NASC: Director.

Dr Sean May

BSc (Sussex), D.Phil (Sussex)

voice : 0115 9513306
Fax : 0115 9513297

sean@arabidopsis.info

Teaching

On-line teaching resources, including undergraduate student projects with NASC.

Research and Interests

Arabidopsis genomics

Genome research using model systems has been adopted by plant and animal biologists to rapidly define genome architecture, gene function and as an aid to the discovery of fundamental biology. Arabidopsis thaliana has become one of the most favoured model systems for the study of many aspects of plant metabolism, development and disease resistance.

Arabidopsis is a typical flowering plant but has special characteristics that recommend it as an ideal model for research. These include its small size, small genome size, prolific seed production and the diverse array of available mutations. The entire sequence of the genome for the Columbia ecotype of Arabidopsis was completed in December 2000. A second ecotype (Landsberg) was shotgun sequenced commercially and has provided a valuable comparison reference. Recently, several more ecotypes have been Solexa sequenced and can be visualised as SNPs in our AtEnsembl browser.

The principle behind using Arabidopsis is that information obtained from this model species can be applied to other flowering plants, including crops ( See the plenary lecture by Richard Flavell at PAG XI). Hence important problems faced by industry and agriculture can be addressed through the adaptation of the knowledge base generated through Arabidopsis research.

Tackling genome research requires a scientific infrastructure to coordinate research and to centralise the provision of biological and information resources. NASC is involved in the provision of biological resources as the primary European Arabidopsis Seed Centre, and in the provision of information relating to our stocks and Arabidopsis genome information in general. NASC operates in parallel with the Arabidopsis Biological Resource Center (ABRC) at Ohio State, providing a safe repository for over half a million accessions and distributing this material to the scientific community. For details of the stocks we distribute, take a look at our NASC www server http://arabidopsis.info. NASC currently distributes around 70,000 tubes of seed per year.

NASC is also involved in the development of genomic information resources to support other elements of the on-going Arabidopsis research project.

  • We originally developed the Arabidopsis Genome Resource (AGR) as part of UKcrop.net . The focus of the database was to integrate Arabidopsis Genome Initiative (AGI) sequence data with the physical and genetic maps of Arabidopsis to provide the necessary components for the study of gene function and the identification of crop plant orthologues of Arabidopsis genes. This database is now only archival and is not actively developed.
  • Our current browser atensembl.arabidopsis.info has replaced AGR inside ukcrop.net and integrates a very wide range of Arabidopsis data in the context of the genome as well as data from brassica and other plant species.
Our primary purpose with NASC's input to the ukcrop.net databases is to focus on comparative genomics between Arabidopsis and crop plant species. The UK Crop Plant Bioinformatics Network ( UKcrop.net ), was established as part of the BBSRC Plant and Animal Genome Analysis initiative. This project comprised 6 groups who established databases originally using the ACEDB software for Arabidopsis, Barley, Brassicas, Forage grass and Millet. For full details of the individual projects and our collaborators, take a look at the UK CropNet server.

Post-Genomics - GARNet

Garnet.arabidopsis.info is the public-funded functional genomics programme for Arabidopsis in the UK. The consortium includes a public array service with the original intention to differentially probe the entire Arabidopsis transcriptome by 2003. During the project, we have significantly changed our direction in order to pursue this goal in a more efficient and effective manner by:
  • becoming a part of CATMA. This allowed us to generate a Complete Arabidopsis Transcriptome MicroArray service and the amplicons are available through our catalogue. The CATMA amplicons have now been cloned into Gateway vectors for use in RNA-I knockdown experiments as a broad set of clones and seed stocks that are now available to the community.
  • We also have an affymetrix facility which provided over 3,000 chip sets of data in the first three years of the service. Array data has been cross-linked into our arabidopsis.info [germplasm catalogue], atensembl.arabidopsis.info [genome browser] and the GARNet proteomics [proteomics.arabidopsis.info] and transcriptomics [affy.arabidopsis.info] output. NASC policy determines that emergent affy data is made public within one year after the experiment takes place.

