Medicine

Ian Clarke

BSc, PhD

Primary position:
Professor of Molecular Microbiology/Virology

Background

The University of Southampton

Professor Clarke was appointed to the Chair of Molecular Microbiology/Virology in 1998. He graduated in Microbiology from the University of Leeds in 1979 and completed his PhD in Molecular Virology at the University of Warwick in 1982 studying genomic variation in rotaviruses. He worked as a research scientist in the food industry (Cadbury Schweppes plc) before appointment to a ‘new blood lectureship’ at the University of Southampton. Subsequently he has held various positions at Southampton including Director of Division and is currently head of the Molecular Microbiology group.

Professor Clarke leads a research team that is interested in host-pathogen interactions with special emphasis on intracellular pathogens and diseases for which there are currently no effective vaccines. He has particular interests in Chlamydia and norovirus research. The Chlamydia research group is focused on genomics, basic chlamydial molecular biology, chlamydial epidemiology and the development of point of care testing. Professor Clarke has retained interests in human noroviruses with a long term aim of developing a vaccine. The Southampton virus was the first norovirus to be characterised at the molecular level (published in Science). His research group is based within the Faculty of Medicine and comprises both clinical and non-clinical scientists with postgraduate students. Potential students, postdoctoral scientists or clinician scientists who are interested in joining his group are encouraged to contact Professor Clarke.

 

Qualifications

BSc, Microbiology University of Leeds (1979)
PhD, University of Warwick (1982) "Genomic variation rotaviruses"

Appointments held

2013 - present Director, sub-Division, Infection and Immunity

1999- 2013 Head, Molecular Microbiology Group

2004– 09 Director, sub-Division of Tissue, Infection and Repair

2001– 04 Director, Molecular Microbiology and Infection

1998- 01 Director, Division of Cell and Molecular Medicine

Professor Ian Clarke's photo

Publications

The University of Southampton's electronic library (e-prints)

