James B. Lewis, PhD

Curriculum Vitae

Electronic addresses:

E-mail: nanojbl@halcyon.com, nanojbl@comast.net
World Wide Web: http://nanoindustries.com/nanojbl/

Education:

Ph.D., 1972, Harvard University, Cambridge, MA., Chemistry
M.A., 1968, Harvard University, Cambridge, MA., Chemistry
B.A., 1967, University of Pennsylvania, Philadelphia, PA., Chemistry

Positions held:

1988-May 31, 1996. Senior Research Investigator, Immunodeficiency and Immunosuppression Dept., Bristol-Myers Squibb Pharmaceutical Research Institute - Seattle, WA

1980-1988. Associate Member, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA

1974-1980. Staff Investigator and Senior Staff Investigator, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

1973-1974. Postdoctoral Researcher, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

1971-1973. Postdoctoral Researcher, Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland

Research Summary

1968-1971. Graduate research in the Chemistry Department of Harvard University, Cambridge, MA, under the supervision of Paul Doty. RNA biochemistry and structure. I developed a method to probe the secondary structure of E. coli 5S ribosomal RNA by equilibrium dialysis against tri- and tetra-ribonucleotides complementary to the 5S rRNA sequence to determine the accessibility of the oligomer antisequence in the 5S rRNA structure. See publications 1 - 4 below.

1971-1973. Postdoctoral Researcher, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland, under the supervision of Bernhard Hirt, supported by a cancer research fellowship from the Damon Runyon Cancer Research Foundation. Molecular biology of small DNA tumor viruses SV40 and polyoma. My goal was the cell-free synthesis of viral tumor antigen by translation of RNA transcribed from viral DNA using E. coli RNA polymerase. One reason for the failure of this approach became obvious several years later with the discovery of RNA splicing. While in Switzerland I learned from M. Schrier and T. Staehelin of the Basel Institute of Immunology (BII) how to set up a highly efficient system for mammalian cell-free translation. See publications 5 - 6 below.

1973-1974. Postdoctoral Researcher, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, under the supervision of Raymond Gesteland. Molecular biology of adenoviruses. As part of a large cancer center project, I set up a modified version of the cell free translation system that I had learned in Switzerland, and used it to translate RNA purified from cells infected with human adenovirus type 2. See publications 7 - 8 below.

1974-1980. Staff Investigator and Senior Staff Investigator, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. Molecular biology of adenoviruses. Working with CW Anderson, JF Atkins, and RF Gesteland, I used cell-free translation to identify proteins encoded by adenovirus and to identify the genes for each protein. We initially used a translation system based on that of Schrier and Staehelin made more efficient by the addition of polyamines. To purify adenoviral mRNA and to fractionate it into populations complementary to specific restriction fragments of Ad DNA, we initially used liquid phase hybridization with fragmented DNA followed by urea-hydroxyapatite chromatography and recovery of the RNA by binding to oligo(dT)-cellulose. In this way various adenovirus proteins produced at early and at late times after infections were identified as coded by specific fragments of the viral DNA. Among the adenovirus early proteins identified by this work were the E1A proteins and one of the small E1B proteins. Investigation of why late protein mRNAs bound weakly to a second segment of DNA contributed in a small way to the discovery by others of RNA splicing in 1976. Later experiments done in collaboration with MB Mathews switched to using hybridization to DNA immobilized on nitrocellulose filters to purify mRNA species and to using nuclease-treated reticulocyte lysates for translation.

My work during this period benefited greatly from numerous collaborations with other scientists having expertise and skills that complemented my own. Of special note, in the research group that I shared with MB Mathews, I worked with postdoctoral fellows ML Harter on adenovirus early proteins, H Esche on adenovirus transforming region mRNAs, and BW Stillman on the adenovirus terminal protein. Outside of our research group, I contributed purified adenoviral mRNAs to LT Chow and TR Broker for their use in electron microscopy of heteroduplexes between viral DNA and RNA molecules to precisely map the structure of most of the adenovirus transcriptome. I was able to synthesize adenovirus proteins in vitro labeled with various amino acids and without N-terminal acetylation so that CW Anderson and JE Smart could determine specific protein sequences for alignment with the viral genome sequence. The last segment of my work at CSH contributed to the discovery of adenovirus region E-2B. See publications 9 - 32 below.

