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John F Antoniw

Contact Information

Projects

• Database of Plant Viruses
• Molecular Biology Notebook

Interests

• microarray analysis
• fungal genome annotation
• virus genome databases and sequence analysis
• educational molecular biology software
• web applications development
• Delphi and Kylix programming

My main interests are in developing databases and software for bioinformatics, especially in the analysis of microarray data from Mycosphaerella graminicola chips with John Keon and Jason Rudd. I am also involved in the annotation of the Fusarium graminearum genome for transcription factors with Kim Hammond-Kosack and Martin Urban, and Richard Coulson at the EBI. I am developing plant virus genome web databases and PC client software with Mike Adams, and the light leafspot forecast web software with Neal Evans. I am also interested in developing molecular biology software (e.g. BioLab in The Molecular Biology Notebook with Nathalie Castells-Brooke) for use in education at A-level in schools and undergraduate level at universities.

Software

Here is a list of some my software:

• RESearch - DNA sequence analysis especially restriction enzyme sites
• MakeGel - agarose gel electrophoresis simulation
• GeneMap - a web browser helper application for displaying sequences
• Descriptions of Plant Viruses on CD-ROM - plant virus database and software
• Molecular Biology Notebook - educational molecular biology course
• BioLab - educational molecular biology lab simulation
• TransMembrane Proteins - 2D model of transmembrane proteins
• PCR primer design - primer database, and analysis and design software
• SNP Enzyme Finder - finds restriction enzymes which can detect SNPs

Links:

The AAB Descriptions of Plant Viruses (DPV)
Based on the highly successful printed publication - Plant Virus Descriptions, but with a lot more information, some new descriptions and improved images. The CDRom which contains plant virus databases and Windows^TM software (versions 3.1, 95 or later) is a unique resource for teaching and research. We are developing an online version at DPV Web (see below for more details).

DPV Web
This site will eventually contain a complete on-line version of the DPV software and databases and much more. You can already find the individual virus descriptions, a classified list of plant virus sequences and some information about the new sequence database and software that we are developing for the analysis of virus genomes - Codon Use analysis is the first module.

Plant virus and viroid sequence information
All the current sequences from the EMBL and Genbank databases classified by virus or viroid name. Viruses of fungi and protozoa are also included.

Electron micrographs of Plant Viruses
A selection of electron micrographs produced by plant pathologists at Rothamsted.

Light Leafspot Forecast
Prediction of the severity of light leafspot disease on Winter oilseed rape.

The Molecular Biology Notebook
A comprehensive package for the hands-on teaching of Molecular Biology.

Selected recent publications

Research Papers

TOGAWA, R.C., ANTONIW, J.F. & MULLINS, J.G.L. (2001) TMCompare: transmembrane region sequence and structure. Bioinformatics, 17, 1238-1239, 2001

ADAMS, M.J., ANTONIW, J.F. & MULLINS, J.G.L. (2001) Plant virus transmission by plasmodiophorid fungi is associated with distinctive transmembrane regions of virus-encoded proteins. Archives of Virology, 146, 1139-1153

TAHIRI-ALAOUI, A., LINGUA, G., AVROVA, A., SAMPO, S., FUSCONI, A., ANTONIW, J.F. & BERTA, G. (2002) A cullin gene is induced in tomato roots forming arbuscular mycorrhizae. Canadian Journal of Botany, 80, 607-616

PASTORI, G.M., KIDDLE, G., ANTONIW, J.F., BERNARD, S., VELJOVIC-JOVANOVIC, S., VERRIER, P.J., NOCTOR, G. & FOYER, C.H. (2003) Leaf vitamin C contents modulate plant defense transcripts and regulate genes that control development through hormone signaling. Plant Cell, 15, 939-951

KIDDLE, G., PASTORI, G.M., BERNARD, S., PIGNOCCHI, C., ANTONIW, J.F., VERRIER, P.J. & FOYER, C.H. (2003) Effects of leaf ascorbate content on defense and photosynthetic gene expression in Arabidopsis thaliana. Antioxidants & Redox Signalling 5, 23-32

ZHENG, H.-Y., CHEN, J., ZHAO, M.-F., LIN, L., CHEN, J.-P., ANTONIW, J.F. & ADAMS, M.J. (2003). Occurrence and sequences of Lily mottle virus and Lily symptomless virus in plants grown from imported bulbs in Zhejiang province, China. Archives of Virology 148, 2419-2428.

