Hall's Lab Publications

Timothy C. Hall Research Publications
tim@idmb.tamu.edu

The publications are separated into five groups:

A. Books and Invited Chapters

Hall, T. C., Sun, S. M., Buchbinder, B. U. and Belozerskii, M. A. 1977. The translation of mRNA for storage globulin of the bean, Phaseolus vulgaris. In: Translation of Natural and Synthetic Polynucleotides. A. Legocki, Ed. Univ. of Agriculture in Poznan, Poland. pp. 217-223.

Hall, T. C. 1979a. Plant messenger RNA. In: Nucleic Acids in Plants. T. C. Hall and J. W. Davies, Eds. CRC Press. I: 217-251. Hall, T. C. 1979b. Transfer RNA-like structures in viral genomes. In: International Review of Cytology. Academic Press, Inc. 60: 1-26. Hall, T. C., and Davies, J. W., Eds. 1979. Nucleic Acids in Plants. (2 vols.) CRC Press.

Hall, T. C., Sun, S. M., Ma, Y., McLeester, R. C., Pyne, J. W., Bliss, F. A. and Buchbinder, B. U. 1979. The major storage protein of French bean seeds: Characterization in vivo and translation in vitro. In: The Plant Seed: Development, Preservation, and Germination. Rubenstein, R. L. Phillips, C. E. Green and B. G. Gengenbach, Eds. Academic Press, Inc., New York. I: 3-26.

Hall, T. C., Sun, S. M., Buchbinder, B. U., Pyne, J. W., Bliss, F. A. and Kemp, J. D. 1980. Bean seed globulin mRNA: Translation, characterization, and its use as a probe towards genetic engineering of crop plants. In: Genome Organization and Expression in Plants. C. J. Leaver, Ed. Plenum Pub. Corp. pp. 259-272.

Hall, T. C. and Kemp, J. D. 1981. Enhancing protein quality and quantity. In: Genetic Engineering. Proceedings of the Batelle Memorial Institute International Conference, V: 36-71.

Brown, J. W. S., Ersland, D. R., and Hall, T. C. 1982. Molecular aspects of storage protein synthesis during seed development. In: The Physiology and Biochemistry of Seed Development, Dormancy and Germination. A. A. Khan, Ed. Elsevier/North-Holland Biomedical Press. pp. 3-42.

Hall, T. C., Miller, W. A. and Bujarski, J. J. 1982. Enzymes involved in the replication of plant viral RNAs. In: Advances in Plant Pathology. D. S. Ingram & P. H. Williams, Eds. Academic Press, Inc., London. I: 179-211.

Ersland, D., Brown, J. W. S., Casey, R. and Hall, T. C. 1983. The storage proteins of Phaseolus vulgaris L., Vicia faba L., and Pisum sativum L. In: Seed Proteins: Biochemistry, Genetics, Nutritive Value. W. Gottschalk and H. P. Muller, Eds. Martinus Nijhoff: The Hague. pp. 355-375.

Hall, T. C. 1983. Workshop summary: From test tube to farm. In: Plant Molecular Biology. U.C.L.A. Symposia on Molecular and Cellular Biology. R. B. Goldberg, Ed. Alan R. Liss, Inc., New York, New Series. 12: 481-484.

Hall, T. C., Miller, W. A. and Bujarski, J. J. 1983. Bromovirus replicases. In: Current Communications in Molecular Biology: Plant Infectious Agents. Cold Spring Harbor Publications. pp. 117-119.

Hall, T. C., Slightom, J. L., Ersland, D. R., Murray, M. G., Hoffman, L. M., Adang, M. J., Brown, J. W. S., Ma, Y., Matthews, J. A., Cramer, J. H., Barker, R. F., Sutton, D. W., and Kemp, J. D. 1983. Phaseolin: Nucleotide sequence explains molecular weight and charge heterogeneity of a small multigene family and also assists vector construction for gene expression in alien tissue. In: Structure and Function of Plant Genomes. O. Ciferri and L. Dure, Eds. Plenum Press. pp. 123-142.

Hall, T. C., Slightom, J. L. Ersland, D. R., Scharf, P., Barker, R. F., Murray, M. G., Brown, J. W. S. and Kemp, J. D. 1983. The phaseolin family of seed protein genes: Sequences and properties. In: Advances in Gene Technology: Molecular Genetics of Plants and Animals. K. Downey, R. W. Voellmy, F. Ahmad and J. Schultz, Eds. Academic Press. pp. 349-367.

Kemp, J. D., Sutton, D. W., Fink, C., Barker, R. F., and Hall, T. C. 1983. Agrobacterium-mediated transfer of foreign genes into plants. In: Beltsville Symposia in Agriculture 7: Genetic Engineering Applications to Agriculture. L. D. Owens, Ed. Rowman & Allenheld, Totowa. pp. 215-228.

Slightom, J. L., Adang, M. J., Ersland, D. R., Hoffman, L. M., Murray, M. J. and Hall, T. C. 1983. French bean storage protein gene family: Organization, nucleotide sequence and expression. In: Manipulation and Expression of Genes in Eukaryotes. P. Nagley, A. W. Linnane, W. J. Peacock and J. A. Pateman, Eds. Academic Press, Inc., Sydney, Australia. pp.203-211.

Hall, T.C. 1985. Expression of plant genes in alien cellular environments. In: Oxford Surveys of Plant Molecular and Cell Biology. B. J. Miflin, Ed. Oxford University Press, N.Y. 2: 329-338.

Hall, T. C., Reichert, N. A., Sengupta-Gopalan, C., Cramer, J. H., Lea, K., Barker, R. F., Slightom, J. L., Klassy, R., Kemp, J. D. 1985. Regulation of bean ß-phaseolin gene expression in yeast and tobacco seed. In: Molecular Form and Function of the Plant Genome. L. van Vloten-Doting, G. S. P. Groot and T. C. Hall, Eds. Plenum Press, New York. pp. 517-529.

van Vloten-Doting, L., Groot, G. S. P. and Hall, T. C., Eds. 1985. Molecular Form and Function of the Plant Genome. Plenum Press, New York.

