquid chromatography. Anal. Biochem. 308:396-400 [PubMed]
518. J. Peter Gogarten, Alireza G. Senejani, Olga Zhaxybayeva, Lorraine Olendzenski, and Elena Hilario (2002) Inteins: Structure, Function, and Evolution. Annu. Rev. Microbiol. 56:263-287
519. Kang, H. M. N. R. Filipenko G. Kassam & D. M. Waisman. (2002) Recombinant annexin II tetramer. Methods Mol.Biol 172:225-234 [PubMed]
520. Karten B., Vance D.E., Campenot R.B., and Vance J.E. (2002) Cholesterol accumulates in cell bodies, but is decreased in distal axons, of Niemann-Pick C1-deficient neurons. J. Neurochem. 83:1154-1163 [PubMed]
521. Keating, M.M., Gong, H., and Byers, D.M. (2002) Identification of a key residue in the conformational stability of acyl carrier protein. Biochim. Biophys. Acta 1601:208-214 [PubMed]
522. Kwon, M. J. F. Caplan N. R. Filipenko K. S. Choi S. L. Fitzpatrick L. Zhang & D. M. Waisman. (2002) Identification of Annexin II Heterotetramer as a Plasmin Reductase. J.Biol.Chem. 277:10903-10911 [PubMed]
523. Mehta, S., Yang, X.M., Chan, C.S., Dobson, M.J., Jayaram, M., and Velmurugan, S. (2002) The 2micron plasmid purloins the yeast cohesion complex: a mechanism for coupling plasmid partitioning and chromosome segregation? J. Cell Biol. 158:625-637 [PubMed]
524. O'Malley, M.A., Roger, A.J. and Doolittle, W.F. (2002) Can commercial protection be good for research? Nature 419:111
525. Olga Zhaxybayeva and J Peter Gogarten (2002) Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses. BMC Genomics 3:4
526. Raymond, J., Zhaxybayeva, O., Gogarten, J.P., Gerdes, S. and Blankenship, R.E. (2002) Whole Genome Analysis of Photosynthetic Prokaryotes. Science 298:1616-1620
527. Roger, A.J., and Silberman, J.D. (2002) Mitochondria in hiding. Nature 418:828-829
528. Rosen K and Filmus J. (2002) Oncogenes as regulators of cell survival: The role of oncogenes and tumor suppressor genes in the induction of resistance to anoikis and hypoxia. Oncogene-directed therapy. Rak J. editor Humana Press. Totowa, NJ:
529. Rosen K, Shi W, Calabretta B, Filmus J. (2002) Cell detachment triggers p38 mitogen-activated protein kinase-dependent overexpression of Fas ligand. A novel mechanism of Anoikis of intestinal epithelial cells. J. Biol. Chem. 277(48):46123-30 [PubMed]
530. Scheid, M., Marignani PA., Woodgett J. (2002) Multiple Phosphoinositide-3-kinase dependent steps in the activation of protein kinase B. Molecular and Cellular Biology 22:6247-6260 [PubMed]
531. Silberman, J.D., Simpson, A.G.B., Kulda, J., Cepicka, I., Hampl, V., Johnson, P.J. and Roger, A.J. (2002) Retortamonad flagellates are closely related to diplomonads and endash, implications for the history of mitochondrial function in eukaryote evolution. Mol. Biol. Evol. 19:777-786
532. Simpson, A.G.B. and Roger, A.J. (2002) Eukaryote evolution: Getting to the root of the problem. Curr. Biol. 12:R691-R693
533. Simpson, A.G.B., Lukes, J. and Roger, A.J. (2002) The evolutionary history of kinetoplastids and their kinetoplasts. Mol. Biol. Evol. 19:2071-2083
534. Simpson, A.G.B., MacQuarrie, E. and Roger, A.J. (2002) Early origin of canonical introns. Nature 419:270
