Pachebat, Justin - Aberystwyth University - Institute of Biological, Environmental and Rural Sciences

个人简介

I am a parasitologist and specialist in single molecule genomics and next generation sequencing (NGS). After degrees in Microbiology at Bristol and Medical Microbiology at the London School of Hygiene and Tropical Medicine, I did a PhD at the MRC National Institute for Medical Research on the characterisation and biosynthesis of a malaria vaccine target: Merozoite Surface Protein 7 in Plasmodium falciparum merozoites. After my PhD I did several post-docs at the MRC Laboratory of Molecular Biology (2000-2007) and the University of Cambridge (2007-2009). At the MRC-LMB, I ran the HAPPY genome mapping project as part of the international Dictyostelium discoideum genome consortium (see Nature papers), I also ran several R&D projects. At the University of Cambridge, I was based in Jim Haseloff's laboratory at Plant Sciences, and developed an interest in synthetic biology; whilst David Baulcombe developed my interest in NGS which lead to collaborations with: Jim Ajioka (Pathology) and Carolina Marcano (Illumina) to characterise Campylobacter bacteriophage genomes; Gareth Bloomfield and Rob Kay (MRC-LMB) on D. discoideum phenotypic mutants (see E Life paper), Sarah Covshoff and Julian Hibberd on Echinochloa and Rice transcriptomics (see Plant Physiology paper). In 2009 and 2010 I organised the annual Cambridge NGS Bioinformatics meetings.

研究领域

Key words: Campylobacter, Cryptosporidium, Diagnostics, Dictyostelium, Enteric Pathogens, Eimeria, Enterococcus, Host-Pathogen interactions, Illumina, Meta-genomics, Meta-transcriptomes, Next Generation Sequencing, Parasites, Phage, Rhodococcus, Sequencing, Single molecule genomics, Toxoplasma, Viruses, Whole genome amplification. My research has two main focuses: 1) using single molecule genomics and NGS technologies to characterise pathogens of animals, humans and plants with the aim of developing novel diagnostics / methods of control; 2) using meta-genomic and meta-transcriptomic approaches to study host - pathogen - microbiome interactions. Current examples of my research include: The detection and characterisation of unknown human viruses (with Public Health England, Liverpool and Cambridge Universities). Meta-genomics to identify microbiota associated with chronic lung disease (MEDLUNG project led by Luis Mur in collaboration with the NHS and Swansea University). Campylobacter jejuni bacteriophage genomics (in collaboration with Jim Ajioka, Cambridge University and Illumina UK Ltd). Control of Campylobacter jejuni in chickens using novel antimicrobial agents (KESS and TSB funded with several commercial partners). Control of Eimeria species in chickens (collaboration with Damer Blake, Royal Veterinary College and Natural Feeds and Fertilizers Ltd). Genomics of commensal gut bacteria isolated from blood sucking Rhodnius prolixus insects (Swansea University). Genomic characterisation of clinical isolates of Cryptosporidium spp. (KESS funded, with Martin Swain & UK Cryptosporidium Reference Lab). Genomics of pathogenic and probiotic Enterococcal spp. (Institute of Experimental Medicine, St. Petersberg, Russia). Slime mould mutant genomics (collaboration with Rob Kay and Gareth Bloomfield, MRC LMB).

近期论文

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Karaseva, A., Tsapieva, A., Pachebat, J.A., Suvorov, A. 2016. Draft Genome Sequence of the probiotic Enterococcus faecium strain L-3. Genome Announcements 4 (1) e01599-15 Cadair Cameron, S., E. Lewis, K., Huws, S., Lin, W., Hegarty, M., D. Lewis, P., Mur, L., Pachebat, J.A. 2016. Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity. PLoS One 11 (2) 0149095 Cadair Brown, M., Hablutzel, P., Friberg, I.M., Thomason, A.G., Stewart, A., Pachebat, J.A., Jackson, J. 2016. Seasonal immunoregulation in a naturally-occurring vertebrate. BMC Genomics 369 Cadair Huws, S., Edwards, J.E., Creevey, C., Rees Stevens, P., Lin, W., Girdwood, S., Pachebat, J., Kingston-Smith, A. 2016. Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass. FEMS Microbiology Ecology 92 (1) fiv 137 Zampini, M., Mur, L., Rees Stevens, P., Pachebat, J.A., Newbold, C., Hayes, F., Kingston-Smith, A. 2016. Terminator Operon Reporter: Combining a transcription termination switch with reporter technology for improved gene synthesis and synthetic biology applications. Scientific Reports 6 26572 Cadair Covshoff, S., Szecowka, M., Hughes, T., Smith-Unna, R., Kelly, S., Bailey, K., Sage, T., Pachebat, J., Leegood, R., Hibberd, J. 2016. Transcriptomics of C4 photosynthesis in rice paddy. Plant Physiology 170 (1) pp. 57-73. Cadair Facey, P.D., Méric, G., Hitchings, M.D., Pachebat, J.A., Hegarty, M.J., Chen, X., Morgan, L.V.A., Hoeppner, J.E., Whitten, M.M.A., Kirk, W.D.J., Dyson, P.J., Sheppard, S.K., Del Sol, R. 2015. Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis. Genome Biology and Evolution 7 (8) pp. 2188-2202. Cadair Hadfield, S.J., Pachebat, J.A., Swain, M.T., Robinson, G., Cameron, S.J.S., Alexander, J., Hegarty, M.J., Elwin, K., Chalmers, R.M. 2015. Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples. BMC Genomics 16 650 Cadair Bloomfield, G., Traynor, D., Sander, S.P., Veltman, D.M., Pachebat, J.A., Kay, R.R. 2015. Neurofibromin controls macropinocytosis and phagocytosis in Dictyostelium. eLife 4 e04940 Cadair Zampini, M., Rees Stevens, P., Pachebat, J., Kingston-Smith, A., Mur, L., Hayes, F. 2015. RapGene: a fast and accurate strategy for synthetic gene assembly in Escherichia coli. Scientific Reports 5 11302 Cadair