William James

University Lecturer

Tutorial Fellow of Brasenose College

 Carla Griffiths

aptamer interactions with HIV-1 gp120

Graduate Student, Wolfson College

Ally Evans

Personal assistant

Karl Karlsson

Human ES cell-derived Macrophages, HIV

Graduate Student, Lincoln College

Veronica Coventry

Aptamer Microbicide Program

Post-doctoral Associate

Sabine Fengler

HIV and neutralizing aptamers

Post-doctoral associate

Aptamer Microbicide Program

Post-doctoral Associate

Remo Gerber

NMR analysis of PrP folding

Graduate Student, Lincoln College

with Prof. Peter J. Hore,  Physical & Theoretical Chemistry

Mike Puklavec

Tissue Culture specialist

with Professor A N Barclay

Emily Spence

Human ES cells

Undergraduate Student, Merton College

Chris Lyons

PrP folding in vitro

Undergraduate student, Temple University

Clement Mitchell

PrP Folding in vitro

Undergraduate student, St John's College

Selected Publications

HIV research

AIDS, which is caused by infection with the retrovirus, HIV, currently kills approximately 3 million people and infects an additional 5 million world-wide every year (see UN AIDS for updates). We have been interested in investigating the molecular cell biology of this virus for two decades, principally focussing on the mechanisms of virus entry into cells and RNA-based methods for inhibiting HIV replication.

We have recently isolated aptamers (see below) that bind to the envelope glycoprotein of HIV (refs 1-4, to the right). The ligands turn out to inhibit the infection of lymphocytes by clinical strains of virus from around the world to an extent that makes them very interesting both for clinical applications (such as prevention and treatment) and as reagents for analysing virus-cell interactions.

TOP

1.         Dey, A.K., M. Khati, M. Tang, R. Wyatt, S.M. Lea, and W. James, An aptamer that neutralizes R5 strains of HIV-1 blocks gp120-CCR5 interaction. submitted.

2.     Dey, A.K., C. Griffiths, S.M. Lea, and W. James, Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. Rna, 2005. 11(6): p. 873-84.

3.      Khati, M., M. Schuman, J. Ibrahim, Q. Sattentau, S. Gordon, and W. James, Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2'F-RNA aptamers. J Virol, 2003. 77(23): p. 12692-8.

4.      Sayer, N., J. Ibrahim, K. Turner, A. Tahiri-Alaoui, and W. James, Structural characterization of a 2(')F-RNA aptamer that binds a HIV-1 SU glycoprotein, gp120. Biochem Biophys Res Commun, 2002. 293(3): p. 924-31.

5.         Khati, M., W. James, and S. Gordon, HIV-macrophage interactions at the cellular and molecular level. Arch Immunol Ther Exp (Warsz), 2001. 49(5): p. 367-78.

6.         Ibrahim, J., P. Griffin, D.R. Coombe, C.C. Rider, and W. James, Cell-surface heparan sulfate facilitates human immunodeficiency virus Type 1 entry into some cell lines but not primary lymphocytes. Virus Res, 1999. 60(2): p. 159-69.

7.         Simon, J.H.M., P. Stumbles, N. Signoret, C. Somoza, M. Puklavec, Q. Sattentau, A.N. Barclay, and W. James, Role of CD4 epitopes outside the gp120-binding site during entry of HIV-1. J Virol, 1997. 71(2): p. 1476-1484.

8.         Sczakiel, G., G. Palu, and W. James, Delivery of Recombinant HIV-1-directed antisense and ribozyme genes, in Recombinant proteins: detection and isolation protocols, R. Tuan, Editor. 1996, Humana Press, Inc: Totowa, NJ, USA. p. 389-400.

9.         Herbein, G., P. Illei, L. Montaner, W. James, and S. Gordon, Comparison of p24 measurement by ELISA versus indicator cells for detecting residual HIV infectivity in vitro. J Virol Methods, 1996. 58: p. 167-173.

10.       de Vreese, K., D. Reymen, P. Griffin, G. Werner, J. Este, W. James, R. Datema, G. Henson, J. Desmyter, J. Anne, and E. de Clercq, Mechanism of action studies on the bicyclams, a new class of potent HIV inhibitors. Antiviral research, 1996. 29: p. 209-219.