Dreher, T. W. and Hall, T. C. 1987. Mutational analysis of the functions of the tRNA-like region of brome mosaic virus RNA. In: Positive Strand RNA Viruses. U.C.L.A. Symposia on Molecular and Cellular Biology. M. A. Brinton and R. R. Rueckert, Eds. Allen R. Liss, Inc., New York. New Series. 54: 317-325.

Hall, T. C., Dreher, T. W. and Marsh, L. E. 1987. Replicase and replication: Strategies for brome mosaic virus. In: Molecular Strategies for Crop Protection. U.C.L.A. Symposia on Molecular and Cellular Biology. C. J. Arntzen and C. Ryan, Eds. Allen R. Liss, Inc., New York. New Series. 48: 295-305.

Hall, T. C. and Thomas, T. L. 1987. Molecular approaches for the manipulation of developmental processes in plants. In: Hormone Action in Plant Development - A Critical Appraisal. Proceedings of the 10th Long Ashton Symposium. G. V. Hoad, J. R. Lenton, M. B. Jackson and R. K. Atkin, Eds. Butterworths, London. pp. 287-297.

Marsh, L. E., Dreher, T. W. and Hall, T. C. 1987. Mutational analysis of the internal promoter for transcription of the subgenomic RNA4 of BMV. In: Positive Strand RNA Viruses. U.C.L.A. Symposia on Molecular and Cellular Biology. M. A. Brinton and R. R. Rueckert, Eds. Allen R. Liss, Inc., New York. New Series. 54: 327-336.

Marsh, L. E. and Hall, T. C. 1987. Evidence implicating a tRNA heritage for the promoters of positive-strand RNA synthesis in brome mosaic and related viruses. In: The Evolution of Catalytic Function. Cold Spring Harbor Symposium on Quantitative Biology. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. 52: 331-341.

Dreher, T. W. and Hall, T. C. 1988. RNA replication of brome mosaic virus and related plant viruses. In: RNA Genetics. E. Domingo, J. J. Holland and P. Ahlquist, Eds. CRC Press, Boca Raton, FL. 1: 91-113. Hall, T. C. and DeRose, R. T. 1988. Transformation of plant cells. In: Applications of Plant Cell and Tissue Culture. Ciba Foundation Symposium No. 137. G. Bock and J. Marsh, Eds. Wiley-Interscience, Chichester, England. pp. 123-143.

Hall, T. C., Bustos, M. M., Anthony, J. L., Yang, L. J., Domoney, C., and Casey, R. 1990. Opportunities for bioactive compounds in transgenic plants. In: Ciba Foundation Symposium No. 154: Bioactive compounds from plants. D. J. Chadwick & J. Marsh, eds. John Wiley and Sons, Chichester, England. 177-197.

Hall, T. C., Rao, A. L. N., Pogue, G. P., Huntley, C. C. and Marsh, L. E. 1990. Replication, repair and recombination of brome mosaic virus RNA. In: New Aspects of Positive Strand RNA Viruses. M. A. Brinton and F. X. Heinz, Eds. A.S.M. Press, Washington D.C. pp. 47-54.

Marsh, L. E., Pogue, G. P., Huntley, C. C. and Hall, T.C. 1991. Insight to replication strategies and evolution of (+) strand RNA viruses provided by brome mosaic virus. In: Oxford Surveys of Plant Molecular and Cell Biology. B. J. Miflin, Ed. Oxford University Press, N.Y. 7: 297-334.

Bustos, M. M., Kalkan, F. A., Begum, D., Battraw, M. J. and Hall, T. C. 1992. Transcriptional and targeting determinants affecting phaseolin accumulation. In: Biotechnology and Nutrition. D. D. Bills and S.-D. Kung, eds. Butterworth-Heinemann, Boston. 215-235.

Hall, T. C. 1993. Revolutionary evolution. In: Transgenic Plants. S.-D. Kung and R. Wu, eds. Academic Press, Inc., Orlando. 247-255.

Duggal, R., Lahser, F. C., Rao, A. L. N. and Hall, T. C. 1994. Cis-acting sequences in the replication of plant viruses with (+)-sense RNA genomes. In: Annual Review of Phytopathology. R. J. Cook, Editor. Annual Reviews, Inc., Palo Alto, CA. 32: 287-309.

Hall, T. C., Xu, Y., Huntley, C. C., Yu, H., Seay, J., Connell, J. C., Lepetit, M., Dong, J., Wallace, D., Way, M. O. and Buchholz, W. G. 1994. Transgene expression and agronomic improvement of rice. In: The Production and Uses of Genetically Transformed Plants. M. W. Bevan, B. D. Harrison and C. J. Leaver, eds. Chapman & Hall, London. pp. 9-13.

Huntley, C. C., Pogue, G. P., Rao, A. L. N., and Hall, T. C. 1994. Strategies for pathogen derived resistance applied to brome mosaic virus. In: Virology in the Tropics. N. Rishi, K. L. Ahuja, and B. P. Singh, Eds. Malhotra Publishing House, New Delhi. pp. 116-135.

Rao, A. L. N., Duggal, R., Lahser, F. C. and Hall, T. C. 1994. Analysis of RNA replication in plant viruses. In: Methods in Molecular Genetics, Vol. 4: Molecular Virology. K. W. Adolph, Editor. Academic Press, Inc., Orlando, FL. pp. 216-236.

Buchholz, W. G., Connell, J. P., Kumpatla, S. and Hall, T. C. 1996. Molecular analysis of transgenic rice. In: Plant Virology Protocols: From Virus Isolation to Transgenic Resistance. Foster, G. and Taylor, S., eds. Humana Press, Inc., Totowa, NJ. pp. 383-396.

Buchholz, W. G., Teng, W., Wallace, D., Ambler, J. R. and Hall, T. C. 1996. Production of transgenic rice (Oryza sativa subspecies japonica cv. Taipei 309). In: Plant Virology Protocols: From Virus Isolation to Transgenic Resistance. Foster, G. and Taylor, S., eds. Humana Press, Inc., Totowa, NJ. pp. 397-416.