Article

Ramsey, K.H., Schripsema, J.H., Smith, B.J., Wang, Y., Jham, B.C., O'Hagan, K.P., Thomson, N.R., Murthy, A.K., Skilton, R.J., Chu, P. and Clarke, I.N. (2014) Plasmid coding sequence-five influences infectivity and virulence in a mouse model of Chlamydia trachomatis urogenital infection. Infection and Immunity, 1-33. (doi:10.1128/IAI.01795-14). (PMID:24866804).
Wang, Yibing, Cutcliffe, Lesley T., Skilton, Rachel J., Ramsey, Kyle H., Thomson, Nicholas R. and Clarke, Ian N. (2014) The genetic basis of plasmid tropism between Chlamydia trachomatis and Chlamydia muridarum. Pathogens and Disease, 1-5. (doi:10.1111/2049-632X.12175). (PMID:24700815).
Herod, Morgan R., Salim, Omar, Skilton, Rachel J., Prince, Cynthia A., Ward, Vernon K., Lambden, Paul R. and Clarke, Ian N. (2014) Expression of the murine norovirus (MNV) ORF1 polyprotein is sufficient to induce apoptosis in a virus-free cell model. PLoS ONE, 9, (3), e90679. (doi:10.1371/journal.pone.0090679). (PMID:15562321).
Seth-Smith, Helena M.B., Harris, Simon R., Scott, Paul, Parmar, Surendra, Marsh, Peter, Unemo, Magnus, Clarke, Ian N., Parkhill, Julian and Thomson, Nicholas R. (2013) Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA. Nature Protocols, 8, (12), 2404-2412. (doi:10.1038/nprot.2013.147 ). (PMID:24202554).
Sigar, Ira M., Schripsema, Justin H., Wang, Yibing, Clarke, Ian N., Cutcliffe, Lesley T., Seth-Smith, Helena M.B., Thomson, Nicholas R., Bjartling, Carina, Unemo, Magnus, Persson, Kenneth and Ramsey, Kyle H. (2013) Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model. Pathogens and Disease (doi:10.1111/2049-632X.12086). (PMID:24022847).
O'Neill, C.E., Seth-Smith, H.M.B., Van Der Pol, B., Harris, S.R., Thomson, N.R., Cutcliffe, L.T. and Clarke, I.N. (2013) Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes. Microbiology , 159, (4), 748-756. (doi:10.1099/mic.0.065391-0 ). (PMID:23378575).
Seth-Smith, Helena M.B., Harris, Simon R., Skilton, Rachel J., Radebe, Frans M., Golparian, Daniel, Shipitsyna, Elena, Duy, Pham Thanh, Scott, Paul, Cutcliffe, Lesley T., O'Neill, Colette, Parmar, Surendra, Pitt, Rachel, Baker, Stephen, Ison, Catherine A., Marsh, Peter, Jalal, Hamid, Lewis, David A., Unemo, Magnus, Clarke, Ian N., Parkhill, Julian and Thomson, Nicholas R. (2013) Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture. Genome Research (doi:10.1101/gr.150037.112). (PMID:23525359).
Wang, Yibing, Cutcliffe, Lesley T., Skilton, Rachel J., Persson, Kenneth, Bjartling, Carina and Clarke, Ian N. (2013) Transformation of a plasmid-free, genital tract isolate of Chlamydia trachomatis with a plasmid vector carrying a deletion in CDS6 revealed that this gene regulates inclusion phenotype. Pathogens and Disease, 67, (2), 100-103. (doi:10.1111/2049-632X.12024).
Wang, Yibing, Kahane, Simona, Cutcliffe, Lesley T., Skilton, Rachel J., Lambden, Paul R., Persson, Kenneth, Bjartling, Carina and Clarke, Ian N. (2013) Genetic Transformation of a Clinical (Genital Tract), Plasmid-Free Isolate of Chlamydia trachomatis: Engineering the Plasmid as a Cloning Vector. PLoS One, 8, (3), e59195. (doi:10.1371/journal.pone.0059195). (PMID:23527131).
Labiran, C., Clarke, Ian N., Cutcliffe, Lesley T., Wang, Yibing, Skilton, Rachel J., Persson, Kenneth, Bjartling, Carina, Herrmann, Björn, Christerson, Linus and Marsh, Peter (2012) Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis. Frontiers in Cellular and Infection Microbiology, 2, (68) (doi:10.3389/fcimb.2012.00068).
Harris, Simon R., Clarke, I., Seth-Smith, Helena M.B., Solomon, Anthony W., Cutcliffe, Lesley T., Marsh, Peter, Skilton, Rachel J., Holland, Martin J., Mabey, David., Peeling, Rosanna W., Lewis, David A., Spratt, Brian G., Unemo, Magnus, Persson, Kenneth, Bjartling, Carina, Brunham, Robert, de Vries, Henry J.C., Morré, Servaas A., Speksnijder, Arjen, Bébéar, Cécile M., Clerc, Maïté, de Barbeyrac, Bertille, Parkhill, Julian and Thomson, Nicholas R. (2012) Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nature Genetics, 44, (4), 413-419. (doi:10.1038/ng.2214). (PMID:22406642).
Baker, Estelle S., Luckner, Sylvia R., Krause, Kurt L., Lambden, Paul R., Clarke, Ian N. and Ward, Vernon K. (2012) Inherent structural disorder and dimerisation of murine norovirus NS1-2 protein. PLoS ONE, 7, (2), e30534-[13pp]. (doi:10.1371/journal.pone.0030534). (PMID:22347381).
Otto, Peter H., Clarke, Ian N., Lambden, Paul R., Salim, Omar, Reetz, Jochen and Liebler-Tenorio, Elisabeth M. (2011) Infection of calves with bovine norovirus Glll.1 strain jena virus: an experimental model to study the pathogenesis of norovirus infection. Journal of Virology, 85, (22), 12013-12021. (doi:10.1128/JVI.05342-11). (PMID:21880760).
Wang, Yibing, Kahane, Simona, Cutcliffe, Lesley T, Skilton, Rachel J, Lambden, Paul R and Clarke, Ian N (2011) Development of a transformation system for chlamydia trachomatis: restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector. PLoS Pathogens, 7, (9), e1002258. (doi:10.1371/journal.ppat.1002258). (PMID:21966270).
Reed, David L., Currier, Russell W., Walton, Shelley F., Conrad, Melissa, Sullivan, Steven A., Carlton, Jane M., Read, Timothy D., Severini, Alberto, Tyler, Shaun, Eberle, R., Johnson, Welkin E., Silvestri, Guido, Clarke, Ian N., Lagergård, Teresa, Lukehart, Sheila A., Unemo, Magnus, Shafer, William M., Beasley, R. Palmer, Bergström, Tomas, Norberg, Peter, Davison, Andrew J., Sharp, Paul M., Hahn, Beatrice H and Blomberg, Jonas (2011) The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms. Annals of the New York Academy of Sciences, 1230, 74-107. (doi:10.1111/j.1749-6632.2011.06133.x). (PMID:21824167).