535. Simpson, A.G.B., Roger, A.J., Silberman, J.D., Leipe, D., Edgcomb, V.E., Jermiin, L.S. Patterson, D.J. and Sogin, M.L. (2002) Molecular phylogenies reveal a novel close relative for diplomonads, the excavate taxon Carpediemonas. Mol. Biol. Evol. 19:1782-1791
536. St. Maurice, M., and Bearne, S.L.* (2002) Kinetics and Thermodynamics of Mandelate Racemase Catalysis. Biochemistry 41:4048-4058 [PubMed]
537. Stechmann A. , Cavalier-Smith T. (2002) Rooting the eukaryote tree by using a derived gene fusion. Science 297(5578):89-91 [PubMed]
538. Susko, E., Inagaki, Y., Field, C., Holder, M.E. and Roger, A.J. (2002) Testing for differences in rates across sites distributions in phylogenetic subtrees. Mol. Biol. Evol. 19:1514-1523
539. T.A. Lagace, J.R. Miller, N.D. Ridgway (2002) Caspase processing and nuclear export of CTP:phosphocholine cytidylyltransferase during farnesol-induced apoptosis. Mol. Cell. Biol. 22:4851-4862 [PubMed]
540. Tuominen,E.K.J., Wallace, C.J.A. and Kinnunen,P.K.J. (2002) Phospholipid-Cytochrome c interaction:Evidence for the extended lipid anchorage. J. Biol. Chem. 277:8822-8826 [PubMed]
541. van der Spoel AC, Jeyakumar M, Butters TD, Charlton HM, Moore HD, Dwek RA, Platt FM. (2002) Reversible infertility in male mice following oral administration of alkylated imino sugars: a non-hormonal approach to male contraception. Proc Natl Acad Sci U S A 99:17173-17178 [PubMed]
542. Vukmirica, J., Nishimaki-Mogami, T., Tran, K., Shan, J., McLeod, R.S., Yuan, J., and Yao, Z. (2002) The N-linked oligosaccharides at the amino terminus of human apolipoprotein B are important for the assembly and secretion of the apolipoprotein B-containing very low density lipoproteins. J. Lipid Res. 43:1496-1507 [PubMed]
543. Wright, M.M., and McMaster, C.R. (2002) Phosphatidylcholine and Phosphatidylethanolamine Synthesis: Mixed Micellar Analysis of the Cholinephosphotransferase and Ethanolaminephosphotransferase Activities of Human CEPT1. Lipids 37:663-672
544. Wright, M.M., and McMaster, C.R. (2002) Phospholipid Synthesis, Diacylglycerol Compartmentation, and Apoptosis. (Review) Biol. Res. 35, 223-229 Biol. Res. 35:223-229
545. Wyles, J., McMaster, C.R., and Ridgway, N.D. (2002) VAMP Associated Protein-A (VAP-A) Interacts with the Oxysterol Binding Protein (OSBP) to Modify Export from the Endoplasmic Reticulum. J. Biol. Chem. 277:29908-29918 [PubMed]
546. Wyles, J.P and Ridgway, N. D. (2002) Oxysterol Binding Proteins: A Multigene Family that Regulates Lipid Metabolism and Vesicle Transport Sterols and Oxysterols: Chemistry, Biology and Pathobiology, S.L. Fliesler (ed). Recent Research Developments in Biochemistry Series, Research Signpost.:141-157
547. Yan, S.R., Al-Hertani, W., Byers, D., and Bortolussi, R. (2002) Lipopolysaccharide-binding protein- and CD14-dependent activation of mitogen-activated protein kinase p38 by lipopolysaccharide in human neutrophils is associated with priming of respiratory burst. Infection and Immunity 70:4068-4074 [PubMed]
548. Yanagisawa, L.L., Marchena, J., Xie, Z., Li, X., Poon, P.P., Singer, R.A., Johnston, G.C., Randazzo, P.A. and Bankaitis, V.A. (2002) Activity of specific lipid-regulated ADP ribosylation factor-GTPase activating proteins is required for Sec14p-dependent Golgi secretory function in yeast. Mol. Biol. Cell 13:2193-2206 [PubMed]