Buchholz, W. G., Xu, Y., Snowden, K. C., Yu, H., Ambler, J., Connell, J. P., Wallace, D., Tanaka, K. and Hall, T. C. 1996. Expression patterns of cyclophilin1, prolamine and RCg2 promoters in transgenic rice. In: Proceedings of the 3rd International Rice Genetics Symposium (Manila, Philippines, Oct 16-29, 1995). 710-718.

Dong, J. J., Teng, W. M., Buchholz, W. G. and Hall, T. C. 1996. Agrobacterium-mediated transformation of an elite cultivar of Texas rice. In: Proceedings of the 3rd International Rice Genetics Symposium (Manila, Philippines, Oct 16-29, 1995). 143-151.

Buchholz, W. G., Connell, J. P., Kumpatla, S. and Hall, T. C. 1998. Molecular analysis of transgenic rice. In: Plant Virology Protocols: From Virus Isolation to Transgenic Resistance. Foster, G. and Taylor, S., eds. Humana Press, Inc., Totowa, NJ. pp. 383-396.

Buchholz, W. G., Teng, W., Wallace, D., Ambler, J. R. and Hall, T. C. 1998. Production of transgenic rice (Oryza sativa subspecies japonica cv. Taipei 309). In: Plant Virology Protocols: From Virus Isolation to Transgenic Resistance. Foster, G. and Taylor, S., eds. Humana Press, Inc., Totowa, NJ. pp. 397- 416.

Hall, T. C., Chandrasekharan, M. B. and Li, G. 1999. Phaseolin: its past, properties, regulation and future. In: Seed Proteins. Casey, R. and Shewry, P. R., eds. Kluwer, Dorderecht, The Netherlands. pp. 209-240.

Hall, T. C., Kumpatla, S. P., Kharb, P., Iyer, L., Cervera, M., Jiang, Y., Wang, T., Yang, G., Teerawanichpan, P. Narangajavana, J. and Dong, J. 2001. Gene silencing and its reactivation in transgenic rice. p. 465-481. In: Rice Genetics IV (G. S. Khush, D. S. Brar and B. Hardy eds) Science Publishers, Inc., New Delhi (India) and International Rice Research Institute, Los Baños (Philippines).

B. Monocot reviewed articles

DeRose, R. T., Ma, D-P., Kwon, I-S., Hasnain, S. E., Klassy, R. C. and Hall, T. C. 1989. Characterization of the kafirin gene family from sorghum reveals extensive homology with zein from maize. Plant Mol. Biol. 12: 245-256.

Battraw, M. J. and Hall, T. C. 1990. Histochemical analysis of CaMV 35S promoter--glucuronidase gene expression in transgenic rice plants. Plant Mol. Biol. 15: 527-538.

Battraw, M. J. and Hall, T. C. 1991. Stable transformation of Sorghum bicolor protoplasts with chimeric neomycin phosphotransferase II and -glucuronidase genes. Theor. Appl. Genet. 82: 161-168.

Battraw, M. and Hall, T. C. 1992. Expression of a chimeric neomycin phosphotransferase II gene in first and second generation transgenic rice plants. Plant Sci. 86: 191-202.

Hall, T. C., Xu, Y., Huntley, C. C., Yu, H., Seay, J., Connell, J. C., Lepetit, M., Dong, J., Wallace, D., Way, M. O. and Buchholz, W. G. 1993. Transgene expression and agronomic improvement of rice. Phil. Tran. R. Soc. London B. 341: 361-374.

Xu, Y. and Hall, T. C. 1993. Cytosolic triosephosphate isomerase is a single gene in rice. Plant Physiol. 101: 683-687.

Xu, Y., Harris-Haller, L. W., McCollum, J. C., Hardin, S. H. and Hall, T. C. 1993. Nuclear gene encoding cytosolic triosephosphate isomerase from rice (Oryza sativa L.). Plant Physiol. 102: 697.

Buchholz, W. G., Harris-Haller, L., DeRose, R. T. and Hall, T. C. 1994. Cyclophilins are encoded by a small gene family in rice. Plant Mol. Biol. 25: 837-843.

Xu, Y., Yu, H. and Hall, T. C. 1994. Rice triosephosphate isomerase gene 5' sequence directs -glucuronidase activity in transgenic tobacco but requires an intron for expression in rice. Plant Physiol. 106: 459-467.

Xu, Y., Buchholz, W. G., DeRose R. T. and Hall, T. C. 1995. Characterization of a novel gene family from rice that encodes root-specific proteins. Plant Mol. Biol. 27: 237-248.

Snowden, K. C., Buchholz, W. G. and Hall, T. C. 1996. Intron position affects expression from the tpi promoter in rice. Plant Mol. Biol. 31: 689-692.

Dong, J. J., Teng, W. M., Buchholz, W. G. and Hall, T. C. 1996. Agrobacterium-mediated transformation of javanica rice. Molecular Breeding 2: 267-276

DeRose, R. T., Begum, D. and Hall, T. C. 1996. Analysis of kafirin promoter activity in transgenic tobacco seeds. Plant Mol. Biol. 32: 1029-1035.

Kumpatla, S., Teng, W., Buchholz, W. G. and Hall, T. C. 1997. Epigenetic transcriptional silencing and 5-azacytidine-mediated reactivation of a complex transgene in rice. Plant Physiol. 115: 361-373.

Kumpatla, S. P., Chandrasekharan, M. B., Iyer, L. M., Li, G. and Hall, T. C. 1998. Genome intruder scanning and modulation systems and transgene silencing. Trends in Plant Science 3: 97-104.

Kumpatla, S.P. and Hall, T. C. 1998. Recurrent onset of epigenetic silencing in rice harboring a multicopy transgene. Plant Journal. 14: 129-135.

Kumpatla, S. P., and Hall, T. C. 1998. Longevity of 5-azacytidine-mediated gene expression and re-establishment of silencing in transgenic rice. Plant Mol. Biol. 38: 1113-1122.

Kumpatla, S. P. and Hall, T. C. 1999. Sequence rearrangements, repeats and extensive methylation in a multicopy silencing-prone transgene locus in rice. IUBMB-Life, 48: 459-467.

Kharb, P., Dong, J., Islam-Faridi, M.N., Stelly, D.M. and Hall, T.C. 2001. Fluorescence in situ hybridization of single copy transgenes in rice chromosomes. In Vitro Cell. Dev. Biol. - Plant 37: 1-5.