ADAMS, M.J. & ANTONIW, J.F. (2004). Codon usage bias amongst plant viruses. Archives of Virology 149, 113-135

CHEN, J., ZHENG, H.-Y., LIN, L., ADAMS, M.J., ANTONIW, J.F., ZHAO, M.-F., SHANG, Y.F., & CHEN, J.-P. (2004). A virus related to Soybean mosaic virus from Pinellia ternata in China and its comparison with local soybean SMV isolates. Archives of Virology 149, 349-363

CHEN, J., ZHENG, H.-Y., ANTONIW, J.F., ADAMS, M.J., CHEN, J.-P. & LIN, L. (2004). Detection and classification of allexiviruses from garlic in China. Archives of Virology 149, 435-445

LIN, L., ZHENG, H.-Y., CHEN, J., CHEN, J.-P., ZHANG, Q.-Y., ZHAO, M.-F., ANTONIW, J.F. & ADAMS, M.J. (2004). A new potyvirus from tuberose (Polianthes tuberosa) in China. Archives of Virology 149, 1469-1480

ADAMS, M.J., ANTONIW, J.F., BAR-JOSEPH, M., BRUNT, A.A., CANDRESSE, T., FOSTER, G.D., MARTELLI, G.P., MILNE, R.G., ZAVRIEV, S.K. & FAUQUET, C.M. (2004). The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Archives of Virology 149, 1045-1060

ADAMS , M.J., ANTONIW, J.F., & FAUQUET, C.M. (2005). Molecular criteria for genus and species discrimination within the family Potyviridae. Archives of Virology 150, 459-479

KEON, J., ANTONIW, J.F., RUDD, J., SKINNER, W., HARGREAVES, J. & HAMMOND-KOSACK, K.E. (2005). Analysis of expressed sequence tags from the wheat leaf blotch pathogen Mycosphaerella graminicola (anamorph Septoria tritici). Fungal Genetics and Biology, IN PRESS

ADAMS, M.J., ANTONIW, J.F. & BEAUDOIN, F. (2005). Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Molecular Plant Pathology, IN PRESS

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Software

ADAMS, M.J., ANTONIW, J.F., BARKER, H., JONES, A.T., MURANT, A.F., & ROBINSON, D. (1998) Software: "Descriptions of Plant Viruses on CD-ROM". Wellesbourne, Warwick, UK: Association of Applied Biologists.

ANTONIW, J.F., CASTELLS-BROOKE, N., DANN, L., MOORE, B., MULLINS, J.G.L. & VERRIER, P.(1999) Software: "Molecular Biology Notebook". Wellesbourne, Warwick, UK: Association of Applied Biologists.

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Book Chapters/Reviews

ANTONIW, J.F. (2002) Alphacryptovirus. Chapter in book: "The Springer Index of Viruses". C.A. Tidona & G. Darai (Editors) Springer-Verlag Heidelberg, ISBN 3-540-67167-6.

ADAMS, M.J. & ANTONIW, J.F. (2005). Membrane proteins in plant viruses. In: Viral membrane proteins: structure, function, drug design. Ed. W. Fisher. Kluwer

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Conference/Workshop Presentations

MULLINS, J.G.L., KNIGHT, G.L., SARAKINOU, K.S. & ANTONIW, J.F. (2000) Conservation of functional site structure across different membrane transport protein families. Biochemical Society Transactions vol 28, part 1, page A40, no. 65.

KNIGHT, G.L., ANTONIW, J.F., SARAKINOU, K.S. & MULLINS, J.G.L. (2000) The Ileal active bile acid transport protein works bi-directionally: evidence that it is structurally evolved for two distinct functions. Biochemical Society Transactions vol 28, part 1, page A42, no. 87.

EVANS, N., ANTONIW, J., FITT, B. D. L., GLADDERS & P., WELHAM, S. J. (2000) Introducing an interactive Internet based forecasting system for light leaf spot of winter oilseed rape in the UK. GCIRC Bulletin 17, 48-52.

ADAMS, M.J. & ANTONIW, J.F. (2001) Descriptions of Plant Viruses ISPP Instructional Technology Symposium (On line symposium, May 15 - June 30, 2001) http://ispp-itsymposium.org.nz

EVANS, N., FITT, B., ANTONIW, J. & WELHAM, S.(2001) Forecasting light leaf spot of winter oilseed rape on the internet. ISPP Instructional Technology Symposium (On line symposium, May 15 - June 30, 2001) http://ispp-itsymposium.org.nz

EVANS, N., STEED, J., WELHAM, S., ANTONIW, J. & FITT, B. (2001) Interactive forecasting of light leaf spot (Pyrenopeziza brassicae) risk of winter oilseed rape on the internet. IOBC Bulletin, 2001