549. Zaremberg, V., and McMaster, C.R. (2002) Differential Partitioning of Lipids Metabolized by Separate Yeast Glycerol-3-phosphate Acyltransferases Reveals that Phospholipase D Generation of Phosphatidic Acid Mediates Sensitivity to Choline-containing Lysolipids and Drugs. J. Biol. Chem. 277:39035-39044

Publications in 2001

550. Archibald, J. M., Blouin , C. and Doolittle, W. F. (2001) Gene duplication and the evolution of group II chaperonins: implications for structure and function. Journal of Structural Biology 135:157-169
551. Archibald, J. M., Cavalier-Smith, T., Maier, U-G. and Douglas, S. (2001) Molecular chaperones encoded by a reduced eukaryotic nucleus: the cryptomonad nucleomorph. J. Mol. Evol. 52:490-501 [PubMed]
552. Bearne, S.L.*, White, R.L.*, MacDonnell, J.E., Bahrami, S., and Gronlund, J. (2001) Purification and characterization of beta-methylaspartase from Fusobacterium varium. Mol. Cell. Biochem. 221:117-126 [PubMed]
553. Bearne, S.L.*, Hekmat, O., and MacDonnell, J.E. (2001) Inhibition of Escherichia coli CTP synthase by glutamate gamma-semialdehyde and the role of the allosteric effector GTP in glutamine hydrolysis. Biochem. J. 356:223-232 [PubMed]
554. Becker, L., McLeod, R.S., Marcovina, S.M., Yao, Z., and Koschinsky, M.L. (2001) Identification of a critical lysine residue in apoB100 which is required for lipoprotein (a) assembly. J. Biol. Chem. 276:36155-36162 [PubMed]
555. Bernhard, D., Stechmann, A. , Foissner, W., Ammermann, D., Hehn, M. & Schlegel, M. (2001) Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences. Mol. Phyl. Evol. 21(1):86-92 [PubMed]
556. Black, K.M., Clark-Lewis, I. and Wallace, C.J.A. (2001) The conserved tryptophan in cytochrome c: importance of the unique side chain features of the indole moiety. Biochem. J. 359:715-720 [PubMed]
557. Blouin, C. and Wallace, C.J.A. (2001) Protein matrix and dielectric effect in cytochrome c. J. Biol. Chem. 276:28814-28818 [PubMed]
558. Blouin, C., Guillemette, J.G., Wallace, C. (2001) Resolving the individual components of a pH-induced conformational change. Biophys J. 81(4):2331-2338. [PubMed]
559. Bonner, S., Yan, S.R., Byers, D.M., and Bortolussi, R. (2001) Activation of ERK 1 and 2 of the MAP kinase family by lipopolysaccharide requires plasma in neutrophils from adult and newborns. Infection and Immunity 69:3143-3149 [PubMed]
560. Brewster, N.K., Johnston, G.C. and Singer, R.A. (2001) A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins modulates transcription. Mol. Cell. Biol. 21:3491-3502 [PubMed]
561. Choi, K. S. S. L. Fitzpatrick N. R. Filipenko D. K. Fogg G. Kassam A. M. Magliocco & D. M. Waisman. (2001) Regulation of plasmin-dependent fibrin clot lysis by annexin II heterotetramer. J.Biol.Chem. 276:25212-25221 [PubMed]
562. Edgcomb, V.E., Roger, A.J., Simpson, A.G.B., Kysela, D.T. and Sogin, M.L. (2001) Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies. Mol.Biol.Evol. 18:514-522
563. Filipenko, N. R. and D. M. Waisman. (2001) The C-terminus of annexin II mediates binding to f-actin. J.Biol.Chem. 276:5310-5315 [PubMed]