Dong, J., Kharb, P., Teng, W. and Hall, T.C. 2001. Characterization of rice transformed via an Agrobacterium-mediated inflorescence transformation. Mol. Breeding 7: 187-194.

C. Dicot reviewed articles

Hall, T. C., McLeester, R. C. and Bliss, F. A. 1972. Electrophoretic analysis of protein changes during the development of the French bean fruit. Phytochemistry 11: 647-649.

Bliss, F. A., Barker, L. N., Franckowiak, J. D. and Hall, T. C. 1973. Genetic and environmental variation of seed yield, yield components, and seed protein quantity and quality of cowpea. Crop Sci. 13: 656-660.

McLeester, R. C., Hall, T. C., Sun, S. M. and Bliss, F. A. 1973. Comparison of globulin proteins from Phaseolus vulgaris with those from Vicia faba. Phytochemistry 2: 85-93.

Sun, S. M., McLeester, R. C., Bliss, F. A. and Hall, T. C. 1974. Reversible and irreversible dissociation of globulins from Phaseolus vulgaris seed. J. Biol. Chem. 249: 2118-2121.

Romero, J., Sun, S. M., McLeester, R. C., Bliss, F. A. and Hall, T. C. 1975. Heritable variation in a polypeptide subunit of the major storage protein of the bean, Phaseolus vulgaris L. Plant Physiol. 56: 776-779.

Sun, S. M., Buchbinder, B. U., and Hall, T. C. 1975. Cell-free synthesis of the major storage protein of the bean, Phaseolus vulgaris L. Plant Physiol. 56: 780-785.

Sun, S. M., and Hall, T. C. 1975. Solubility characteristics of globulins from Phaseolus seeds in regard to their isolation and characterization. Agr. and Food Chem. 23: 184-189.

Stockman, D. R., Hall T. C. and Ryan, D. S. 1976. Affinity chromatography of the major seed protein of the bean (Phaseolus vulgaris L.) Plant Physiol. 58: 272-275.

Bliss, F. A. and Hall, T. C. 1977. Food legumes -- Compositional and nutritional changes induced by breeding. Cereal Foods World 22: 106-113.

Hall, T. C., Bliss, F. A., Ryan, D. S., and Sun, S. M. 1977. The subunit structure and cell-free synthesis of the major storage protein from bean (Phaseolus vulgaris L.) seeds. Colloques Internationaux du C.N.R.S. 261: 335-343.

Hall, T. C., McLeester, R. C. and Bliss, F. A. 1977. Equal expression of the maternal and paternal alleles for the polypeptide subunits of the major storage protein of the bean Phaseolus vulgaris L. Plant Physiol. 59: 1122-1124.

Hall, T. C., Ma, Y., Buchbinder, B. U., Pyne, J. W., Sun, S. M. and Bliss, F. A. 1978. Messenger RNA for G1 protein of French bean seeds: Cell-free translation and product characterization. Proc. Natl. Acad. Sci. USA 75: 3196-3200.

Sun, S. M., Mutschler, M. A., Bliss, F. A., and Hall, T. C. 1978. Protein synthesis and accumulation in bean cotyledons during growth. Plant Physiol. 61: 918-923.

Brown, J. W. S., Bliss, F. A. and Hall, T. C. 1980. Microheterogeneity of globulin-1 storage protein from French bean with isoelectrofocusing. Plant Physiol. 66: 838-840.

Ma, Y., Bliss, F. A. and Hall, T. C. 1980. Peptide mapping reveals considerable sequence homology among the three polypeptide subunits of G1 storage protein from French bean seed. Plant Physiol. 66: 897-902.

Mutschler, M. A., Bliss, F. A. and Hall, T. C. 1980. Variation in the accumulation of seed storage protein among genotypes of Phaseolus vulgaris (L.) Plant Physiol. 65: 627-630.

Brown, J. W. S., Bliss, F. A. and Hall, T. C. 1981. Linkage relationships between genes controlling seed proteins in French bean. Theoret. Appl. Genet. 60: 251-259.

Brown, J. W. S., Ma, Y., Bliss, F. A. and Hall, T. C. 1981. Genetic variation in the subunits of globulin-1 storage protein of French bean. Theoret. Appl. Genet. 59: 83-88.

Brown, J. W. S., Osborn, T. C., Bliss, F. A. and Hall, T. C. 1981. Genetic variation in the subunits of globulin-2 and albumin seed proteins of French bean. Theoret. Appl. Genet. 60: 245-250.

Matthews, J. A., Brown, J. W. S., and Hall, T. C. 1981. Phaseolin mRNA is translated to yield glycosylated polypeptides by Xenopus oocytes. Nature 294: 175-176.

Sun, S. M., Slightom, J. L. and Hall, T. C. 1981. Intervening sequences in a plant gene -- Comparison of the partial sequence of cDNA and genomic DNA of French bean phaseolin. Nature 289: 37-41.

Brown, J. W. S., McFerson, J. R., Bliss, F. A. and Hall, T. C. 1982. Genetic divergence among commercial classes of Phaseolus vulgaris in relation to phaseolin pattern. HortScience 17: 752-754.

Brown, J. W. S., Osborn, T. C., Bliss, F. A., and Hall, T. C. 1982a. Bean lectins I: Relationships between agglutinating activity and electrophoretic variation in the lectin-containing G2/albumin seed proteins of French bean (Phaseolus vulgaris L.) Theoret. Appl. Genet. 62: 263-271.

Brown, J. W. S., Osborn, T. C., Bliss, F. A., and Hall, T. C. 1982b. Bean lectins II: Relationship between qualitative lectin variation in Phaseolus vulgaris L. and previous observations on purified bean lectins. Theoret. Appl. Genet. 62: 361-367.

Murai, N., Sutton, D. W., Murray, M. G., Slightom, J. L., Merlo, D. J., Reichert, N. A., Sengupta-Gopalan, C., Stock, C. A., Barker, R. F., Kemp, J. D. and Hall, T. C. 1983. Phaseolin gene from bean is expressed after transfer to sunflower via tumor-inducing plasmid vectors. Science 222: 476-482.