Systems Biology

From 2006 I have been Director for Outreach within the Centre for Plant Integrative Biology (CPIB). This is a UK centre based in Nottingham regarding the development of systems biology for plants based on work centred around the Arabidopsis root.

Grants Held

NASC grant details. * = solely NASC
+ = shared with other groups.

  1. * BBSRC: 2007 - 2012 Nottingham Arabidopsis Stock Centre (core germplasm grant) £1.46 Million
  2. * BBSRC (BBE01772X1): 2007 - 2010 GARNet III (core bioinformatics grant) £791,918
  3. + BBSRC (BBD0196131): 2006 - 2011 Centre for Plant Integrative Biology (CPIB) £9,177,261
  4. * BBSRC (BBSB1356X): 2004 - 2009 UKcropnetIII £257,205
  5. * Horseracing Betting Levy Board (link to a review of the award): 2008 - 2009
  • + EU: 2006 - 2011 Agron-omics. 12.5 Million Euro- Theoretically we are part of this and were awarded the grant, but the executive committee has excluded us from salary claims due to a change in direction from data storage/curation to data analysis. Our budget has been reallocated through WIllem Gruissem in Switzerland.

    Recently finished

    • * BBSRC: 2002 - 2007, Nottingham Arabidopsis Stock Centre; provision of Arabidopsis thaliana genetic resources to the research community. £798 928
    • BBSRC 2003-2006, The GARNet Transcriptomics and bioinformatics service (continuation grant II). NASC award £392,064.
    • BBSRC: 1999 - 2004 UKCropNet99.  – A bioinformatics consortium including the John Innes Centre (Norwich); IGER (Aberystwyth) and the SCRI (Dundee). NASC award £831 352  (approximately 5/6ths   to be re-distributed amongst our consortium).
    • BBSRC: 2000 - 2004, NASC transcriptome project (array and bioinformatics facility) – a part of GARnet (genomics Arabidopsis resource net). NASC award £1 062 556.
    • BBSRC: 2001-2004, Prediction of protein function in plant genomes using data mining. A joint grant between IGER, the University of Wales - Aberystwyth, and NASC.
    • BBSRC: 2002-2005, Computational Approaches to identifying gene regulatory systems in Arabidopsis. A joint grant between John Innes Centre, University of Norwich and NASC. NASC award £123,556
    • EU: 2002-2005, PLANET, European Plant Genome Database Network. A joint grant between NASC, MIPS (Germany), INRA (France), VIB (Belgium), INFOBIOGEN (France), John Innes Centre (UK), Plant Research International (Holland), and CNB - CSIC (Spain). NASC award € 210,975
    • BBSRC: 2001-2003, Oligo array service for the Arabidopsis community. NASC award £487,552
    • BBSRC: 1997 - 2002, Nottingham Arabidopsis Stock Centre; provision of Arabidopsis thaliana genetic resources to the research community. £725 656
    • BBSRC: 1999 - (Feb) 2001, Provision of SLAT collection to researchers. A joint grant between the University of York, NASC and the John Innes Centre. NASC award ~ £10 000.
    • Plant Sciences Research Fund - (1999-2000) Arabidopsis seed storage / longevity research project - collaboration with Wakehurst place (Kew Gardens)
    • BBSRC : 1996-1999, UK Crop Plant Bioinformatics Network, a consortia between NASC, Mike Gale (JIC, Norwich), Robbie Waugh and David Marshall (SCRI, Dundee), Helen Ougham (IGER, Aberystwyth), Martin Trick (JIC, Norwich). NASC award £103445
    • EU: 1995-1999, Arabidopsis Biotechnologial Resources, a consortium between NASC, Zoe Wilson (Uni Nott), Andy Pereira (CPRO-DLO Wageningen, Netherlands), George Pelletier (INRA, Versailles, France). NASC award ECU 206000
    • Gatsby: 1999, NASC stock database integration with external Arabidopsis datasets. NASC award £10,680 Gatsby: 1998 - 1999, Gatsby Foundation SLAT collection. NASC award  £10000
    • University of Nottingham Research Opportunity fund, 1998 - 1999 Arabidopsis seed storage / longevity research project - collaboration with Wakehurst place (Kew Gardens).