Turner, Katy, Clarke, Ian, Timpson, Nicholas and Horner, Patrick (2011) Chlamydia trachomatis in the age of the genome: application of molecular genotyping to improve our understanding of the immunopathogenesis of Chlamydia genital tract disease. Sexually Transmitted Diseases, 38, (6), 495-498. (doi:10.1097/OLQ.0b013e3182185744). (PMID:22256335).
Seth-Smith, H M B, Harris, S R, Rance, R, West, A , Severin, J, Ossewaarde, J, Cutcliffe, L.T., Skilton, R.J., Marsh, P., Parkhill, J, Clarke, Ian N. and Thomson, N (2011) Genome sequence of the zoonotic pathogen Chlamydophila psittaci. Journal of Bacteriology, 193, (5), 1282-1283. (doi:10.1128/JB.01435-10). (PMID:21183672).
Unemo, Magnusa and Clarke, Ian N. (2011) The Swedish new variant of Chlamydia trachomatis. Current Opinion in Infectious Diseases, 24, (1), 62-69. (doi:10.1097/QCO.0b013e32834204d5). (PMID:21157332).
Wang, Yibing, Skilton, Rachel J., Cutcliffe, Lesley T., Andrews, Emma, Clarke, Ian N. and Marsh, Pete (2011) Evaluation of a high resolution genotyping method for Chlamydia trachomatis using routine clinical samples. PLoS ONE, 6, (2), e16971. (doi:10.1371/journal.pone.0016971). (PMID:21347295).
Hussey, Robert J., Coates, Leighton, Gill, Raj S., Erskine, Peter T., Coker, Shu-Fen, Mitchell, Ed, Cooper, Jonathan B., Wood, Steve, Broadbridge, Robert, Clarke, Ian N., Lambden, Paul R. and Shoolingin-Jordan, Peter M. (2010) A structural study of norovirus 3C protease specificity: Binding of a designed active site-directed peptide inhibitor. Biochemistry, 50, (2), 240-249. (doi:10.1021/bi1008497). (PMID:21128685).
Hussey, R.J., Coates, L., Gill, R.S., Wright, J. Neville, Sarwar, M., Coker, S., Erskine, P.T., Cooper, J.B., Wood, S.P., Clarke, I.N., Lambden, P.R., Broadbridge, R. and Shoolingin-Jordan, P.M. (2010) Crystallization and preliminary X-ray diffraction analysis of the protease from Southampton norovirus complexed with a Michael acceptor inhibitor. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications, 66, (11), 1544-1548. (doi:10.1107/S1744309110039059). (PMID:21045318).
Unemo, Magnus, Seth-Smith, Helena M.B., Cutcliffe, Lesley T., Skilton, Rachel J., Barlow, David, Goulding, David, Persson, Kenneth, Harris, Simon, Kelly, Anne, Bjartling, Carina, Fredlund, Hans, Olcén, Per, Thomson, N icholas R. and Clarke, Ian N. (2010) The Swedish new variant of chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization. Microbiology, 156, (5), 1394-404. (doi:10.1099/mic.0.036830-0 ). (PMID:20093289).
Thomson, Nicholas R. and Clarke, Ian N. (2010) Chlamydia trachomatis: small genome, big challenges. Future Microbiology, 5, (4), 555-561. (doi:10.2217/fmb.10.31). (PMID:20353297).
Skilton, Rachel J., Cutcliffe, Lesley T., Barlow, David, Wang, Yibing, Salim, Omar, Lambden, Paul R. and Clarke, Ian N. (2009) Penicillin induced persistence in Chlamydia trachomatis: high quality time lapse video analysis of the developmental cycle. PloS one, 4, (11), e7723. (doi:10.1371/journal.pone.0007723). (PMID:19542292).
Seth-Smith, Helena M.B., Harris, Simon R., Persson, Kenneth, Marsh, Pete, Barron, Andrew, Bignell, Alexandra, Bjartling, Carina, Clark, Louise, Cutcliffe, Lesley T., Lambden, Paul R., Lennard, Nicola, Lockey, Sarah J., Quail, Michael A., Salim, Omar, Skilton, Rachel J., Wang, Yibing, Holland, Martin J., Parkhill, Julian, Thomson, Nicholas R. and Clarke, I.N. (2009) Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain. BMC Genomics, 10, (239) (doi:10.1186/1471-2164-10-239). (PMID:19460133).
McCormick, Christopher J., Salim, Omar, Lambden, Paul R. and Clarke, Ian N. (2008) Translation termination reinitiation between open reading frame 1 (ORF1) and ORF2 enables capsid expression in a bovine norovirus without the need for production of viral subgenomic RNA. Journal of Virology, 82, (17), 8917-8921. (doi:10.1128/JVI.02362-07). (PMID:18579601).
Salim, Omar, Skilton, Rachel J., Lambden, Paul R., Fane, Bentley A. and Clarke, Ian N. (2008) Behind the chlamydial cloak: the replication cycle of chlamydiaphage Chp2, revealed. Virology, 377, (2), 440-445. (doi:10.1016/j.virol.2008.05.001).
Salim, Omar, Clarke, Ian N. and Lambden, Paul R. (2008) Functional analysis of the 5' genomic sequence of a bovine norovirus. PLoS ONE, 3, (5), e2169-[8pp]. (doi:10.1371/journal.pone.0002169).
Thomson, Nicholas R., Holden, Matthew T.G., Carder, Caroline, Lennard, Nicola, Lockey, Sarah J., Marsh, Pete, Skipp, Paul, O'Connor, C. David, Goodhead, Ian, Norbertzcak, Halina, Harris, Barbara, Ormond, Doug, Rance, Rrichard, Quail, Michael A., Parkhill, Julian, Stephens, Richard S. and Clarke, Ian N. (2008) Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates. Genome Research, 18, (1), 161-171. (doi:10.1101/gr.7020108). (PMID:18032721).
Pelosi, E and Clarke, I (2008) Hepatitis E: a complex and global disease. Emerging Health Threats Journal, 1 (doi:10.3134/ehtj.08.008).
Oliver, S.L., Wood, E., Asobayire, E., Wathes, D.C., Brickell, J.S., Elschner, M., Otto, P., Lambden, P.R., Clarke, I.N. and Bridger, J.C. (2007) Serotype 1 and 2 bovine noroviruses are endemic in cattle in the United kingdom and Germany. Journal of Clinical Microbiology, 45, (9), 3050-3052. (doi:10.1128/JCM.02015-06).
Skilton, R.J., Cutcliffe, L.T., Pickett, M.A., Lambden, P.R., Fane, B.A. and Clarke, I.N. (2007) Intracellular parasitism of chlamydiae: specific infectivity of chlamydiaphage Chp2 in Chlamydophila abortus. Journal of Bacteriology, 189, (13), 4957-4959. (doi:10.1128/JB.00235-07).