Slightom, J. L., Sun, S. M. and Hall, T. C. 1983. Complete nucleotide sequence of a French bean storage protein gene: Phaseolin. Proc. Natl. Acad. Sci. USA 80: 1897-1901.

Blagrove, R. J., Lilley, G. G., Van Donkelaar, A., Sun, S. M. and Hall, T. C. 1984. Structural studies of a French bean storage protein: phaseolin. Int. J. Biol. Macromol. 6: 137-141.

Talbot, D.R., Adang, M.J., Slightom, J.L. and Hall, T.C. 1984. Size and organization of a multigene family encoding phaseolin, the major seed storage protein of Phaseolus vulgaris L. Mol. Gen. Genet. 198: 42-49.

Sengupta-Gopalan, C., Reichert, N. A., Barker, R. F., Hall, T. C., and Kemp, J. D. 1985. Developmentally regulated expression of the bean ß-phaseolin gene in tobacco seed. Proc. Natl. Acad. Sci. USA 82: 3320-3324.

Paaren, H. E., Slightom, J. L., Hall, T. C., Inglis, A. S. and Blagrove, R. J. 1987. Purification of a seed glycoprotein: N-terminal and deglycosylation analysis of phaseolin. Phytochemistry 26: 335-343.

Thomas, T. L. and Hall, T. C. 1987. Gene transfer and expression in plants: Implications and potential. Bioessays 3: 149-153.

Bustos, M. M., Luckow, V. A., Griffing, L. R., Summers, M. D. and Hall, T. C. 1988. Expression, glycosylation and secretion of phaseolin in a baculovirus system. Plant Mol. Biol. 10: 475-488.

Bustos, M. M., Guiltinan, M. J., Jordano, J., Begum, D., Kalkan F. A. and Hall, T. C. 1989. Regulation of -Glucuronidase expression in transgenic tobacco plants by an A/T rich, cis-acting sequence found upstream of a French bean ß-phaseolin gene. Plant Cell 1: 839-853.

Anthony, J. L., Vonder Haar, R. A. and Hall, T. C. 1990. Nucleotide sequence of an ß-phaseolin gene from Phaseolus vulgaris. Nucleic Acids Res. 18: 3396.

Yang, L., Domoney, C., Casey, R. and Hall, T. C. 1990. Processing Pisum sativum seed storage protein precursors in vitro. Cell Research 2: 153-162.

Anthony, J. L., Vonder Haar, R. A. and Hall, T. C. 1991. Nucleotide sequence of a genomic clone encoding arcelin, a lectin-like seed protein from Phaseolus vulgaris. Plant Physiol. 97: 839-840.

Bustos, M. M., Battraw, M. J., Kalkan, F. A., and Hall, T. C. 1991. Transient gene expression in electroporated bean cotyledon protoplasts. Plant Mol. Biol. Reporter 9: 322-332.

Bustos, M. M., Begum, D., Kalkan, F. A., Battraw, M. J. and Hall, T. C. 1991. Positive and negative cis-acting DNA domains are required for spatial and temporal regulation of gene expression by a seed storage protein promoter. EMBO J. 10: 1469-1479.

Bustos, M. M., Kalkan, F. A., VandenBosch, K. A. and Hall, T. C. 1991. Differential accumulation of four phaseolin glycoforms in transgenic tobacco. Plant Mol. Biol. 16: 381-395.

van der Geest, A. H. M., Hall, G. E., Spiker, S. and Hall, T. C. 1994. The ß-phaseolin gene is flanked by matrix attachment regions. Plant J. 6: 413-423.

Frisch, D. A., Harris-Haller, L., Yokubaitis, N. T., Thomas, T. L., Hardin, S. H., and Hall, T. C. 1995. Complete sequence of the binary vector Bin 19. Plant Mol. Biol. 27: 405-409.

Frisch, D. A., van der Geest, A. H. M., Dias, K. and Hall, T. C. 1995. Chromosomal integration is required for spatial regulation of expression from the ß-phaseolin promoter. Plant J. 7: 503-512.

van der Geest, A. H. M., Frisch, D. A., Kemp, J. D. and Hall, T. C. 1995. Cell ablation reveals that expression from the phaseolin promoter is confined to embryogenesis and microsporogenesis. Plant Physiol. 109: 1151-1158.

van der Geest, A. H. M. and Hall, T. C. 1996. A 68 bp element of the ß-phaseolin promoter functions as a seed-specific enhancer. Plant Mol. Biol. 32: 579-588.

van der Geest, A. H. M. and Hall, T. C. 1997. The ß-phaseolin 5' matrix attachment region acts as an enhancer facilitator. Plant Mol. Biol. 33: 553-557.

Li, G., Chandler, S. P., Wolffe, A. and Hall, T. C. 1998. Architectural specificity in chromatin structure at the TATA box in vivo: Nucleosome displacement upon ß-phaseolin gene activation. Proc. Natl. Acad. Sci. USA. 95: 4772-4777.

Vaucheret, H., Elmayan, T., Thierry, D., van der Geest, A., Hall, T., Conner, A. J., Mlynarova, L. and Nap, J. P. 1998. Flank matrix attachment regions (MARs) from chicken, bean, yeast or tobacco do not prevent homology-dependent trans-silencing in transgenic tobacco plants. Mol. Gen. Genet. 259: 388-392.

Hall, T.C., Li, G., and Chandrasekharan, M. 1998. Participation of chromatin in the regulation of phaseolin gene expression. J. Plant Physiol. 152: 614-620.

Li, G., Bishop, K. J., Chandrasekharan, M. B. and Hall, T. C. 1999. ß-phaseolin gene activation is a two-step process: PvAlf-facilitated chromatin modification followed by abscisic acid-mediated gene activation. Proc. Natl. Acad. Sci., U.S.A. 96: 7104-7109.

Li, G. and Hall, T. C. 1999. Footprinting in vivo reveals changing profiles of multiple factor interactions with the ß-phaseolin promoter during embryogenesis. Plant J. 18: 633-642.

Li, G., Bishop, K.J. and Hall, T.C. 2001. De novo activation of the ß-phaseolin promoter by phosphatase or protein synthesis inhibitors. J. Biol. Chem. 276: 2062-2068.