    Members of Group

    Seed Centre

    • Rebecca Roberts (Research Assistant)
    • Marcos Castellanos (Research Assistant)
    • Lubomira Kacinova (full time technician)
    • Nicola Leftley (full time technician)
    • Linda Lucas (part time technician)
    • Alan Mortimore (part time technician)
    • Mo Topham (part time Technician)

    Bioinformatics

    • Daisy Belfield (Research Assistant)
    • Graeme Gill (Research Assistant)
    • Neil Graham (Research Assistant)
    • Nick James (Research Assistant)
    • Bob Parkinson (Research Assistant)
    • Beatrice Amos (Experimental Officer)

    Molecular biology

    • Zoe Emmerson (Research technician)

    Informal enquiries are welcome to: arabidopsis@arabidopsis.info

    Publications

    2008

    M. R. Broadley, P. J. White, J. P. Hammond, N. S. Graham, H. C. Bowen, Z. F. Emmerson, R. G. Fray, P. P. M. Iannetta, J. W. McNicol and S. T. May Evidence of neutral transcriptome evolution in plants. New Phytologist (2008) Vol. 180, no. 3 (p 587-593).

    ...Reviewed in 'Editors' Choice: Neutral Plantings - Science 3 October 2008; Vol. 322. no. 5898, p. 17'

    Kamal Swarup, Eva Benková,, Ranjan Swarup, Ilda Casimiro, Benjamin Péret, Yaodong Yang, Geraint Parry, Erik Nielsen, Ive De Smet, Steffen Vanneste, Mitch P. Levesque, David Carrier, Nicholas James, Vanessa Calvo, Karin Ljung, Eric Kramer, Rebecca Roberts, Neil Graham, Sylvestre Marillonnet, Kanu Patel, Jonathan D.G. Jones, Christopher G. Taylor, Daniel P. Schachtman, Sean May, Goran Sandberg, Philip Benfey, Jiri Friml, Ian Kerr, Tom Beeckman, Laurent Laplaze & Malcolm J. Bennett. 2008. The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology 10, 946 - 954 (2008).

    Klara Hoyerova , Lucie Perry, Paul Hand , Martina Lankova , Tomas Kocabek , Sean May , Jana Kottova , Jan Paces , Richard Napier , and Eva Zazimalova. (2008) Functional characterization of PaLAX1, a putative auxin permease, in heterologous plant systems. Plant Physiology 146 (3): 1128.

    2007

    GRAHAM, BROADLEY, HAMMOND, WHITE, and MAY, 2007. Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection. BMC Genomics, 8(1), 344.

    BAKER, C., NIELSON, H.M., MINTHON, L., WRIGHT, H.T., CHAPPELL, S., OKYERE, J., MAY, S., MORGAN, K., KALSHEKER, N. and JANCIAUSKIENE, S.M., 2007. Effects of Alzheimer's peptide and a1_antichymotrypsin on astrocyte gene expression. Neurobiology of Aging, 28(1), 51-61.

    Nick James, Neil Graham, Debbie Clements, Beatrice Schildknecht, and Sean May. 2007. AtEnsEMBL - A Post-Genomic Resource Browser for Arabidopsis. in Plant Bioinformatics - Methods and Protocols (ed. Edwards, D) Humana Press. ISBN10:1-58829-653-9.

    2006

    Spaniolas S, May ST, Bennett MJ, Tucker GA. J Agric Food Chem. 2006 Oct 4;54(20):7466-7470. Authentication of Coffee by Means of PCR-RFLP Analysis and Lab-on-a-Chip Capillary Electrophoresis.