Ward, V.K., McCormick, C.J., Clarke, I.N., Salim, O., Wobus, C.F., Thackray, L.B., Virgin, H.W. and Lambden, P.R. (2007) Recovery of infectious murine norovirus using pol II-driven expression of full-length cDNA. Proceedings of the National Academy of Sciences of the United States of America, 104, (26), 11050-11055. (doi:10.1073/pnas.0700336104).
Lambden, Paul R., Pickett, Mark A. and Clarke, Ian N. (2006) The effect of penicillin on Chlamydia trachomatis DNA replication. Microbiology, 152, (9), 2573-2578. (doi:10.1099/mic.0.29032-0).
Oliver, S.L., Batten, C.A., Deng, Y., Elschner, M., Otto, P., Charpilienne, A., Clarke, I.N., Bridger, J.C. and Lambden, P.R. (2006) Genotype 1 and Genotype 2 Bovine Noroviruses Are Antigenically Distinct but Share a Cross-Reactive Epitope with Human Noroviruses. Journal of Clinical Microbiology, 44, (3), 992-998. (doi:10.1128/JCM.44.3.992-998.2006).
Batten, Carrie A., Clarke, Ian N., Kempster, Sarah L., Oliver, Stefan L., Bridger, Janice C. and Lambden, Paul R. (2006) Characterization of a cross-reactive linear epitope in human genogroup I and bovine genogroup III norovirus capsid proteins. Virology, 356, (1-2), 179-187. (doi:10.1016/j.virol.2006.07.034). (PMID:16934306).
Skipp, Paul, Robinson, Jo, O'Connor, C. David and Clarke, Ian N. (2005) Shotgun proteomic analysis of Chlamydia trachomatis. Proteomics, 5, (6), 1558-1573. (doi:10.1002/pmic.200401044).
Iturriza-Gómara, Miren, Clarke, Ian, Desselberger, Ulrich, Brown, David, Thomas, Daniel and Gray, Jim (2004) Seroepidemiology of group C rotavirus infection in England and Wales. European Journal of Epidemiology, 19, (6), 589-595. (doi:10.1023/B:EJEP.0000032381.36658.cb). (PMID:15330133).
Garner, Sarah A., Everson, J. Sylvia, Lambden, Paul R., Fane, Bentley A. and Clarke, Ian N. (2004) Isolation, molecular characterisation and genome sequence of a bacteriophage (Chp3) from Chlamydophila pecorum. Virus Genes, 28, (2), 207-214. (doi:10.1023/B:VIRU.0000016860.53035.f3).
Froggatt, Pippa C., Vipond, I. Barry, Ashley, Charles R., Lambden, Paul R., Clarke, Ian N. and Caul, E. Owen (2004) Surveillance of norovirus infection in a study of sporadic childhood gastroenteritis in South West England and South Wales, during one winter season (1999-2000). Journal of Medical Virology, 72, (2), 307-311. ( doi:10.1002/jmv.10569).
Vipond, I.B., Caul, E.O., Hirst, D., Carmen, B., Curry, A., Lopman, B.A., Pead, P., Pickett, M.A., Lambden, P.R. and Clarke, I.N. (2004) National epidemic of Lordsdale Norovirus in the UK. Journal Of Clinical Virology, 30, (3), 243-247. (doi:10.1016/j.jcv.2003.11.011).
Clarke, Ian N., Cutcliffe, Leslie T., Everson, J. Sylvia, Garner, Sarah A., Lambden, Paul R., Pead, Paddy J., Pickett, Mark A., Brentlinger, Karie L. and Fane, Bentley A. (2004) Chlamydiaphage Chp2, a skeleton in the φX174 closet: scaffolding protein and procapsid identification. Journal of Bacteriology, 186, (22), 7571-7574. (doi:10.1128/JB.186.22.7571-7574.2004).
Everson, J.S., Garner, S.A., Lambden, P.R., Fane, B.A. and Clarke, I.N. (2003) Host range of chlamydiaphages fCPAR39 and Chp3. Journal of Bacteriology, 185, (21), 6490-6492. (doi:10.1128/JB.185.21.6490-6492.2003).
Deng, Y., Batten, C.A., Liu, B.L., Lambden, P.R., Elschner, M., Gunther, H., Otto, P., Schnurch, P., Eichhorn, W., Herbst, W. and Clarke, I.N. (2003) Studies of epidemiology and seroprevalence of bovine noroviruses in Germany. Journal of Clinical Microbiology, 41, (6), 2300-2305. (doi:10.1128/JCM.41.6.2300-2305.2003).
Everson, J.S., Garner, S.A., Fane, B., Liu, B.L., Lambden, P.R. and Clarke, I.N. (2002) Biological properties and cell tropism of Chp2, a bacteriophage of the obligate intracellular bacterium Chlamydophila abortus. Journal of Bacteriology, 184, (10), 2748-2754. (doi:10.1128/JB.184.10.2748-2754.2002).
Robinson, Samantha, Clarke, Ian N., Vipond, I. Barry, Caul, E. Owen and Lambden, Paul R. (2002) Epidemiology of human sapporo-like caliciviruses in the South West of England: molecular characterisation of a genetically distinct isolate. Journal of Medical Virology, 67, (2), 282-288. (doi:10.1002/jmv.2219).
Chen, Zhilin, Lambden, Paul R., Lau, Jeshen, Caul, E. Owen and Clarke, Ian N. (2002) Human group C rotavirus: completion of the genome sequence and gene coding assignments of a non-cultivatable rotavirus. Virus Research, 83, (1-2), 179-187. (doi:10.1016/S0168-1702(01)00442-7).
Schachter, J., Stephens, R.S., Timms, P., Kuo, C., Bavoil, P.M., Birkelund, S., Boman, J., Caldwell, H., Campbell, L.A., Chemesky, M., Christiansen, G, Clarke, I.N., Gaydos, C., Grayston, J.T., Hackstadt, T., Hsia, R., Kaltenboeck, B., Leinonnen, M., Ojcius, D., McClarty, G., Orfila, J., Peeling, R., Puolakkainen, M., Quinn, T.C., Rank, R.G., Raulston, J., Ridgeway, G.L., Saikku, P., Stamm, W.E., Taylor-Robinson, D., Wang, S.P. and Wyrick, P.B. (2001) Radical changes to chlamydial taxonomy are not necessary just yet (letter and reply). International Journal of Systematic and Evolutionary Microbiology, 51, (1), 249-253.
Clarke, Ian N. and Lambden, Paul R. (2001) The molecular biology of human caliciviruses. Gastroenteritis Viruses. Novartis Foundation Symposium, 238, 191-196. (doi:10.1002/0470846534.ch11).
Clarke, Ian N. and Lambden, Paul R. (2000) Organization and expression of calicivirus genes. The Journal of Infectious Diseases, 181, supplement 2, S309-S316. (doi:10.1086/315575). (PMID:10804143).
Green, K.Y., Ando, T., Balayan, M.S., Berke, T, Clarke, I.N., Estes, M.K., Matson, D.O., Nakata, S., Neill, J.D., Studdert, M.J. and Thiel, H.J. (2000) Taxonomy of the caliciviruses. The Journal of Infectious Diseases, 181, supplement 2, S322-S330. (doi:10.1086/315591). (PMID:10804145).