564. Filipenko, N. R. H. M. Kang & D. M. Waisman. (2001) Characterization of the Ca2+-binding sites of annexin II tetramer. J.Biol.Chem. 276:3718-PM [PubMed]
565. Flaman, A.S., Chen, J.M., Van Iderstine, S.C., and Byers, D.M. (2001) Site-directed mutagenesis of acyl carrier protein reveals amino acid residues important for ACP structure and acyl-ACP synthetase activity. J. Biol. Chem. 276:35934-35939 [PubMed]
566. Frankel A, Rosen K, Filmus J, Kerbel R.S. (2001) Induction of anoikis and suppression of human ovarian tumor growth in vivo by down-regulation of Bcl-XL. Cancer Res. 61:4837-4841 [PubMed]
567. Henneberry, A.L., Lagace, T.A., Ridgway, N.D., and McMaster, C.R. (2001) Phosphatidylcholine Synthesis Influences the Diacylglycerol Homeostasis Required for Sec14p Dependent Golgi Function and Cell Growth. Mol. Biol. Cell 12:511-520
568. Howard J.C., Li Q, Chu W, Zochodne B, Kapoor M, Ung Y, Rosen K, Ben-David Y. (2001) Bcl-2 expression in F-MuLV-induced erythroleukemias: a role for the anti-apoptotic action of Bcl-2 during tumor progression. Oncogene 20:2291-2300 [PubMed]
569. Johnson, L.M. and Too, C.K.L. (2001) Prolactin, interleukin-2 and FGF-2 stimulate expression, nuclear distribution and DNA-binding of rat homolog of pombe Cdc5 in Nb2 T lymphoma cells. Mol. Cell. Endocrinol. 184:151-161 [PubMed]
570. Kassam, G. M. Kwon C. S. Yoon K. S. Graham M. K. Young S. Gluck & D. M. Waisman. (2001) Purification and characterization of A_61 ,.an angiostatin-like plasminogen fragment produced by plasmin autodigestion in the absence of sulfhydryl donors J.Chem.Biol. 276:8924-8933 [PubMed]
571. Kim, S., Muise, A.M., Lyons, P.J., Ro, H.-S. (2001) Regulation of adipogenesis by a transcriptional repressor that modulates MAPK. J. Biol. Chem. 276:10199-10206 [PubMed]
572. Klein, M., Friedrich, M., Roger, A.J., Hugenholtz, P., Fishbain, S., Abicht, H., Blackall, L.L., Stahl, D.A. and Wagner, M. (2001) Multiple lateral transfer events of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bact. 183:6028-6035
573. Ko, K.W.S., Avramoglu, R.K., McLeod, R.S., Vukmirica, J., and Yao, Z. (2001) The insulin-stimulated cell surface presentation of low density lipoprotein receptor-related protein in 3T3-L1 adipocytes is sensitive to phosphatidylinositide 3-kinase inhibition. Biochemistry 40:752-759 [PubMed]
574. Kwon, M. C. S. Yoon S. Fitzpatrick G. Kassam K. S. Graham M. K. Young & D. M. Waisman. (2001) p22 is a novel plasminogen fragment with antiangiogenic activity. Biochemistry 40:13246-13253 [PubMed]
575. Marignani PA and Carpenter CL (2001) Vav2 is required for cell spreading. Journal of Cell Biology 154:177-186 [PubMed]
576. Marignani PA., Kanai F and Carpenter CL (2001) LKB1 associates with Brg1 and is necessary for Brg1 induced growth arrest. Journal of Biological Chemistry 276:32415-32418 [PubMed]
577. Morrison, H.G., Roger, A.J., Nystul, T.G., Gillin, F.D. and Sogin, M.L. (2001) Giardia lamblia expresses a proteobacterial-like3 DnaK homologue. Mol.Biol.Evol. 18:530-541