    Love, C., Logan, E., Erwin, T., Kaur, J., Lim, G.A.C., Hopkins, C., Batley, J., James, N., May, S., Spangenberg, G. and Edwards, D. 2006. Integrating and interrogating diverse Brassica data within an ensembl structured database. Acta Hort. (ISHS) 706:77-82

    Frank F Millenaar, John Okyere, Sean T May, Martijn van Zanten, Laurentius A C J Voesenek, Anton J M Peeters. BMC Bioinformatics 2006, 7:137 (15 March 2006) How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results.

    John P. Hammond, Helen C. Bowen, Philip J. White, Victoria Mills, Kevin A. Pyke, Alan J. M. Baker, Steven N. Whiting, Sean T. May and Martin R. Broadley New Phytol 2006 170(2):239-60 A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes.

    Philip Zimmermann, Beatrice Schildknecht, David Craigon, Margarita Garcia-Hernandez, Wilhelm Gruissem, Sean May, Gaurab Mukherjee, Helen Parkinson, Seung Rhee, Ulrich Wagner, Lars Hennig. Plant Methods 2006, 2:1 MIAME/Plant adding value to plant microarrray experiments.

    2005

    Crystal Baker, Henrietta M. Nielsen, Lennart Minthon, H.T. Wright, Sally Chappell, John Okyere, Sean May, Kevin Morgan, Noor Kalsheker and Sabina M. Janciauskiene. Neurobiol Aging. 2005 Dec 16. Effects of Alzheimer's peptide and alpha1-antichymotrypsin on astrocyte gene expression.

    John P Hammond, Martin R Broadley, David J Craigon, Janet Higgins, Zoe Emmerson, Henrik Townsend, Philip J White, Sean T May. Plant Methods 2005, 1:10. Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species.

    Joke Allemeersch, Steffen Durinck, Rudy Vanderhaeghen, Philippe Alard, Ruth Maes, Kurt Seeuws, Tom Bogaert, Kathleen Coddens, Kirsten Deschouwer, Paul Van Hummelen, Marnik Vuylsteke, Yves Moreau, Jeroen Kwekkeboom, Andre H.M. Wijfjes, Sean May, Jim Beynon, Pierre Hilson, and Martin T.R. Kuiper. Benchmarking the CATMA microarray. A novel tool for 'Arabidopsis' transcriptome analysis. Plant Physiology (2005), Vol. 137, pp. 588

    Sean Mayes, Kate Parsley, Roger Sylvester-Bradley, Sean May and John Foulkes. Annals of Applied Biology (2005), 146:223-237 Integrating genetic information into plant breeding programmes: how will we produce varieties from molecular variation, using bioinformatics?

    PAG XIII

    2004

    Swarup R., Kargul J., Marchant A., Zadik D., Rahman A., Mills R., Yemm A., May S., Williams L., Millner P., Tsurumib S., Moore I., Napier R., Kerr ID and Bennett MJ. Structure-Function Analysis of the Presumptive Arabidopsis Auxin Permease AUX1. The Plant Cell 16:3069-3083 (2004).

    Craigon DJ., James N., Okyere J., Higgins J., Jotham J., May S. NASCArrays: A repository for Microarray Data generated by NASC's Transcriptomics Service. Nucleic Acids Research, (2004). volume 32, Database issue D575-D577.

    Okyere, J., Sun, G-a., Craigon, D.J., Higgins, J. and May, S.T. (2004). Cross-species Hybridization and Analysis using Affymetrix GeneChip. Comparative Biochemistry and Physiology 137A (3), S191-S197.

    Janciauskiene, S., Minthon, L., Vincic, G., Sun, Y-X., Baker, C., Plummer, S., Okyere, J., May, S., Morgan, K. and Kalsheker, N. (2004) Gene expression profiles of primary human astrocytes exposed to Abeta and ACT/Abeta complexes assessed using a global DNA microarray. Neurobiology of Aging (25), Sup 2, p303-654.

    PAG XII

    2003

    Schrader J, Baba K, May ST, Palme K, Bennett M, Bhalerao RP, Sandberg G. Polar auxin transport in the wood-forming tissues of hybrid aspen is under simultaneous control of developmental and environmental signals. Proc Natl Acad Sci U S A. (2003) Aug 19;100(17):10096-101. Epub 2003 Aug 08.