Chadwick, P. R., Beards, G., Brown, D., Caul, E. O., Cheesbrough, J., Clarke, I. N., Curry, A., O'Brien, S., Quigley, K., Sellwood, J. and Westmoreland, D. (2000) Management of hospital outbreaks of gastro-enteritis due to small round structured viruses. Journal of Hospital Infection, 45, (1), 1-10. (PMID:10833336).
Liu, B.L., Everson, J., Fane, B., Giannikopoulou, P., Vretou, E., Lambden, P.R. and Clarke, I.N. (2000) Molecular characterization of a bacteriophage (Chp2) from chlamydia psittaci. Journal of Virology, 74, (8), 3464-3469. (PMID:8375644).
Vipond, I. Barry, Pelosi, Emmanuela, Williams, Judith, Ashley, Charles R., Lambden, Paul R., Clarke, Ian N. and Caul, E. Owen (2000) A diagnostic EIA for detection of the prevalent SRSV strain in United Kingdom outbreaks of gastroenteritis. Journal of Medical Virology, 61, (1), 132-137. (doi:10.1002/(SICI)1096-9071(200005)61:1<132::AID-JMV21>3.0.CO;2-8). (PMID:10745245).
Clarke, I.N. and Lambden, P.R. (2000) Viral gastroenteritis: the human caliciviruses. CPD Infection, 2, (1), 14-17.
James, Vivenna L.A., Lambden, Paul R., Deng, Yu, Caul, E. Owen and Clarke, Ian N. (1999) Molecular characterization of human group C rotavirus genes 6, 7 and 9. Journal of General Virology, 80, (12), 3181-3187. (PMID:10567650).
Pelosi, Emanuela, Lambden, Paul R., Caul, E. Owen, Liu, Binlei, Dingle, Kate, Deng, Yu and Clarke, Ian N. (1999) The seroepidemiology of genogroup 1 and genogroup 2 Norwalk-like viruses in Italy. Journal of Medical Virology, 58, (1), 93-99. (doi:10.1002/(SICI)1096-9071(199905)58:1<93::AID-JMV15>3.0.CO;2-P). (PMID:10223553).
Liu, B.L., Viljoen, GJ, Clarke, I.N. and Lambden, P.R. (1999) Identification of further proteolytic cleavage sites in the Southampton calicivirus polyprotein by expression of the viral protease in E. coli. Journal of General Virology, 80, (2), 291-296. (PMID:10073687).
Liu, B.L., Lambden, P.R., Günther, H., Otto, P., Elschner, M. and Clarke, I.N. (1999) Molecular characterization of a bovine enteric calicivirus: relationship to the Norwalk-like viruses. Journal of Virology, 73, (1), 819-825. (PMID:8380940).
James, V.L.A., Lambden, P.R., Caul, E.O. and Clarke, I.N. (1998) Enzyme-linked immunosorbent assay based on recombinant human group C rotavirus inner capsid protein (VP6) To detect human group C rotaviruses in fecal samples. Journal of Clinical Microbiology, 36, (11), 3178-3181. (PMID:9431910).
Thomas, N.S., Lusher, M., Storey, C. and Clarke, IN. (1997) Plasmid diversity in chlamydia. Microbiology, 143, (6), 1847-1854. (doi:10.1099/00221287-143-6-1847). (PMID:9202459).
Noel, J.S., Liu, B.L., Humphrey, C.D., Rodriguez, E.M., Lambden, P.R., Clarke, I.N., Dwyer, D.M., Ando, T., Glass, R.I. and Monroe, S.S. (1997) Parkville virus: a novel genetic variant of human calicivirus in the Sapporo virus clade, associated with an outbreak of gastroenteritis in adults. Journal of Medical Virology, 52, (2), 173-178. (doi:10.1002/(SICI)1096-9071(199706)52:2<173::AID-JMV10>3.0.CO;2-M). (PMID:9179765).
Green, Steve M., Lambden, Paul R., Caul, E. Owen and Clarke, Ian N. (1997) Capsid sequence diversity in small round structured viruses from recent UK outbreaks of gastroenteritis. Journal of Medical Virology, 52, (1), 14-19. (doi:10.1002/(SICI)1096-9071(199705)52:1<14::AID-JMV3>3.0.CO;2-U). (PMID:9131452).
James, V.L.A., Lambden, P.R., Caul, E.O., Cooke, S.J. and Clarke, I.N. (1997) Seroepidemiology of human group C rotavirus in the UK. Journal of Medical Virology, 52, (1), 86-91. (doi:10.1002/(SICI)1096-9071(199705)52:1<86::AID-JMV14>3.0.CO;2-Z). (PMID:9131463).
Clarke, I.N. and Lambden, P.R. (1997) The molecular biology of caliciviruses. Journal of General Virology, 78, (2), 291-301. (PMID:9018049).
Johnson, Nicholas, Pickett, Mark A., Watt, Peter J., Clarke, Ian N. and Heckels, John E. (1997) Construction of an epitope vector utilising the diphtheria toxin B-subunit. FEMS Microbiology Letters, 146, (1), 91-96. (doi:10.1016/S0378-1097(96)00459-4). (PMID:8997711).
Liu, B, Clarke, Ian N., Caul, E and Lambden, Paul R. (1997) The genomic 5' terminus of Manchester calicivirus. Virus Genes, 15, (1), 25-28. (doi:10.1023/A:1007946628253). (PMID:9354265).
Ward, Stephen J., Scopes, Deborah, Christodoulides, Myron, Clarke, Ian N. and Heckels, John E. (1996) Expression of Neisseria meningitidis class 1 porin as a fusion protein in Escherichia coli: the influence of liposomes and adjuvants on the production of a bactericidal immune response. Microbial Pathogenesis, 21, (6), 499-512. (doi:10.1006/mpat.1996.0079). (PMID:8971689).
Liu, B., Clarke, I.N. and Lambden, P.R. (1996) Polyprotein processing in Southampton virus: identification of 3C-like protease cleavage sites by in vitro mutagenesis. Journal of Virology, 70, (4), 2605-2610. (PMID:8642693).
Samarbaf-Zadeh, Ali Reza, Lambden, Paul R., Green, Steve, Deng, Yu, Caul, E. Owen and Clarke, Ian N. (1996) The VP3 gene of human group C rotavirus. Virus Genes, 13, (2), 169-173. (doi:10.1007/BF00568909). (PMID:8972570).
Watson, M.W., Clarke, I.N., Everson, J.S. and Lambden, P.R. (1995) The CrP operon of Chlamydia psittaci and Chlamydia pneumoniae. Microbiology, 141, (10), 2489-2497. (doi:10.1099/13500872-141-10-2489). (PMID:7582008).
Dingle, Kate E., Lambden, Paul R., Caul, E. Owen and Clarke, Ian N. (1995) Human enteric Caliciviridae: the complete genome sequence and expression of virus-like particles from a genetic group II small round structured virus. Journal of General Virology, 76, (9), 2349-2355. (doi:10.1099/0022-1317-76-9-2349). (PMID:7561776).
Liu, B.L., Clarke, I.N., Caul, E.O. and Lambden, P.R. (1995) Human enteric caliciviruses have a unique genome structure and are distinct from the Norwalk-like viruses. Archives of Virology, 140, (8), 1345-1356. (doi:10.1007/BF01322662). (PMID:7661689).