578. Murphy, P.R., Limoges, M., Dodd, F., Boudreau, R.T.M., Too, C.K.L. (2001) FGF-2 stimulates endothelial nitric oxide synthase expression and inhibits apoptosis by a nitric oxide-dependent pathway in Nb2 lymphoma cells. Endocrinology 142:81-88 [PubMed]
579. Ohashi M., Kanai F., Tateishi K.,Taniguchi H., Marignani PA., Yoshida Y., Shiratori Y., Hamada H., Omata H. (2001) Target gene therapy for alpha-fetoprotein producing hepatocellularcarcinoma by E1B55k-attenuated adenovirus. BBRC 282:529-535 [PubMed]
580. Paige, M.F., Rainey, J.K. and Goh, M.C. (2001) A study of fibrous long spacing collagen ultrastructure and assembly by atomic force microscopy. Micron 32:341-353 [PubMed]
581. Parrish JC, Guillemette JG, Wallace CJ. (2001) Contribution of leucine 85 to the structure and function of Saccharomyces cerevisiae iso-1 cytochrome c. Biochem Cell Biol. 79(4):517-24 [PubMed]
582. Parrish, J.C., Guillemette, J.G. and Wallace, C.J.A. (2001) A tale of two charges: distinct roles for an acidic and a basic amino acid in the structure and function of cytochrome c. Biochem. Cell. Biol. 79:83-91 [PubMed]
583. Poon, P.P., Nothwehr, S.F., Singer, R.A. and Johnston, G.C. (2001) The Gcs1 and Age2 ArfGAP proteins provide essential overlapping function for transport from the yeast trans-Golgi network. J. Cell Biol. 155:1239-1250 [PubMed]
584. Ro, H.-S., Kim, S.-W., Wu, D., Webber, C., and Nicholson, T.E. (2001) Gene structure and expression of the mouse adipocyte enhancer-binding protein. Gene 280:123-133 [PubMed]
585. Rosen K, Coll M.L., Li A, Filmus J. (2001) Transforming growth factor-alpha prevents detachment-induced inhibition of c-Src kinase activity, Bcl-XL down-regulation, and apoptosis of intestinal epithelial cells. J. Biol. Chem. 276:3723-3729 [PubMed]
586. Sengupta, A., Blomqvist, K., Pickett, A., Zhang, Y., Chew, J.S.K. and Dobson, M.J. (2001) Functional domains of yeast plasmid-encoded Rep proteins. J.Bacteriol. 183:2306-2315 [PubMed]
587. Stechmann, A. (2001) Phylogenetic relationships of brachiopods within the Metazoa based on mitochondrial amino acid sequences. The Systematics Association Special Volume Series 63, Brachipods Past and Present, eds Brunton, C. H. C., Cocks, L. R. M. & Long, S. L. (eds.) Taylor and Francis, London:138-141
588. Too, C.K.L., Vickaryous, N., Boudreau, R.T.M. and Sangster, S.M. (2001) Identification and nuclear localization of a novel prolactin and cytokine-responsive carboxypeptidase D. Endocrinology 142:1357-1367 [PubMed]
589. Tuominen, E.K.J., Zhu, K., Wallace, C.J.A., Clark-Lewis, I., Craig, D.B., Rytomaa, M. and Kinnunen, P.K.J. (2001) ATP induces a conformational change in lipid-bound cytochrome c. J. Biol. Chem. 276:19356-19362 [PubMed]

Publications in 2000

590. Archibald, J.M., Logsdon, J.M. Jr., and Doolittle, W.F. (2000) Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes Mol. Biol. Evol. 17:1456-1466 [PubMed]
591. Baldauf, S.L., Roger, A.J., Wenk-Siefert, I. and Doolittle, W.F. (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977
592. Bearne, S.L.*, and Blouin, C. (2000) Inhibition of Escherichia coli glucosamine-6-phosphate synthase by reactive intermediate analogues. The role of the 2-amino function in catalysis. J. Biol. Chem. 275:135-140 [PubMed]