    John P. Hammond, Malcolm J. Bennett, Helen C. Bowen, Martin R. Broadley, Dan C. Eastwood, Sean T. May, Clive Rahn, Ranjan Swarup, Kathryn E. Woolaway, and Philip J. White (2003). Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants. Plant Physiology, Vol. 132, pp. 1.19.

    Fiona R. Hay, Andrew Mead, Kirstine Manger and Fiona J. Wilson. (2003) One-step analysis of seed storage data and the longevity of Arabidopsis thaliana seeds. J. Exp Bot. 54: 384, pp993-1011 (NASC publication)

    May, S. (2003) NASC Affymetrix service and Data services. Comparative Biochemistry and Physiology Part A 134 (2003) S1.

    PAG XI

    2002

    Deeken R, Geiger D, Fromm J, Koroleva O, Ache P, Langenfeld-Heyser R, Sauer N, May S, Hedrich R (2002) Loss of the AKT2/3 potassium channel affects sugar loading into the phloem of Arabidopsis. Planta 216:334-344.

    Michael Beale, Paul Dupree, Kathryn Lilley, Jim Beynon, Martin Trick, Jonathan Clarke, Michael Bevan, Ian Bancroft, Jonathan Jones, Sean May et al.(2002), GARNet, the Genomic Arabidopsis Resource Network, Trends in Plant Science, Volume 7, Issue 4, 1 April 2002, Pages 145-147.

    Molecular Biotechnology (2002) 20, 209-221. Finding Your knockout. May, S.T., Clements, D., Bennett, M.J.

    D. Craigon, L. Daugherty, P. Dennis, G. Gill, C. Hall, J. Higgins, E. Humphries, J. Jotham, J. Okyere, G.-an Sun, M. Topham, L. Zhang and S. May (2002) Standards in arraying. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology Volume 132, Supplement 1 , April 2002, Pages S139-S141.

    Online: Genomics Meets Grid Meeting. Paper presented.

    2001

    Journal of Plant Growth Regulation (2001) 20, 217-225. Quick on the uptake: characterization of a family of plant auxin influx carriers. Parry,G., Marchant,A., May,S., Swarup,R., Swarup,K., James,N., Graham,N.S., Allen,T., Martucci,T., Yemm,A., Napier,R., Manning,K., King,G. and Bennett,M.J.

    J. Kincaid, K. Bradnam, K. Searle, P. Dennis, C. Hall, S. Kitchingman and S. May (NASC) DNA arrays as a tool for investigating gene function.

    Molecular Plant-Microbe Interactions. (2001) 14, 267-277. Expression studies on AUX1-like genes in Medicago truncatula suggest that auxin is required at two steps in early nodule development. De Billy, F., Grosjean, C., May, S.T., Bennett, M.J. and Cullimore, J.V.

    PAX IX

    2000

    Sean. T. May, Deborah. Clements & Malcolm. J. Bennett. (2000) Reverse Genetics: Screening plant populations for gene knockouts. In. Plant Hormone Protocols - Methods in Molecular Biology (eds. Gregory A. Tucker & Jeremy A. Roberts) Humana Press.

    BBC interview article (Dec 2000). Wild Weedy and Famous: http://news.bbc.co.uk/1/hi/sci/tech/1070301.stm

    Scholl RL, May ST, Ware DH. (2000) Seed and molecular resources for Arabidopsis. Plant Physiol. 124(4):1477-80

    Bradnam K, May S. (2000) Website update: The UK Crop Plant Bioinformatics Network (UK CropNet). Yeast. 17(4):335-8.

    Jo Dicks, Mary Anderson, Linda Cardle, Sam Cartinhour, Matthew Couchman, Guy Davenport, Jeremy Dickson, Mike Gale, David Marshall, Sean May, Hamish McWilliam, Andrew O Malia, Helen Ougham, Martin Trick, Sean Walsh, and Robbie Waugh. (2000) UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics Nucleic Acids Res. 28: 104-107.

    pre-2000

    EMBO J 1999 Apr 15;18(8):2066-2073. AUX1 regulates root gravitropism in Arabidopsis by facilitating auxin uptake within root apical tissues: A. Marchant,J. Kargul, S.T. May, P. Muller, A. Delbarre, C. Perrot-Rechenmann, M.J. Bennett.