Li, G., Chandrasekharan, M.B., Wolffe, A.P. and Hall, T.C. 2001b. Chromatin structure and phaseolin gene regulation. Plant Mol. Biol. 46: 121-129

Ng, D. W-K, Chandrasekharan, M.B., Hall, T.C. 2004. The 5' UTR negatively regulates expression from the ABI3 promoter. Plant Mol. Biol. In press.

Zhou X.,. Chandrasekharan M.B., Hall T.C. 2004. High rooting frequency and functional analysis of GUS and GFP expression in transgenic Medicago truncatula A17. New Phytol. in press.

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D. Viruses - reviewed articles

Hall, T. C., Shih, D. S. and Kaesberg, P. 1972. Enzyme-mediated binding of tyrosine to brome-mosaic-virus ribonucleic acid. Biochem. J. 129: 969-976.

Chen, J. M. and Hall, T. C. 1973. Comparison of tyrosyl transfer ribonucleic acid and brome mosaic virus tyrosyl ribonucleic acid as amino acid donors in protein synthesis. Biochemistry 12: 4570-4574.

Hall, T. C., Wepprich, R. K., Davies, J. W., Weathers, L. G. and Semancik, J. S. 1974. Functional distinctions between the ribonucleic acids from citrus exocortis viroid and plant viruses: Cell-free translation and aminoacylation reactions. Virology 61: 486-492.

Kohl, R. J. and Hall, T. C. 1974. Aminoacylation of RNA from several viruses: Amino acid specificity and differential activity of plant, yeast and bacterial synthetases. J. Gen. Virol. 25: 257-261.

Shih, D. S., Kaesberg, P., and Hall, T. C. 1974. Messenger and aminoacylation functions of brome mosaic virus RNA after chemical modification of 3' terminus. Nature 249: 353-355.

Bastin, M., Dasgupta, R., Hall, T. C. and Kaesberg, P. 1976. Similarity in structure and function of the 3'-terminal region of the four brome mosaic viral RNAs. J. Mol. Biol. 103: 737-745.

Bastin, M. and Hall, T. C. 1976. Interaction of elongation factor 1 with aminoacylated brome mosaic virus and tRNA's. J. Virol. 20: 117-122.

Hall, T. C. and Wepprich, R. K. 1976. Functional possibilities for aminoacylation of viral RNA in transcription and translation. Ann. Microbiol. (Inst. Pasteur) 127A: 143-152.

Kohl, R. J. and Hall, T. C. 1977. Loss of infectivity of brome mosaic virus RNA after chemical modification of the 3' or 5' terminus. Proc. Natl. Acad. Sci. USA 74: 2682-2686.

German, T. L., de Zoeten, G. A. and Hall, T. C. 1978. Pea enation mosaic virus genome RNA contains no polyadenylate sequences and cannot be aminoacylated. Intervirology 9: 226-230.

Pinck, M. and Hall, T. C. 1978. Aminoacylation properties of eggplant mosaic virus RNA: Separation and association of tRNAs. Virology 88: 281-285.

Hall, T. C., Pinck, M., Ma, Y., Duranton, H. M. and German, T. L. 1979. Aminoacylation and messenger functions of eggplant mosaic virus RNA. Virology 97: 354-365.

Hardy, S. F., German, T. L., Loesch-Fries, L. S. and Hall, T. C. 1979. Highly active template-specific RNA-dependent RNA polymerase from barley leaves infected with brome mosaic virus. Proc. Natl. Acad. Sci. USA 76: 4956-4960.

Pyne, J. W. and Hall, T. C. 1979. Efficient ribosome binding of brome mosaic virus (BMV) RNA4 contributes to its ability to outcompete the other BMV RNAs for translation. Intervirology 11: 23-29.

Loesch-Fries, L. S. and Hall, T. C. 1980. Synthesis, accumulation and encapsidation of individual brome mosaic virus RNA components in barley protoplasts. J. Gen. Virol. 47: 323-332.

Kiberstis, P. A., Loesch-Fries, L. S. and Hall, T. C. 1981. Viral protein synthesis in barley protoplasts inoculated with native and fractionated brome mosaic virus RNA. Virology 112: 804-808.

Bujarski, J. J., Hardy, S. F., Miller, W. A. and Hall, T. C. 1982. Use of dodecyl--d maltoside in the purification and stabilization of RNA polymerase from brome mosaic virus-infected barley. Virology 119: 465-473.

Loesch-Fries, L. S. and Hall, T. C. 1982. In vivo aminoacylation of brome mosaic and barley stripe mosaic virus RNAs. Nature 298: 771-773.

Barker, R. F., Jarvis, N. P., Thompson, D. V., Loesch-Fries, L. S. and Hall, T. C. 1983. Complete nucleotide sequence of alfalfa mosaic virus RNA3. Nucl. Acids Res. 11: 2881-2891.

Kiberstis, P. A. and Hall, T. C. 1983. N-acetyl-tyrosine at the 3' end of brome mosaic virus RNA has little effect on infectivity. J. Gen. Virol. 64: 2073-2077.

Miller, W. A. and Hall, T. C. 1983. Use of micrococcal nuclease in the purification of highly template dependent RNA-dependent RNA polymerase from brome mosaic virus-infected barley. Virology 125: 236-241.

Ahlquist, P. Bujarski, J. J., Kaesberg, P. and Hall, T. C. 1984. Localization of the replicase recognition site within brome mosaic virus RNA by hybrid-arrested RNA synthesis. Plant Mol. Biol. 3: 37-44.

Dreher, T. W., Bujarski, J. J. and Hall, T. C. 1984. Mutant viral RNAs synthesized in vitro show altered aminoacylation and replicase template activities. Nature 311: 171-175.

Miller, W. A. and Hall, T. C. 1984. RNA-dependent RNA polymerase isolated from cowpea chlorotic mottle virus-infected cowpeas is specific for bromoviral RNA. Virology 132: 53-60.

Bujarski, J. J., Dreher, T. W. and Hall, T. C. 1985. Deletions in the 3'-terminal tRNA-like structure of brome mosaic virus RNA differentially affect aminoacylation and replication in vitro. Proc. Natl. Acad. Sci. USA 82: 5636-5640.