593. Dodd, F., Limoges, M., Boudreau, R.T.M., Rowden, G., Murphy, P.R. and Too, C.K.L. (2000) L-arginine inhibits apoptosis via an NO-dependent mechanism in Nb2 lymphoma cells. J. Cell. Biochemistry 77:624-634 [PubMed]
594. Evans, Jr., T.C., Martin, D., Lolly, R., Panne, D., Sun, L., Ghosh, I., Chen, L., Benner, J., Liu, X.-Q., Xu, M.-Q. (2000) Protein trans-splicing and cyclization by naturally split intein from the dnaE gene of Synechocystis species PCC6803. J. Biol. Chem. 275:9091-9094
595. Fitzpatrick, S. L. G. Kassam A. Manro C. E. Braat P. Louie & D. M. Waisman. (2000) Fucoidan-Dependent Conformational Changes in Annexin II Tetramer. Biochemistry 39:2140-2148
596. Fitzpatrick, S. L. G. Kassam K. S. Choi H.-M. Kang Fogg.D.K. & D. M. Waisman. (2000) Regulation of plasmin activity by annexin II tetramer. Biochemistry 39:1021-1028
597. Kanai F., Marignani PA., Sarbassova D., Yagi R., Hall RA., Donowitz M., Hisaminato A., Fujiwara T., Ito Y., Cantley LC. and Yaffe MB. (2000) TAZ: a novel transcriptional co-activator regulated by interactions with 14-3-3 and PDZ domain proteins. Embo. J. 19:6778-6791 [PubMed]
598. Liu, X.-Q. (2000) Protein-splicing intein: genetic mobility, origin, and evolution. Ann. Rev. Genet. 34:61-76 [PubMed]
599. Mai, J. D. M. Waisman & B. F. Sloane. (2000) Cell surface complex of cathepsin B/annexin II tetramer in malignant progression. Biochim.Biophys.Acta 1477:215-230 [PubMed]
600. Mai, J. R. L. Finley, Jr. D. M. Waisman & B. F. Sloane. (2000) Human Procathepsin B Interacts with the Annexin II Tetramer on the Surface of Tumor Cells. J.Biol.Chem. 275:12806-12812 [PubMed]
601. Olendzenski, L., Liu, L., Zhaxybayeva, O., Murphey, R., Shin, D.G., and Gogarten, J.P. (2000) Horizontal Transfer of Archaeal Genes into the Deinococcaceae: Detection by molecular and computer based approaches. Journal of Molecular Evolution 51:587-599 [PubMed]
602. Rosen K, Rak J, Leung T, Dean N.M., Kerbel R.S., Filmus J. (2000) Activated Ras prevents downregulation of Bcl-XL triggered by detachment from the extracellular matrix. A mechanism of ras-induced resistance to anoikis in intestinal epithlial cells. J. Cell Biol. 149:447-456 [PubMed]
603. St. Maurice, M., and Bearne, S.L.* (2000) Reaction intermediate analogues for mandelate racemase: interaction between Asn 197 and the alpha-hydroxyl of the substrate promotes catalysis. Biochemistry 39:13324-13335 [PubMed]
604. Thomas, L.N., Wright, A.S., Lazier, C.B., Cohen, P. and Rittmaster, R.S. (2000) Prostate Involution in Men Taking Finasteride Is Associated With Elevated Levels of Insulin-like Growth Factor Binding Proteins (IGFBPs)-2-4 and -5. The Prostate 42:203-210 [PubMed]
605. Velmurugan, S., Yang, X., Chan, C, Dobson, M.J., and Jayaram, M. (2000) Partitioning of the 2µm circle plasmid of Saccharomyces cerevisiae: functional coordination with chromosome segregation and plasmid-encoded Rep protein distribution. J. Cell Biol. 149:553-566 [PubMed]
606. Wallace, C.J.A. (2000) Protein Engineering by Semisynthesis. CRC Press Boca Raton. FL:
607. Wallace, C.J.A. and Clark-Lewis, I. (2000) Site-specific independent double-labelling of proteins with reporter atoms. Biochem. Cell. Biol. 78:79-86 [PubMed]