11.       James, W., R. Weiss, and J. Simon, The Receptor for HIV:  dissection of CD4 and studies on putative accessory factors, in The CD4 molecule, D. Littman, Editor. 1995, Springer-Verlag: Berlin. p. 137-158.

12.       Meier, U.-C., P. Klenerman, P. Griffin, W. James, B. Koppe, B. Larder, A. McMichael, and R. Phillips, Cytotoxic T Lymphocyte lysis inhibited by viable HIV mutants. Science, 1995. 270: p. 1360-1362.

13.       Fischer, P., M. Collin, G. Karlsson, W. James, T. Butters, S. Davis, S. Gordon, R. Dwek, and F. Platt, The alpha-glucosidase inhibitor N-butyldeoxynojirimycin inhibits HIV entry at the post-CD4 binding level. J Virol, 1995. 68(9): p. 5791-5797.

14.       Ashe, M.P., P. Griffin, W. James, and N.J. Proudfoot, Poly(A) site selection in the HIV-1 Provirus: inhibition of promoter-proximal polyadenylation by the downstream major splice donor site. Genes & Development, 1995. 9(12): p. 3008-3025.

15.       Simon, J.H.M. and W. James, Heterokaryons formed between a rat myeloma and a mouse fibroblast are permissive for entry of HIV-1. AIDS Res Hum Retroviruses, 1994. 10(12): p. 1609-1611.

16.       Simon, J., G. Schockmel, P. Illei, and W. James, A rodent cell line permissive for entry and reverse transcription of HIV-1 has a pre-integration block to productive infection. J Gen Virol, 1994. 75: p. 2615-2623.

17.       Collin, M., P. Illei, W. James, and S. Gordon, Definition of the range and distribution of HIV macrophage tropism using PCR-based infectivity measurements. J Gen Virol, 1994. 75: p. 1597-1603.

18.       Simon, J.H., C. Somoza, G.A. Schockmel, M. Collin, S.J. Davis, A.F. Williams, and W. James, A rat CD4 mutant containing the gp120-binding site mediates human immunodeficiency virus type 1 infection. J Exp Med, 1993. 177(4): p. 949-54.

19.       Montaner, L., A. Doyle, M. Collin, G. Herbein, P. Illei, W. James, A. Minty, D. Caput, P. Ferrara, and S. Gordon, Interleukin 13 inhibits HIV-1 production in primary blood-derived human macrophages in vitro. J Exp Med, 1993. 178: p. 743-747.

20.       Gregory, S., R. Collman, W. James, S. Gordon, F. Gonzalez-Scarano, and N. Nathanson, HIV-1 pseudotype virus containing a Cocal virus genome: construction, assay and use. J Virol Met, 1993. 44: p. 287-304.

21.       Davis, S., W. James, G. Schockmel, J. Simon, and C. Somoza, The recognition of chimeras of rat and human CD4 by HIV-1 gp120 and monoclonal antibodies. Phil Trans R Soc Lond B, 1993. 342: p. 75-81.

22.       Crisell, P., S. Thompson, and W. James, Inhibition of HIV-1 replication by ribozymes that show poor activity in vitro. Nuc Acids Res, 1993. 21: p. 5251-5.

23.       James, W., P. Crisell, and A. Rhodes, Gene Inhibition of HIV-1 replication. A comparative and mechanistic study. Ann NY Acad Sci, 1992. 660: p. 274-6.

24.       Rhodes, A. and W. James, Inhibition of heterologous strains of HIV by antisense RNA [see comments]. Aids, 1991. 5(2): p. 145-51.

25.       Collin, M., W. James, and S. Gordon, Development of techniques to analyse the formation of HIV provirus in primary human macrophages. Res Virol, 1991. 142(2-3): p. 105-12.

26.       Rhodes, A. and W. James, Inhibition of human immunodeficiency virus replication in cell culture by endogenously synthesized antisense RNA. J Gen Virol, 1990. 71(owned): p. 1965-74.

Aptamers 

Aptamers are artificial  nucleic acid ligands that are isolated from complex libraries of synthetic oligos. They can be used, like antibodies, to investigate biological systems but are small, protease resistant and do not suffer from the limitations of tolerance, antigen processing and so on. For a reviews, follow the links opposite.