Green, Steve M., Lambden, Paul R., Caul, E. Owen, Ashley, Charles R. and Clarke, Ian N. (1995) Capsid diversity in small round-structured viruses: molecular characterization of an antigenically distinct human enteric calicivirus. Virus Research, 37, (3), 271-283. (doi:10.1016/0168-1702(95)00041-N). (PMID:8533462).
Lambden, P.R. and Clarke, I.N. (1995) Genome organization in the caliciviridae. Trends in Microbiology, 3, (7), 261-265. (doi:10.1016/S0966-842X(00)88940-4). (PMID:7551638).
Green, Steve M., Lambden, Paul R., Deng, Yu, Clarke, Ian N., Lowes, J. Andrew, Lineham, Sarah, Bushell, Julie, Rogers, John, Caul, E. Owen and Ashley, Charles R. (1995) Polymerase chain reaction detection of small round-structured viruses from two related hospital outbreaks of gastroenteritis using inosine-containing primers. Journal of Medical Virology, 45, (2), 197-202. (doi:10.1002/jmv.1890450215). (PMID:7775939).
Lambden, Paul R. and Clarke, Ian N. (1995) Cloning of viral double-stranded RNA genomes. Methods in Molecular Genetics, 7, 359-372. (doi:10.1016/S1067-2389(06)80055-5).
Deng, Yu, Fielding, Patrick A., Lambden, Paul R., Caul, E. Owen and Clarke, Ian N. (1995) Molecular characterization of the 11th RNA segment from human group C rotavirus. Virus Genes, 10, (3), 239-243. (doi:10.1007/BF01701813). (PMID:8560785).
Lambden, P.R., Liu, B.L. and Clarke, I.N. (1995) A conserved sequence motif at the 5' terminus of the Southampton virus genome is characteristic of the Caliciviridae. Virus Genes, 10, (2), 149-152. (doi:10.1007/BF01702595). (PMID:8560774).
Fielding, P.A., Lambden, P.R., Caul, E.O. and Clarke, I.N. (1994) Molecular characterization of the outer capsid spike protein (VP4) gene from human group C rotavirus. Virology, 204, (1), 442-446. (doi:10.1006/viro.1994.1551). (PMID:8091676).
Grice, Alexander S., Lambden, Paul R., Caul, E. Owen and Clarke, Ian N. (1994) Sequence conservation of the major outer capsid glycoprotein of human group C rotaviruses. Journal of Medical Virology, 44, (2), 166-171. (doi:10.1002/jmv.1890440209). (PMID:7852957).
Green, Steve M., Dingle, Kate E., Lambden, Paul R., Caul, E. Owen, Ashley, Charles R. and Clarke, Ian N. (1994) Human enteric Caliciviridae: a new prevalent small round-structured virus group defined by RNA-dependent RNA polymerase and capsid diversity. Journal of General Virology, 75, (8), 1883-1888. (doi:10.1099/0022-1317-75-8-1883). (PMID:8046390).
Watson, M.W., Lambden, P.R., Everson, J.S. and Clarke, I.N. (1994) Immunoreactivity of the 60 kDa cysteine-rich proteins of Chlamydia trachomatis, Chlamydia psittaci and Chlamydia pneumoniae expressed in Escherichia coli. Microbiology, 140, (8), 2003-2011. (doi:10.1099/13500872-140-8-2003). (PMID:7522846).
Lambden, Paul R., Caul, E. Owen, Ashley, Charles R. and Clarke, Ian N. (1994) Human enteric caliciviruses are genetically distinct from small round structured viruses. The Lancet, 343, (8898), 666-667. (doi:10.1016/S0140-6736(94)92658-1). (PMID:7906820).
Lambden, P.R., Caul, E.O., Ashley, C.R. and Clarke, I.N. (1993) Sequence and genome organization of a human small round-structured (Norwalk-like) virus. Science, 259, (5094), 516-519. (doi:10.1126/science.8380940 ). (PMID:8380940).
Hayes, Lyn J., Bailey, Robin L., Mabey, David C.W., Clarke, Ian N., Pickett, Mark A., Watt, Peter J. and Ward, Michael E. (1992) Genotyping of Chlamydia trachomatis from a trachoma-endemic village in the Gambia by a nested polymerase chain reaction: identification of strain variants. The Journal of Infectious Diseases, 166, (5), 1173-1177. (doi:10.1093/infdis/166.5.1173). (PMID:1402030).
Cooke, S.J., Clarke, I.N., Freitas, R.B., Gabbay, Y.B. and Lambden, P.R. (1992) The correct sequence of the porcine group C/Cowden rotavirus major inner capsid protein shows close homology with human isolates from Brazil and the U.K. Virology, 190, (1), 531-537. (doi:10.1016/0042-6822(92)91248-S). (PMID:1326817).
Lambden, P.R., Cooke, S.J., Caul, E.O. and Clarke, I.N. (1992) Cloning of noncultivatable human rotavirus by single primer amplification. Journal of Virology, 66, (3), 1817-1822. (PMID:1371174).
Cooke, S.J, Lambden, P.R., Caul, E.O. and Clarke, I.N. (1991) Molecular cloning, sequence analysis and coding assignment of the major inner capsid protein gene of human group C rotavirus. Virology, 184, (2), 781-785. (doi:10.1016/0042-6822(91)90452-H). (PMID:1653500).
McGarity, B.H., Robertson, D.A., Clarke, I.N. and Wright, R. (1991) Deoxyribonucleic acid amplification and hybridisation in Crohn's disease using a chlamydial plasmid probe. Gut, 32, (9), 1011-1015. (doi:10.1136/gut.32.9.1011). (PMID:1916481).
Hayes, L.J., Conlan, J.W., Everson, J.S., Ward, M.E. and Clarke, I.N. (1991) Chlamydia trachomatis major outer membrane protein epitopes expressed as fusions with LamB in an attenuated aroA strain of Salmonella typhimurium; their application as potential immunogens. Journal of General Microbiology, 137, (7), 1557-1564. (doi:10.1099/00221287-137-7-1557). (PMID:1720166).
Watson, M.W., Lambden, P.R. and Clarke, I.N. (1991) Genetic diversity and identification of human infection by amplification of the chlamydial 60-kilodalton cysteine-rich outer membrane protein gene. Journal of Clinical Microbiology, 29, (6), 1188-1193. (PMID:1864938).
McGuinness, B.T., Clarke, I.N., Lambden, P.R., Barlow, A.K., Heckels, J.E., Poolman, J.T. and Jones, D.M. (1991) Point mutation in meningococcal por A gene associated with increased endemic disease. The Lancet, 337, (8740), 514-517. (doi:10.1016/0140-6736(91)91297-8). (PMID:1705642).