Loesch-Fries, L. S., Jarvis, N. P., Krahn, K. J., Nelson, S. E. and Hall, T. C. 1985. Expression of alfalfa mosaic virus RNA 4 cDNA transcripts in vitro and in vivo. Virology 146: 177-187.

Miller, W. A., Dreher, T. W. and Hall, T. C. 1985. Synthesis of brome mosaic virus subgenomic RNA in vitro by internal initiation on (-)-sense genomic RNA. Nature 313: 68-70.

Bujarski, J. J., Ahlquist, P., Hall, T. C., Dreher, T. W. and Kaesberg, P. 1986. Modulation of replication, aminoacylation and adenylation in vitro and infectivity in vivo of BMV RNAs containing deletions within the multifunctional 3' end. EMBO J. 5: 1769-1774.

Miller, W. A., Bujarski, J. J., Dreher, T. W. and Hall, T. C. 1986. Minus strand initiation by brome mosaic virus replicase within the 3' tRNA-like structure of native and modified RNA templates. J. Mol. Biol. 187: 537-546.

Hall, T. C., Marsh, L. E. and Dreher, T. W. 1987. Analysis of brome mosaic virus replication and aminoacylation functions by site-specific mutagenesis. J. Cell Sci. Suppl. 7: 287-301.

Dreher, T. W. and Hall, T. C. 1988a. Mutational analysis of the sequence and structural requirements in brome mosaic virus RNA for minus strand promoter activity. J. Mol. Biol. 201: 31-40.

Dreher, T. W. and Hall, T. C. 1988b. Mutational analysis of the tRNA mimicry of brome mosaic virus RNA: Sequence and structural requirements for aminoacylation and 3'-adenylation. J. Mol. Biol. 201: 41-55.

Marsh, L. E., Dreher, T. W. and Hall, T. C. 1988. Mutational analysis of the core and modulator sequences of the BMV RNA3 subgenomic promoter. Nucl. Acids Res. 16: 981-995.

Dreher, T. W., Rao, A. L. N. and Hall, T. C. 1989. Replication in vivo of mutant brome mosaic virus RNAs defective in aminoacylation. J. Mol. Biol. 206: 425-438.

Marsh, L. E., Pogue, G. P. and Hall, T. C. 1989. Similarities among plant virus (+) and (-) RNA termini imply a common ancestry with promoters of eukaryotic tRNAs. Virology 172: 415-427.

Rao, A. L. N., Dreher, T. W., Marsh, L. E. and Hall, T. C. 1989. Telomeric function of the tRNA-like structure of brome mosaic virus RNA. Proc. Natl. Acad. Sci. USA 86: 5335-5339.

Pogue, G. P., Marsh, L. E. and Hall, T. C. 1990. Point mutations in the ICR2 motif of brome mosaic virus RNAs debilitate (+)-strand replication. Virology 178: 152-160.

Rao, A. L. N. and Hall T. C. 1990. Requirement for a viral trans-acting factor encoded by brome mosaic virus RNA-2 provides strong selection in vivo for functional recombinants. J. Virol. 64: 2437-2441.

Rao, A. L. N., Huntley, C. C., Marsh, L. E. and Hall, T. C. 1990. Analysis of RNA stability and (-) strand content in viral infections using biotinylated RNA probes. J. Virol. Methods 30: 239-250.

Rao, A. L. N., Sullivan, B. P. and Hall T. C. 1990. Use of Chenopodium hybridum facilitates isolation of brome mosaic virus RNA recombinants. J. Gen. Virol. 71: 1403-1407.

Marsh, L. E., Huntley, C. C., Pogue, G. P., Connell, J. P. and Hall, T. C. 1991. Regulation of (+):(-)-strand asymmetry in replication of brome mosaic virus RNA. Virology 182: 76-83.

Marsh, L. E., Pogue, G. P., Connell, J. P., and Hall, T. C. 1991. Artificial defective interfering RNAs derived from brome mosaic virus. J. Gen. Virol. 72: 1787-1792.

Marsh, L. E., Pogue, G. P., Szybiak, U., Connell, J. P. and Hall, T. C. 1991. Non-replicating deletion mutants of brome mosaic virus RNA-2 interfere with viral replication. J. Gen. Virol. 72: 2367-2374.

Rao, A. L. N. and Hall, T. C. 1991. Interference in trans with brome mosaic virus replication by RNA-2 bearing aminoacylation-deficient mutants. Virology 180: 16-22.

Duggal, R., Rao, A. L. N. and Hall, T. C. 1992. Unique nucleotide differences in the conserved 3' termini of brome mosaic virus RNAs are maintained through their optimization of genome replication. Virology 187: 261-270.

Pogue, G. P. and Hall, T. C. 1992. The requirement for a 5' stem-loop structure in brome mosaic virus replication supports a new model for viral positive-strand RNA initiation. J. Virol. 66: 674-684.

Pogue, G. P., Marsh, L. E., Connell, J. P. and Hall, T. C. 1992. Requirement for ICR-like sequences in the replication of brome mosaic virus genomic RNA. Virology 188: 742-753.

Duggal, R. and Hall, T. C. 1993. Identification of domains in brome mosaic virus RNA-1 and coat protein necessary for specific interaction and encapsidation. J. Virol. 67: 6406-6412.

Huntley, C. C. and Hall, T. C. 1993a. Minus sense transcripts of brome mosaic virus RNA-3 intercistronic region interfere with viral replication. Virology 192: 290-297.

Huntley, C. C. and Hall, T. C. 1993b. Interference with brome mosaic virus replication by targeting the minus strand promoter. J. Gen. Virol. 74: 2445-2452.

Lahser, F. C., Marsh, L. E. and Hall, T. C. 1993. Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to replication and translation. J. Virol. 67: 3295-3303.

Rao, A. L. N. and Hall, T. C. 1993. Recombination and polymerase error facilitate restoration of infectivity in brome mosaic virus. J. Virol. 67: 969-979.

Pogue, G. P., Huntley, C. C. and Hall, T. C. 1994. Common replication strategies emerging from the study of diverse groups of positive-strand RNA viruses. Archives of Virology Suppl. 9: 181-194.