TOP

1.         James, W., Aptamers, in The Encyclopedia of Analytical Chemistry: Instrumentation and Applications, R. Myers, Editor. 2000, John Wiley. p. 22pp.

2.         James, W., Nucleic acid and polypeptide aptamers: a powerful approach to ligand discovery. Current Opinion in Pharmacology, 2001. 1: p. 540-546.

3.         Sayer, N., J. Ibrahim, K. Turner, A. Tahiri-Alaoui, and W. James, Structural characterization of a 2(')F-RNA aptamer that binds a HIV-1 SU glycoprotein, gp120. Biochem Biophys Res Commun, 2002. 293(3): p. 924-31.

4.         Rhie, A., L. Kirby, N. Sayer, R. Wellesley, P. Disterer, I. Sylvester, A. Gill, J. Hope, W. James, and A. Tahiri-Alaoui, Characterization of 2'-Fluoro-RNA Aptamers That Bind Preferentially to Disease-associated Conformations of Prion Protein and Inhibit Conversion. J Biol Chem, 2003. 278(41): p. 39697-705.

5.         Khati, M., M. Schuman, J. Ibrahim, Q. Sattentau, S. Gordon, and W. James, Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2'F-RNA aptamers. J Virol, 2003. 77(23): p. 12692-8.

6.         Tahiri-Alaoui, A., L. Frigotto, N. Manville, J. Ibrahim, P. Romby, and W. James, High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands. Nucleic Acids Res, 2002. 30(10): p. e45.

7.         Sayer, N.M., M. Cubin, A. Rhie, M. Bullock, A. Tahiri-Alaoui, and W. James, Structural determinants of conformationally selective, prion-binding aptamers. J Biol Chem, 2004. 279(13): p. 13102-9.

8.         Dey, A.K., C. Griffiths, S.M. Lea, and W. James, Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. Rna, 2005. 11(6): p. 873-84.

 Prions

Transmissible spongiform encephalopathies (TSEs), including scrapie, BSE and variant CJD, are associated with the the deposition of an abnormally folded version of the cellular PrP protein in amyloid plaques in the brain. This mis-folded protein may itelf be the infectious agent - a prion - but we structural basis for the process is obscure. We are using the aptamer approach to investigate the problem

TOP

1.         Tahiri-Alaoui, A. and W. James, Rapid formation of amyloid from {alpha}-monomeric recombinant human PrP in vitro. Protein Sci, 2005. 14(4): p. 942-7.

2.         Baskakov, I., P. Disterer, L. Breydo, M. Shaw, A. Gill, W. James, and A. Tahiri-Alaoui, The presence of valine at residue 129 in human prion protein accelerates amyloid formation. FEBS Lett, 2005. in press.

3.         Sayer, N.M., M. Cubin, A. Rhie, M. Bullock, A. Tahiri-Alaoui, and W. James, Structural determinants of conformationally selective, prion-binding aptamers. J Biol Chem, 2004. 279(13): p. 13102-9.

4.         Tahiri-Alaoui, A., A.C. Gill, P. Disterer, and W. James, Methionine 129 Variant of Human Prion Protein Oligomerizes More Rapidly than the Valine 129 Variant: IMPLICATIONS FOR DISEASE SUSCEPTIBILITY TO CREUTZFELDT-JAKOB DISEASE. J. Biol. Chem., 2004. 279(30): p. 31390-31397.

5.         Tahiri-Alaoui, A., M. Bouchard, J. Zurdo, and W. James, Competing intrachain interactions regulate the formation of beta-sheet fibrils in bovine PrP peptides. Protein Sci, 2003. 12(3): p. 600-8.

6.         Rhie, A., L. Kirby, N. Sayer, R. Wellesley, P. Disterer, I. Sylvester, A. Gill, J. Hope, W. James, and A. Tahiri-Alaoui, Characterization of 2'-Fluoro-RNA Aptamers That Bind Preferentially to Disease-associated Conformations of Prion Protein and Inhibit Conversion. J Biol Chem, 2003. 278(41): p. 39697-705. 