Conlan, J.W., Ferris, S., Clarke, I.N. and Ward, M.E. (1990) Isolation of recombinant fragments of the major outer-membrane protein of Chlamydia trachomatis: their potential as subunit vaccines. Journal of General Microbiology, 136, (10), 2013-20. (PMID:1702826).
Watson, M.W., al-Mahdawi, S., Lamden, P.R. and Clarke, I.N. (1990) The nucleotide sequence of the 60 kDa cysteine rich outer membrane protein of Chlamydia pneumoniae strain IOL-207. Nucleic Acids Research, 18, (17), 5299. (doi:10.1093/nar/18.17.5299). (PMID:2402463).
Watson, M.W., Lambden, P.R. and Clarke, I.N. (1990) The nucleotide sequence of the 60 kDa cysteine rich outer membrane protein of Chlamydia psittaci strain EAE/A22/M. Nucleic Acids Research, 18, (17), 5300. (doi:10.1093/nar/18.17.5300). (PMID:2612891).
Hayes, L.J., Pickett, M.A., Conlan, J.W., Ferris, S., Everson, J.S., Ward, M.E. and Clarke, I.N. (1990) The major outer-membrane proteins of Chlamydia trachomatis serovars A and B: intra-serovar amino acid changes do not alter specificities of serovar- and C subspecies-reactive antibody-binding domains. Journal of General Microbiology, 136, (8), 1559-1566. (doi:10.1099/00221287-136-8-1559). (PMID:1702141).
McGuinness, Brian, Barlow, Ann K., Clarke, Ian N., Farley, John E., Anilionis, Algis, Poolman, Jan T. and Heckels, John E. (1990) Deduced amino acid sequences of class 1 protein (PorA) from three strains of Neisseria meningitidis. Synthetic peptides define the epitopes responsible for serosubtype specificity. Journal of Experimental Medicine, 171, (6), 1871-1882. (doi:10.1084/jem.171.6.1871). (PMID:1693651).
White, D.A., Barlow, A.K., Clarke, I.N. and Heckels, J.E. (1990) Stable expression of meningococcal class 1 protein in an antigenically reactive form in outer membranes of Escherichia coli. Molecular Microbiology, 4, (5), 769-776. (doi:10.1111/j.1365-2958.1990.tb00647.x). (PMID:2117694).
Lambden, P.R., Everson, J.S., Ward, M.E. and Clarke, I.N. (1990) Sulfur-rich proteins of Chlamydia trachomatis: developmentally regulated transcription of polycistronic mRNA from tandem promoters. Gene, 87, (1), 105-112. (doi:10.1016/0378-1119(90)90500-Q). (PMID:2332164).
Watson, M.W., Lambden, P.R., Ward, M.E. and Clarke, I.N. (1989) Chlamydia trachomatis 60 kDa cysteine rich outer membrane protein: sequence homology between trachoma and LGV biovars. FEMS Microbiology Letters, 53, (3), 293-297. (PMID:2612891).
Conlan, J.W., Ferris, S., Clarke, I.N. and Ward, M.E. (1989) Surface-exposed epitopes on the major outer-membrane protein of Chlamydia trachomatis defined with peptide antisera. Journal of General Microbiology, 135, (12), 3219-3228. (PMID:2483992).
Conlan, J.W., Kajbaf, M., Clarke, I.N., Chantler, S. and Ward, M.E. (1989) The major outer membrane protein of Chlamydia trachomatis: critical binding site and conformation determine the specificity of antibody binding to viable chlamydiae. Molecular Microbiology, 3, (3), 311-318. (doi:10.1111/j.1365-2958.1989.tb00176.x). (PMID:2473372).
Clarke, I.N., Ward, M.E. and Lambden, P.R. (1988) Molecular cloning and sequence analysis of a developmentally regulated cysteine-rich outer membrane protein from Chlamydia trachomatis. Gene, 71, (2), 307-314. (PMID:3066701).
Pickett, M.A., Everson, J.S. and Clarke, I.N. (1988) Chlamydia psittaci ewe abortion agent: omplete nucleotide sequence of the major outer membrane protein gene. FEMS Microbiology Letters, 55, (2), 229-234. (doi:10.1111/j.1574-6968.1988.tb13939.x).
Barlow, A.K., Heckels, J.E. and Clarke, I.N. (1988) Molecular cloning and expression of Neisseria meningitidis class 1 outer-membrane protein in Escherichia coli K-12. Journal of Medical Microbiology, 55, (11), 2734-2740. (PMID:3117690).
Hatt, Christopher, Ward, Michael E. and Clarke, Ian N. (1988) Analysis of the entire nucleotide sequence of the cryptic plasmid of Chlamydia trachomatis serovar L1. Evidence for involvement in DNA replication. Nucleic Acids Research, 16, (9), 4053-4067. (doi:10.1093/nar/16.9.4053). (PMID:6307876).
Pickett, M.A., Ward, M.E. and Clarke, I.N. (1987) Complete nucleotide sequence of the major outer membrane protein gen from Chlamydia trachomatis serovar L1. FEMS Microbiology Letters, 42, (2), 185-190. (doi:10.1111/j.1574-6968.1987.tb02069.x).
Gilbert, Harry J., Clarke, Ian N., Gibson, Raymond K., Stephenson, John R. and Tully, Michael (1985) Molecular cloning of the phenylalanine ammonia lyase gene from Rhodosporidium toruloides in Escherichia coli K-12. Journal of Bacteriology, 161, (1), 314-320. (2981805). (PMID:7041889).
Clarke, Ian N. and McCrae, Malcolm A. (1983) The molecular biology of rotaviruses. VI. RNA species-specific terminal conservation in rotaviruses. The Journal of General Virology, 64, (9), 1877-1884. (PMID:6310030).
Clarke, I. N. and McCrae, M. A. (1982) Structural analysis of electrophoretic variation in the genome profiles of rotavirus field isolates. Infection and Immunity, 36, (2), 492-497. (PMID:225545).
Bridger, Janice C., Clarke, Ian N. and McCrae, Malcolm A. (1982) Characterization of an antigenically distinct porcine rotavirus. Infection and Immunity, 35, (3), 1058-1062. (PMID:6175575).
Clarke, I. N. and McCrae, M. A. (1981) A sensitive method for the production of diagnostic fingerprints of the genome segments of field isolates of rotavirus. Journal of Virological Methods, 3, (5), 261-9. (PMID:6277973).
Clarke, I. N. and McCrae, M. A. (1981) A rapid and sensitive method for analysing the genome profiles of field isolates of rotavirus. Journal of Virological Methods, 2, (4), 203-209. (PMID:6262345).