Duggal, R. and Hall, T. C. 1995. Interaction of host proteins with the plus-strand promoter of brome mosaic virus RNA-2. Virology. 214: 638-641.

Huntley, C. C. and Hall, T. C. 1996. Interference with brome mosaic virus replication in transgenic rice. Mol. Plant-Microbe Interactions 9:164-170.

Iyer, L. M. and Hall, T. C. 2000. Virus recovery is induced in Brome mosaic virus p2 transgenic plants showing synchronous complementation and RNA-2 specific silencing. Mol. Plant-Microbe Interactions. 13: 247-258.

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E. Miscellaneous

1. Hall, T. C. and Cocking, E. C. 1965. High-efficiency liquid-scintillation counting of ¹⁴C-labelled material in aqueous solution and determination of specific activity in labelled proteins. Biochem. J. 96: 626-633.

2. Hall, T. C. and Cocking, E. C. 1966a. Amino acid incorporation into protein by aseptic cell-free systems from tomato cotyledons and leaves. Biochem. Biophys. Acta. 123: 163-171.

3. Hall, T. C. and Cocking, E. C. 1966b. Studies on protein synthesis in tomato cotyledons and leaves. I. Protein synthesis and turnover in intact cotyledons and leaves. Plant and Cell Physiol. 7: 329-341.

4. Hall, T. C. and Cocking, E. C. 1966c. Studies on protein synthesis in tomato cotyledons and leaves. II. Intermediate stages of protein synthesis. Plant and Cell Physiol. 7: 343-356.

5. Hall, T. C. and Weiser, C. J. 1966. Liquid scintillation counting at ambient temperature. Anal. Biochem. 17: 294-299.

6. Hurst, C., Hall, T. C. and Weiser, C. J. 1967. Reception of the light stimulus for cold acclimation in Cornus stolonifera Michx. HortScience 2: 164-165.

7. Hall, T. C. 1968. Protein, amino acid and chlorophyll metabolism during the ontogeny of snap beans. Proc. Amer. Soc. Hort. Sci. 93: 379-387.

8. McCown, B. H., Beck, G. E. and Hall, T. C. 1968. Plant leaf and stem proteins. I. Extraction and electrophoretic separation of the basic, water-soluble fraction. Plant Physiol. 43: 578-582.

9. McLeester, R. C., Weiser, C. J. and Hall, T. C. 1968. Seasonal variations in freezing curves of stem sections of Cornus stolonifera Michx. Plant & Cell Physiol. 9: 807-817.

10. Arglebe, C. and Hall, T. C. 1969. Extraction and comparison of bean cytoplasmic and chloroplast ribosomes. Plant and Cell Physiol. 10: 171-182.

11. Davies, J. W. and Hall, T. C. 1969. Liquid scintillation counting methods for accurate assay of beta-radioactivity in biological experiments. Anal. Biochem. 27: 77-90.

12. Hall, T. C., McCown, B. H., Desborough, S., McLeester, R. C. and Beck, G. E. 1969. A comparative investigation of isozyme fractions separated from plant tissues. Phytochemistry, 8: 385-391.

13. McCown, B. H., Beck, G. E., and Hall, T. C. 1969. The hardening response of three clones of Dianthus and the corresponding complement of peroxidase isoenzymes. J. Amer. Soc. Hort. Sci. 94: 691-693.

14. McCown, B. H., Hall, T. C. and Beck, G. E. 1969. Plant leaf and stem Proteins. II. Isozymes and environmental change. Plant Physiol. 44: 210-216.

15. McCown, B. H., McLeester, R. C., Beck, G. E. and Hall, T. C. 1969. Environment-induced changes in peroxidase zymograms in the stems of deciduous and evergreen plants. Cryobiol. 5: 410-412.

16. McLeester, R. C., Weiser, C. J. and Hall, T. C. 1969. Multiple freezing points as a test for viability of plant stems in the determination of frost hardiness. Plant Physiol. 44: 37-44.

17. Hall, T. C. 1970. Distribution and separation of some proteins from the bean plant. J. Amer. Soc. Hort. Sci. 95: 355-359.

18. Hall, T. C. and Tao, K. L. 1970. Rates of aminoacyl-transfer-ribonucleic acid synthesis in vivo and in vitro by bean leaves. Biochem. J. 117: 853-859.

19. Hall, T. C., McLeester, R. C., McCown, B. H. and Beck, G. E. 1970. Enzyme changes during deacclimation of willow stem. Cryobiol. 7: 130-135.

20. McCown, B. H., McCown, D. D., Beck, G. E. and Hall, T. C. 1970. Isoenzyme complements of Dianthus callus cultures: Influence of light and temperature. Amer. J. Bot. 57: 148-152.

21. Tao, K. L. and Hall, T. C. 1971a. Factors controlling aminoacyl-transfer-ribonucleic acid synthesis in vitro by a plant system. Biochem. J. 121: 495-501.

22. Tao, K. L. and Hall, T. C. 1971b. Extensive charging of transfer ribonucleic acid by bean leaf extracts in vitro. Biochem. J. 125: 975-981.

23. Sun, S. M., and Hall, T. C. 1974. Application of Remazol dye for isolation of protein subunits by preparative SDS-polyacrylamide gel electrophoresis. Anal. Biochem. 61: 237-242.

24. Farhoomand, M. B., Peterson, L. A., and Hall, T. C. 1974. Hydrogen ion concentration of the root media in relation to transpiration rates. Iran. J. Agric. Res. 2: 89-98.

25. Huber, S. C., Hall, T. C. and Edwards, G. E. 1976. Differential localization of Fraction I protein between chloroplast types. Plant Physiol. 57: 730-733.

26. Huber, S. C., Hall, T. C. and Edwards, G. E. 1977. Light dependent incorporation of ¹⁴CO₂ into protein by mesophyll protoplasts and chloroplasts isolated from Pisum sativum. Z. Pflanzenphysiol. 85: 153-163.

27. McLeester, R. C. and Hall, T. C. 1977. Simplification of amino acid incorporation and other assays using filter paper techniques. Anal. Biochem. 79: 627-630.

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