    May S. (1999) Carrot brains NEW SCI 164 (2208): U1-U1 OCT 16

    Plant J. 1998 Sep;15(6):843-51. Cell marking in A. thaliana and its application to patch-clamp studies: 15(6), 843-851. May S.T*., Maathuis F.J.M*., Graham N.S., Bowen H.C., Jellito T.C., Trimmer P., Bennett M.J., Sanders D., White P.J. *joint first authorship.

    Philos Trans R Soc Lond B Biol Sci. (1998) Sep 29;353(1374):1511-5. Going the distance with auxin: unravelling the molecular basis of auxin transport. Bennett MJ, Marchant A, May ST, Swarup R.

    Laboratory News (1998) Latin studies of plant architecture. Sean May.

    Science 1996 Aug 16;273(5277):948-50. Arabidopsis AUX1 gene: a permease-like regulator of root gravitropism. Bennett MJ, Marchant A, Green HG, May ST, Ward SP, Millner PA, Walker AR, Schulz B, Feldmann KA

    Peptides. (1995) 16(1):95-104. Cellular colocalization of diuretic peptides in locusts: a potent control mechanism. Thompson KS, Rayne RC, Gibbon CR, May ST, Patel M, Coast GM, Bacon JP.

    Online: Protocol**. Drosophila brain dissection (one of the first web publications in science - Dec 21st 1993).
    Diagram

    Online: Protocol**. Drosophila wholemount dissection (one of the first web publications in science - Dec 21st 1993).
    Photomicrograph

    **Summarised in May.S.T. and O'Kane. C.-.Neurogenetics (1993) 8 (4); 237-238

    J Comp Physiol [A]. (1991) May;168(5):605-17 The vasopressin-like immunoreactive (VPLI) neurons of the locust, Locusta migratoria. I. Anatomy. . Thompson KS, Tyrer NM, May ST, Bacon JP.

    Patents:

    • Method of using transactivation proteins to control gene expression in transgenic plants - Bennett, May & Ramsay - GB patent 9502456.8 ; US patents: US6127606; US5801027. [link]
    • Plant gene (encompassing all Aux-1 family sequences within higher plants) - Bennett, May & Marchant - GB patent 9523153.6
    • Cross-species Microarrays - WO2005093630

    Public media appearances (live, newspaper & radio)

    Currently being constructed retrospectively

    NASC publications prior to 1999

    Arabidopsis. Annual Plant Reviews, Vol 1 (1998) eds Mary Anderson and Jeremy A. Roberts Sheffield Academic Press pp.407

    Walsh, S., Anderson, M.L. and Cartinhour, S.W (1998) ACEDB a database for genome information. In Bioinformatics: A practical guide to the analysis of genes and proteins. (eds. F. Ouelette and A. Baxevanis) John Wiley & Sons, Inc., New York pp. 299-318

    Anderson, M. and Cartinhour, S. (1997) Internet resources for the biologist. In Biotechnology and Plant Genetic Resources eds J.A. Callow, B.V. Ford Lloyd and H.J. Newbury. p281-300 CABI International.

    Anderson, M. (1997) Control of pests and diseases in Arabidopsis In Arabidopsis Protocols eds J. M. Martinez-Zapater and J. Salinas p19-26 Humana Press.

    Mulligan, B and Anderson, M. (1995) Arabidopsis thaliana: a versatile plant for teaching and research projects in genetics and plant biology. Journal of Biological Education 29, 259-269.

    Web sites of interest

    Personal

    Member of the Arabidopsis Biological Resource Center (ABRC) advisory committee
    Member of the UK Plant Genetic Resources Group.
    MASC committee member (Multinational Arabidopsis Steering Committee).

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