Book Section

Clarke, I.N., Estes, M.K., Green, K.Y., Hansman, G.S., Knowles, N.J., Koopmans, M.K., Matson, D.O., Meyers, G., Neill, J.D., Radford , A, Smith, A.W, Studdert, M.J., Vinje, J and Thiel, H-J (2012) Caliciviridae. In, King, Andrew M., Adams, Michael J., Carstens, Eric B. and Lefkowitz, Elliot J. (eds.) Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Oxford, GB, Elsevier, 977-986.
Clarke, I.N. (2011) Evolution of chlamydia trachomatis. In, Nahmias, Andre, Danielsson, Dan and Beckman Nahmais, Susa (eds.) The Evolution of Infectious Agents in Relation to Sex. Chichester, GB, Wiley, E11-E18. (Annals of the New York Academy of Sciences, 1230 1). (doi:10.1111/j.1749-6632.2011.06194.x).
Clarke, Ian N. (2010) Chlamydial transformation: facing up to the challenge. In, Chlamydial Infections. Twelfth International Symposium on Human Chlamydial Infections San Francisco, US, Twelfth International Symposium on Human Chlamydial Infections, 295-304.
O'Connor, C. David, Clarke, Ian N. and Skipp, Paul (2006) Quest for complete proteome coverage. In, Humphery-Smith, Ian and Hecker, Michael (eds.) Microbial Proteomics: Functional Biology of Whole Organisms. Hoboken, US, John Wiley & Sons, 27-38. (Methods of Biochemical Analysis, 49). (doi:10.1002/0471973165.ch3).
Clarke, Ian N. and Lambden, Paul R. (1997) Viral zoonoses and food of animal origin: caliciviruses and human disease. In, Kaaden, O-.R., Czerny, C.P. and Eichhorn, W. (eds.) Viral Zoonoses and Food of Animal Origin: A RE-Evaluation of Possible Hazards for Human Health. Berlin, DE, Springer Verlag, 141-152. (Archives of Virology. Supplement, 13).

Conference or Workshop Item

Viljoen, GJ, Liu, B.L., Clarke, Ian N. and Lambden, Paul R. (1998) Regulation of gene expression in mammalian cells using the LAC repressor. In, Proceedings of an International Symposium on Diagnosis and Control of Livestock Diseases Using Nuclear and Related Techniques, Wien, AT, 07 - 11 Apr 1997. , 245-267.
 

Research

Green fluorescence of transformed chlamydia trachomatis. Wang et al 2011.

Chlamydial Research Group

The ability to diagnose accurately and rapidly treat Chlamydia infections is necessary to reduce the burden of this disease. We are involved in a major programme to define the nature and extent of diversity in C.trachomatis with the overall research goal of understanding the role of C.trachomatis in complications of infection such as infertility and pelvic inflammatory disease. This work is multidisciplinary and involves many international partners most recently (August 2013) we have been supported by the Wellcome Trust to develop a biobank of C. trachomatis. Our genomics programme is supported by the Wellcome Trust and is performed in partnership with the Sanger Centre, Prof Nick Thomas. We also have funding from the HPA for investigating the epidemiology of C.trachomatis in the UK and work in close partnership with the Southampton HPA laboratory, Dr Peter Marsh. The Chlamydia research group is also a joint partner with the Department of Chemistry in a work programme funded by the Technology Strategy Board, together with industrial partners to develop a point of care test for C.trachomatis. Our basic cell and molecular biology research is also funded by the Wellcome Trust to develop transformation protocols and use plasmid-based chlamydial genetics to understand virulence. Our long term plans are to develop a vaccine to C.trachomatis. We have research partners in both Israel Dr. Simona Kahane -(Ben Gurion University) and USA (Prof. Bentley Fane - BIO5 University of Arizona, Prof Kyle Ramsay - Midwestern University).

Norovirus replication

Norovirus replication in the differentiated epithelial cells of the tips of villi in the distal jejunum. Otto et al 2011.

Norovirus replication

Norovirus Research Group

Norovirus research in Southampton has been established for over 20 years . Work is focused on the ‘Southampton virus' one of the prototype human noroviruses and characterization of this virus represented the culmination of many years work to pinpoint the causative viral agent of epidemic non bacterial gastroenteritis. This advance allowed the characterisation of other noroviruses leading to the identification of the most prevalent norovirus in the world, the so called GII.4 viruses. The prototype of these viruses ‘Lordsdale virus' came from a patient at the Southampton General Hospital. The immediate research goal of the team is to develop a cell culture system that supports human norovirus replication using Southampton and Lordsdale virus. We are also engaged in a programme to understand the basic biology of noroviruses using the murine virus as a model system, this work is performed in collaboration with Professor Vernon Ward (University of Otago) and makes use of the first reverse genetics system for noroviruses developed jointly between Otago and Southampton. In collaboration with Professor Jon Cooper (UCL) we are determining the structure of human norovirus proteins with the aim of developing novel antiviral agents. We also have a long term collaboration with Dr. Peter Otto at the Friederich-Loeffler Institue in Jena to investigate the pathogenesis of norovirus infection. Noroviruses are a major source of environmental contamination and we are funded by the food standards agency to develop highly sensitive diagnostics for noroviruses.

Academic unit:  Clinical and Experimental Sciences Academic Units

Affiliate academic units:  Infection and Immunity Research group

Responsibilities

Postgraduate student supervision

(22 completed PhDs)

Current PhD Students

Clare Labiran
Cate Winstanley 

National and International responsibilities

Chair, Calicivirus study group, International Committee on the Taxonomy of Viruses (2nd term 2012 - 2015)
Chair scientific committee, European society for Chlamydia research (2012 - 2016)

Teaching Responsibilities

Personal tutor BM5/BM6

BM5. Delivers lectures and group teaching that introduce virology and microbiology and also specialist lectures in enteric virology, hepato-virology, respiratory virology and neurovirology.

Contact

Professor Ian Clarke
Phone: (023) 8120 6975
Email: inc@soton.ac.uk

Room Number: SGH/LC70/MP814