Arboviruses

Arthropod-borne viruses are an important source of morbidity and mortality, especially in the developing world. We have had a long-standing interest in investigating the molecualr biology of Flaviviruses, such as Dengue virus, and Bunyaviruses.

TOP

1.         James, W.S. and D. Millican, Host-adaptive antigenic variation in Bunyaviruses. J Gen Virol, 1986. 67(owned): p. 2803-6.

2.         Solomon, T., N.M. Dung, D.W. Vaughn, R. Kneen, L.T. Thao, B. Raengsakulrach, H.T. Loan, N.P. Day, J. Farrar, K.S. Myint, M.J. Warrell, W.S. James, A. Nisalak, and N.J. White, Neurological manifestations of dengue infection. Lancet, 2000. 355(9209): p. 1053-9.

3.         Uzcategui, N.Y., G. Comach, D. Camacho, M. Salcedo, M. Cabello De Quintana, M. Jimenez, G. Sierra, R. Cuello De Uzcategui, W.S. James, S. Turner, E.C. Holmes, and E.A. Gould, Molecular epidemiology of dengue virus type 3 in Venezuela. J Gen Virol, 2003. 84(Pt 6): p. 1569-1575.

 Immunology

We are interested in the immunological aspects of virus-cell interaction, particularly macrophage-tropic strains of HIV and investigate the properties of selected cell-surface glycoproteins of immunological interest using the aptamer approach. Our collaborators in this area are Neil Barclay and Siamon Gordon

TOP

       Al-Shamkhani, A., M. Birkeland, M. Puklavec, M. Brown, W. James, and A. Barclay. 1996. OX40 is differentially expressed on activated rat and mouse T cells and is the sole receptor for the OX40 ligand. Eur J Immunol. 26:1695-1699.

       Al-Shamkhani, A, Mallett, S, Brown, MH, James, W and Barclay, AN 1997. Affinity and kinetics of the interaction between soluble trimeric OX40 ligand, a member of the TNF superfamily, and its receptor, OX40, on activated T cells. J Biol Chem 272:5275-82. 

       Meier, U.-C., P. Klenerman, P. Griffin, W. James, B. Koppe, B. Larder, A. McMichael, and R. Phillips. 1995. Cytotoxic T Lymphocyte lysis inhibited by viable HIV mutants. Science. 270:1360-1362.

       Montaner, L., A. Doyle, M. Collin, G. Herbein, P. Illei, W. James, A. Minty, D. Caput, P. Ferrara, and S. Gordon. 1993. Interleukin 13 inhibits HIV-1 production in primary blood-derived human macrophages in vitro. J Exp Med. 178:743-747.

 Antisense & Ribozymes

Understanding the determinants of their activity in mammalian cells (illustrated discussion here)

Developing a gene therapy against AIDS

Using them to ablate cellular gene expression (Review of the field here )

Computer modelling of RNA-RNA interactions discussed here

We no longer research in this area.

TOP

       Crisell, P., S. Thompson, and W. James. 1993. Inhibition of HIV-1 replication by ribozymes that show poor activity in vitro. Nuc Acids Res. 21:5251-5.

       James, W. 1991. Towards gene-inhibition therapy: a review of progress and prospects in the field of antiviral antisense nucleic acids and ribozymes. Antivir Chem Chemother. 2(4):191-214.

       James, W., and A. Al-Shamkhani. 1995. RNA enzymes as tools for gene ablation. Current Optinion in Biotechnology. 6(1):44-49.

       James, W., and E. Cowe. 1996. Computational approaches to the Identification of ribozyme target sites. In P. Turner (ed.), Methods in Molecular Biology, vol. (in press). Humana Press

       Rhodes, A., and W. James. 1991. Inhibition of heterologous strains of HIV by antisense RNA. Aids. 5(2):145-51.

       Rhodes, A., and W. James. 1990. Inhibition of human immunodeficiency virus replication in cell culture by endogenously synthesized antisense RNA. J Gen Virol. 71:1965-74.

       Sczakiel, G., G. Palu, and W. James. 1996. Delivery of Recombinant HIV-1-directed antisense and ribozyme genes, p. 12pp. In R. Tuan (ed.), Recombinant proteins: detection and isolation protocols, vol. 63. Humana Press, Inc, Totowa, NJ, USA.