1980-1988. Associate Member, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA. Adenovirus gene expression and oncogenesis. I led a small research group (2-6) studying various aspects of the molecular biology of adenoviruses, with special emphasis on gene expression and oncogenic properties. I continued a collaboration with Carl W. Anderson of Brookhaven National Laboratory using amino terminal sequencing of proteins and peptides synthesized in vitro to identify where proteins were encoded on the adenovirus genome. Circa 1982, working together with Robert Eisenman, I set up in my lab the first peptide synthesis machine to be used at the Fred Hutchinson. To complete the identification of region E1B proteins, I used RP-HPLC to separate two adenovirus E1B proteins that comigrated on SDS-PAGE. Within my research group, AW Senear demonstrated morphological transformation of rodent cell lines by high-level expression of the adenovirus E1A gene, RC Schmitt demonstrated differences in the nuclear localization of different E1A proteins, and ML Fahnestock mutagenized the E1A genes to define functions. My research was supported by several research grants, of which I was the principal investigator, from the National Institutes of Health, the National Science Foundation, and the American Cancer Society. See publications 33 - 43 below.

1988-1996. Senior Research Investigator, Immunodeficiency and Immunosuppression Dept., Bristol-Myers Squibb Pharmaceutical Research Institute - Seattle, WA. I supervised a small group of two to five scientists working on HIV and cancer vaccines within a department of 25-30 scientists headed by Shiu-Lok Hu. The work primarily involved recombinant vaccinia viruses and DNA vaccines. We first did some work on HIV proteins, and then spent 6 years working on active immunotherapy for cancer (cancer vaccines). During my last six months at BMS, I switched projects again, returning to molecular virology to begin a project to identify viral protein - cellular protein interactions that are important for the pathogenicity of HIV in the hope that these interactions would prove useful targets for drug screening. We were in the process of setting up yeast two-hybrid screens when my time at BMS came to an end. See publications 44 - 46 below.