SARAKINOU, K.S., ANTONIW, J.F., TOGAWA, R.C. & MULLINS, J.G.L. (2001) TMAlpha: a software tool for analysis of transmembrane region alpha helices. Biochemical Society Transactions, 10-12 April 2001

EVANS, N., STEED, J.M., WELHAM, S.J., ANTONIW, J.F., TURNER, J.A., GLADDERS, P. & FITT, B.D.L. (2001) Interactive forecasting on the internet of light leaf spot (Pyrenopeziza brassicae) risk of winter oilseed rape. IOBC WPRS Bulletin, 2001

SARAKINOU, K.S., ANTONIW, J.F. & MULLINS, J.G.L. (2002) Measuring transmembrane region helix tilts in membrane proteins Abstract of International Conference on Bioinformatics (InCoB2002) talk, Bangkok, Thailand, 6-8 February 2002

ADAMS, M.J. & ANTONIW, J.F. (2002) A database and web site for plant virus sequence analysis. Abstract 5 pages. 5th Symposium of the International Working Group on Plant Viruses with Fungal Vectors (IWGPVFV), Zurich, Switzerland. 22-25th July 2002.

ADAMS, M.J. & ANTONIW, J.F. (2002) A database and interactive web site for sequences of plant viruses. Abstract V-513 p. 176 XIIth International Congress of Virology, Paris, France. 27th July - 1st August 2002

EVANS, N., STEED, J.M., WELHAM, S.J., ANTONIW, J.F., TURNER, J.A., GLADDERS, P. & FITT, B.D.L. (2002) Interactive forecasting on the internet of light leaf spot (Pyrenopeziza brassicae) risk for winter oilseed rape. Integrated Control in Oilseed Crops. IOBC/wprs Bulletin, 25(2), 103-107

ADAMS, M.J. & ANTONIW, J.F. (2003). A database and web site for plant virus sequence analysis. In: Proceedings of the Fifth Symposium of the International Working Group on Plant Viruses with Fungal Vectors, Eds. C. M. Rush & U. Merz, pp. 25-28. Denver: American Society of Sugar Beet Technologists.

COULSON, R., URBAN, M., ANTONIW, J. & HAMMOND-KOSACK, K. (2005). The transcription-associated proteins of Fusarium graminearum identified by TAP-TRIBE and PFAM analyses. Asilomar Fungal Genetics Conference, poster abstract.

LASS0-CABRERA, G., ANTONIW, J. & MULLINS, J. (2005). Pattern Recognition of Interhelical Associations in Membrane Proteins. FEBS IUBMB Conference in Budapest, July 2005, poster abstract.

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Work in progress

KEON, J., RUDD, J., ANTONIW, J.F., SKINNER, W., HARGREAVES, J. & HAMMOND-KOSACK, K.E. (2005). Global transcription profiling of a fungal pathogen during interaction with its host plant provide insights into nutrition and mechanisms of infection. SUBMITTED

Publications

Reference Type: Journal Article

2006

• Zhou, J. J. , Kan, Y. C. , Antoniw, J. , Pickett, J. A. and Field, L. M. (2006) "Genome and Est Analyses and Expression of a Gene Family with Putative Functions in Insect Chemoreception", Chemical Senses, 31, 453-465
  See Paper
• Evans, N. , Welham, S. J. , Antoniw, J. and Fitt, B. D. L. (2006) "Development and Uptake of a Scheme for Predicting Risk of Severe Light Leaf Spot on Oilseed Rape", Outlooks on Pest Management, 243-245
  See Paper

2005

• Pavet, V. , Olmos, E. , Kiddle, G. , Mowla, S. , Kumar, S. , Antoniw, J. , Alvarez, M. E. and Foyer, C. H. (2005) "Ascorbic Acid Deficiency Activates Cell Death and Disease Resistance Responses in Arabidopsis Thaliana", Plant Physiology, accepted
  See Paper
• Keon, J. , Rudd, J. , Antoniw, J. F. , Skinner, W. , Hargreaves, J. and Hammond-Kosack, K. E. (2005) "Metabolic Stress Adaptation by Mycosphaerella Graminicola During Sporulation in Its Host Revealed through Microarray Transcription", Molecular Plant Pathology, 6,, 527-540
  See Paper
• Keon, J. , Antoniw, J. F. , Rudd, J. , Skinner, W. , Hargreaves, J. and Hammond-Kosack, K. E. (2005) "Analysis of Expressed Sequence Tags from the Wheat Leaf Blotch Pathogen Mycosphaerella Graminicola Anamorph Septoria Tritici)", Fungal Genetics and Biology, 42, 376-389
  See Paper
• Antoniw, J. F. and Beaudoin, F. (2005) "Polyprotein Cleavage Sites in the Plant Virus Family Potyviridae", Molecular Plant Pathology, 6, 471-487
  See Paper
• Adams, M. J. , Antoniw, J. F. and Fauquet, C. M. (2005) "Molecular Criteria for Genus and Species Discrimination within the Family Potyviridae", Archives of Virology, 159, 459-479
  See Paper
• Adams, M. J. and Antoniw, J. F. (2005) "Dpvweb: A Comprehensive Database of Plant and Fungal Virus Genes and Genomes - under Review", Nucleic Acids Research, D382-D385

2003

• Pastori, G. M. , Kiddle, G. , Antoniw, J. F. , Bernard, S. M. , Veljovic-Jovanovic, S. , J., V. P. , Noctor, G. and Foyer, C. H. (2003) "Leaf Vitamin C Contents Modulate Plant Defense Transcripts and Regulate Genes That Control Development through Hormone Signaling.", Plant Cell , 15 , 939-951
  See Paper
• Kiddle, G. , Pastori, G. M. , Bernard, S. M. , Pignocchi, C. , Antoniw, J. F. , J., V. P. and Foyer, C. H. (2003) "Effects of Leaf Ascorbate Content on Defense and Photosynthesis Gene Expression in Arabidopsis Thaliana. ", Antioxidants and Redox Signaling , 5 , 23-32
• Kiddle, G. , Pastori, G. M. , Antoniw, J. , Bernard, S. , Veljovic-Jovanovic, S. , J., V. P. , Noctor, G. and Foyer, C. H. (2003) "Vitamin C Contents Modulate Genes Involved in Plant Defense and Development. ", Comparative Biochemistry and Physiology Part A , 134 , S131

2002

• Foyer, C. H. , Pastori, G. M. , Kiddle, G. , Antoniw, J. , Bernard, S. , Veljovic-Jovanovic, S. , Noctor, G. and J., V. P. (2002) "Vitamin C Contents Modulate Defence and Plant Development Via Transcriptional Regulation.", Free Radical Biology and Medicine, 33, S170
• Foyer, C. H. , Kiddle, G. , Pastori, G. M. , Antoniw, J. F. , Bernard, S. , Veljovic-Jovanovic, S. , J., V. P. and Noctor, G. (2002) "Vitamin C Contents Modulate Defense Processes and Plant Development.", In Abstracts 13th Congress of the Federation of European Societies of Plant Physiology, Heraklion, 1-6 September 2002, 196

1999

• Souter, S. D. , Castells-Brooke, N. I. D. , Antoniw, J. F. , Welham, S. J. , Fitt, B. D. L. , Evans, N. , Gladders, P. , Turner, J. A. and Sutherland, K. (1999) "Forecasting Light Leaf Spot (Pyrenopeziza Brassicae ) of Winter Oilseed Rape (Brassica Napus ) on the Internet.", In Information Technology for Crop Protection. Aspects of Applied Biology, 55 , 37-42
• Castells-Brooke, N. , Mullins, R. , Antoniw, J. and Verrier, P. (1999) "The Molecular Biology Notebook on Cd-Rom, a Step toward the Virtual Laboratory", Journal of Biological Education, 33, 223-225

Reference Type: Conference Proceedings

2005

• Adams, M. J. and Antoniw, J. F. (2005) "Membrane Proteins in Plant Viruses", Viral membrane proteins: structure, function, drug design.

2003

• Kiddle, G. , Pastori, G. M. , Antoniw, J. F. , Bernard, S., Veljovic-Jovanovic, S. , J., V. P. , Noctor, G. and Foyer, C. H. (2003) "Vitamin C Contents Modulate Genes Involved in Plant Defense and Development.", In Abstracts Keystone Meeting on Plant Biology: Functions and Control of Cell Death
• Foyer, C. H. , Kiddle, G. , Antoniw, J. F. , Bernard, S. M. , J., V. P. , Pastori, G. M. and Noctor, G. (2003) "The Role of Antioxidant-Mediated Signal Transduction During Stress. ", In Abstracts Keystone Meeting on Plant Biology: Functions and Control of Cell Death, Snowbird, Utah, 10-15 April 2003

Reference Type: Computer Program

1999

• Antoniw, J. , Castells-Brooke, N. , Dann, L. , Moore, B. , Mullins, J. G. L. and Verrier, P. (1999) "Molecular Biology Notebook - Simulation Software and Interactive Encyclopaedia"

List of Publications while at Rothamsted

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