Research Publications 1970-1993

1. Lewis JB, Doty P. Derivation of the secondary structure of 5S RNA from its binding of complementary oligonucleotides. Nature 225: 510-512, 1970. http://dx.doi.org/10.1038/225510a0
2. Schimmel PR, Uhlenbeck OC, Lewis JB, Dickson LA, Eldred EW, Schreier AA. Binding of complementary oligonucleotides to free and aminoacyl transfer ribonucleic acid synthetase bound transfer ribonucleic acid. Biochemistry 11: 642-646, 1972. http://dx.doi.org/10.1021/bi00754a028
3. Lewis JB, Brass LF, Doty P. A comparison of the binding to polynucleotides of complementary and noncomplementary oligonucleotides. Biochemistry 14: 3164-3171, 1975. http://dx.doi.org/10.1021/bi00685a020
4. Lewis JB, Doty P. Identification of the single-strand regions in Escherichia coli 5S RNA, native and A forms, by the binding of oligonucleotides. Biochemistry 16: 5016-5025, 1977. http://dx.doi.org/10.1021/bi00642a012
5. Lewis JB. In vitro synthesis of SV40 and polyoma proteins. Experientia 29: 776, 1973.
6. Béard P, Lewis J. Separation of the strands of polyoma DNA. Experientia 30: 699, 1974.
7. Anderson CW, Lewis JB, Atkins JF, Gesteland RF. Cell-free synthesis of adenovirus 2 proteins programmed by fractionated messenger RNA: a comparison of polypeptide products and messenger RNA lengths. Proc. Nat. Acad. Sci. USA 71: 2756-2760, 1974. abstract PDF
8. Lewis JB, Anderson CW, Atkins JF, Gesteland RF. The origin and destiny of adenovirus proteins. Cold Spring Harbor Symp. Quant. Biol. 39: 581-590, 1974.
9. Atkins JF, Lewis JB, Anderson CW, Gesteland RF. Enhanced differential synthesis of proteins in a mammalian cell-free system by addition of polyamines. J. Biol. Chem. 250: 5688-5695, 1975. abstract PDF
10. Lewis JB, Atkins JF, Anderson CW, Baum PR, Gesteland RF. Mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments. Proc. Nat. Acad. Sci. USA 72: 1344-1348, 1975. abstract PDF
11. Atkins JF, Lewis JB, Anderson CW, Baum PR, Gesteland RF. Mapping of adenovirus 2 genes by translation of RNA selected by hybridization. In INSERM Symposium: 47, AL Haenni and G Beaud, eds. (Paris). pp. 293-298.
12. Lewis JB, Atkins JF, Baum PR, Solem R, Gesteland RF, Anderson CW. Location and identification of the genes for adenovirus type 2 early polypeptides. Cell 7: 141-151, 1976. http://dx.doi.org/10.1016/0092-8674(76)90264-6
13. Anderson CW, Lewis JB, Baum PR, Gesteland RF. Simian virus 40-specific polypeptides in Ad2⁺ND1- and Ad2⁺ND4-infected cells. J. Virol. 18: 685-692, 1976. abstract PDF
14. Grodzicker T, Lewis JB, Anderson CW. Conditional lethal mutants of adenovirus type 2-simian virus 40 hybrids: II. Ad2⁺ND1 host-range mutants that synthesize fragments of the Ad2⁺ND1 30K protein. J. Virol. 19: 559-571, 1976. abstract PDF
15. Chow LT, Roberts JM, Lewis JB, Broker TR. A map of cytoplasmic RNA transcripts from lytic adenovirus type 2, determined by electron microscopy of RNA:DNA hybrids. Cell 11: 819-836, 1977. http://dx.doi.org/10.1016/0092-8674(77)90294-X
16. Lewis JB, Anderson CW, Atkins JF. Further mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments. Cell 12: 37-44, 1977. http://dx.doi.org/10.1016/0092-8674(77)90183-0
17. Gesteland RF, Wills N, Lewis JB, Grodzicker T. Identification of amber and ochre mutants of the human virus Ad2⁺ND1. Proc. Nat. Acad. Sci. USA 74: 4567-4571, 1977. abstract PDF
18. Harter ML, Lewis JB. Adenovirus coded proteins in extracts of human cells early after infection. In INSERM Symposium: 69, P May, R Monier, and R Weil, eds. (Paris). pp. 153-160.
19. Harter ML, Lewis JB. Adenovirus type 2 early proteins in synthesized in vitro and in vivo: identification in infected cells of the 38,000- to 50,000-molecular-weight protein encoded by the left end of the adenovirus type 2 genome. J. Virol. 26: 736-749, 1978. abstract PDF
20. Broker TR, Chow LT, Dunn AR, Gelinas RE, Hassell JA, Klessig DF, Lewis JB, Roberts RJ, and Zain BS. Adenovirus-2 messengers—an example of baroque molecular architecture. Cold Spring Harbor Symp. Quant. Biol. 42: 531-553, 1977.
21. Fey G, Lewis JB, Grodzicker T, Bothwell A. Characterization of a fused protein specified by the adenovirus type 2-simian virus 40 hybrid Ad2⁺ND1 dp2. J. Virol. 30: 201-217, 1979. abstract PDF
22. Harter ML, Lewis JB, Anderson CW. Adenovirus type 2 terminal protein: purification and comparison of tryptic peptides with known adenovirus-coded proteins. J. Virol. 31: 823-835, 1979. abstract PDF
23. Chow LT, Broker TR, Lewis JB. Complex splicing patterns of RNAs from the early regions of adenovirus-2. J. Mol. Biol. 134: 265-303, 1979. http://dx.doi.org/10.1016/0022-2836(79)90036-6
24. Chow LT, Lewis JB, Broker TR. RNA transcription and splicing at early and intermediate times after adenovirus-2 infection. Cold Spring Harbor Symp. Quant. Biol. 44: 401-414, 1979.
25. Lewis JB, Esche H, Smart JE, Stillman BW, Harter ML, Mathews MB. Organization and expression of the left third of the genome of adenovirus. Cold Spring Harbor Symp. Quant. Biol. 44: 493-508, 1979.
26. Anderson CW, Lewis JB. Amino-terminal sequence of adenovirus type 2 proteins: hexon, fiber, component IX, and early protein 1B-15K. Virology 104: 27-41, 1980. http://dx.doi.org/10.1016/0042-6822(80)90363-3
27. Lewis JB, Mathews MB. Control of adenovirus early gene expression: a class of immediate early products. Cell 21: 303-313, 1980. http://dx.doi.org/10.1016/0092-8674(80)90138-5
28. Mathews MB, Lewis JB. Regulation of adenovirus early gene expression. In ICN-UCLA Symposium on Animal Virus Genetics, pp. 327-338. Academic Press, New York.
29. Esche H, Mathews MB, Lewis JB. Proteins and messenger RNAs of the transforming region of wild-type and mutant adenoviruses. J. Mol. Biol. 142: 399-417, 1980. http://dx.doi.org/10.1016/0022-2836(80)90279-X
30. Stillman BW, Lewis JB, Chow LT, Mathews MB, Smart JE. Identification of the gene and mRNA for the adenovirus terminal protein precursor. Cell 23: 497-508, 1981. http://dx.doi.org/10.1016/0092-8674(81)90145-8
31. Smart JE, Lewis JB, Mathews MB, Harter ML, Anderson CW. Adenovirus type 2 early proteins: assignment of the early region 1A proteins synthesized in vivo and in vitro to specific mRNAs. Virology 112: 703-713, 1981. http://dx.doi.org/10.1016/0042-6822(81)90315-9
32. Lewis JB, Mathews MB. Viral messenger RNAs in six lines of adenovirus-transformed cells. Virology 115: 345-360, 1981. http://dx.doi.org/10.1016/0042-6822(81)90116-1
33. Galloway DA, Goldstein LC, Lewis JB. Identification of proteins encoded by a fragment of herpes simplex virus type 2 DNA that has transforming activity. J. Virol. 42: 530-537, 1982. abstract PDF
34. Lewis JB, Anderson CW. Proteins encoded near the adenovirus late messenger RNA leader segments. Virology 127: 112-123, 1983. http://dx.doi.org/10.1016/0042-6822(83)90376-8
35. Anderson CW, Schmitt RC, Smart JE, Lewis JB. Early region 1B of adenovirus 2 encodes two coterminal proteins of 495 and 155 amino acid residues. J. Virol. 50: 387-396, 1984. abstract PDF
36. Trüeb B, Lewis JB, Carter WG. Translatable mRNA for GP140 (a subunit of type VI collagen) is absent in SV40 transformed fibroblasts. J. Cell Biol. 100: 638-641, 1985. abstract PDF
37. Lewis JB, Fahnestock ML, Hardy MM, Anderson CW. Presence in infected cells of nonvirion proteins encoded by adenovirus messenger RNAs of the major late transcription regions L0 and L1. Virology 143: 452-466, 1985. http://dx.doi.org/10.1016/0042-6822(85)90385-X
38. Senear AW, Lewis JB. Morphological transformation of established rodent cell lines by high-level expression of the adenovirus type 2 E1a gene. Mol. Cell. Biol. 6: 1253-1260, 1986. abstract PDF
39. Schmitt RC, Fahnestock ML, Lewis JB. Differential nuclear localization of the major adenovirus type 2 E1a proteins. J. Virol. 61: 247-255, 1987. abstract PDF
40. Lewis JB, Anderson CW. Identification of adenovirus type 2 early region 1B proteins that share the same amino terminus as do the 495R and 155R proteins. J. Virol. 61: 3879-3888, 1987. abstract PDF
41. Anderson CW, Hardy MM, Lewis JB. Abnormal expression of a late gene family L1 protein in monkey cells abortively infected with adenovirus type 2.Virus Genes 1: 149-164, 1988. http://dx.doi.org/10.1007/BF00555934
42. Fahnestock ML, Lewis JB. Genetic dissection of the transactivating domain of the E1a 289R protein of adenovirus type 2. J. Virol. 63: 1495-1504, 1989. abstract PDF
43. Fahnestock ML, Lewis JB. Limited temperature-sensitive transactivation by mutant adenovirus type 2 E1a proteins. J. Virol. 63: 2348-2351, 1989. abstract PDF
44. Klaniecki J, Dykers T, Travis B, Schmitt R, Wain M, Watson A, Sridhar P, McClure J, Morein B, Ulrich JT, Hu S-L, Lewis J. Cross-neutralizing antibodies in rabbits immunized with HIV-1 gp160 purified from simian cells infected with a recombinant vaccinia virus. AIDS Res. Human Retroviruses 7: 791-798, 1991.
45. Travis BM, Dykers TI, Hewgill D, Ledbetter J, Tsu TT, Hu S-L, Lewis JB. Functional roles of the V3 hypervariable region of HIV-1 gp160 in the processing of gp160 and in the formation of syncytia in CD4⁺ cells. Virology 186: 313-317, 1992. http://dx.doi.org/10.1016/0042-6822(92)90088-7
46. Bu D, Domenech N, Lewis J, Taylor-Papadimitriou J, Finn OJ. Recombinant vaccinia mucin vector: in vitro analysis of expression of tumor-associated epitopes for antibody and human cytotoxic T-cell recognition. J. Immunotherapy 14: 127-135, 1993.