Molecular Microbiology

1. Molecular Microbiology Alan Ward

2. Molecular Microbiology Definition Molecular microbiology is the branch of microbiology devoted to the study of the molecular basis of the physiological processes that occur in microorganisms studyof the formation, structure, and function of macromolecules essential to life the manipulation of DNA

3. Molecular Microbiology Example syllabus (from Newcastle University Mres course) • Introduction; Regulation of bacterial growth and the stringent response • The translation apparatus, multidrug resistance and tolerance • Bacterial cell division and its regulation • Control of DNA replication in bacteria • Bacterial cell wall biosynthesis • Cell shape and bacteria without cell wall (L-forms) • Bacterial flagellar assembly and structure • Macromolecular X-ray crystallography in Gram-positive bacteria • Bacterial transcription and its regulation • The bacterial genome and bioinformatics

4. Molecular Microbiology

5. Molecular Microbiology Lab growth – flask/plates Pathogenesis Symbiosis Biofilms My equivalent syllabus might be: • Bacterial growth • DNA replication in bacteria • Bacterial transcription • The translation apparatus • Regulation of transcription • Post-translational regulation • Enzyme regulation • Cell shape • Bacterial cell division and its regulation • Bacterial cell wall biosynthesis • Bacterial flagellar assembly and structure • The bacterial genome and bioinformatics • Protein structure Classic undergraduate Central Dogma Genetics and Biochemistry Macromolecular machines

6. Bioinformatics • Basic concepts of molecular biology: genomes, transcriptomes, proteomes • Sequence analysis: genome annotation, sequence alignment, multiple sequence alignment • Phylogenetic analysis • Protein families • Database searching • Tools • Post-genome analysis: Gene and genome comparisons, protein structure, proteomics Introduction to bioinformatics, 3rd Edition Lesk, Arthur M Oxford University Press, 2008

7. Molecular MicrobiologyMethods • Sample preparation • DNA extraction RNA extraction cDNA • PCR • Band patterns • Multiplex PCR • RT-PCR (Reverse Tramscription/Real Time) • PFGE RAPD AFLP DGGE • Restriction • Hybridisation • Probes • Southern/Northern blots • Microarrays • DNA melting – RT-PCR product validation %GC DNA:DNA similarity • Sequencing • Sanger sequencing • NGS – Next/New Generation Sequencing

8. Expertise • Application of data analysis methods, including linear and non-linear multivariate statistics and neural networks • to microbial systematics, the classification and identification of micro-organisms; • search and discovery of novel organisms for screening and the development of bio-active compounds; • marine microbial ecology • process control and optimization of fermentation processes, both for research and development and in large scale industrial application. • My personal research themes are: • bioinformatics and bacterial taxonomy • identification of microbes, molecular identification • comparative genomics and expression data analysis • MALDI mass spectrometry and chemical fingerprinting • data analysis and poly-phasic taxonomy • Bioprocess modelling, supervision and control

9. Expertise PhD students Anne Barrett Characterization and discrimination of the clinically significant members of the Mycobacterium chelonae clade NithyaRajarajan Identification, characterization and expression of biofilm disrupting nuclease from Bacillus licheniformis Ahmed abd-el-Raza Screening, isolation and optimization of culture conditions for the production of omega-3 and omega-6 fatty acids from marine microorganisms. NagamaniBora Actinomycete diversity of European smear-ripened cheeses

10. Expertise Current projects Whole genome sequence of a clinical isolate of Mycobacterium chelonae from cystic fibrosis patient on the Ion Torrent next generation sequencing personal gene machine – assembly and annotation in progress. Metagenomic analysis of cystic fibrosis patient sputum microflora on the Ion Torrent – analysed by MG-RAST In silico taxonomy-guided identification of the hfq gene (non-coding RNA regulatory chaperone) in the actinobacteria 16S phylogeny of the Streptomycetaceae Taxonomy-guided identification of classes of chaplin genes in the Streptomyces

11. Expertise Recent papers Ward AC Bora N (2014) The Actinobacteria. In Practical Handbook of Microbiology, Third Edition (Edited by Goldman E Green LH) CRC Press (2nd edition Chapter 27 pp. 375-444) AbdElrazak A, Ward AC, Glassey J (2013) Polyunsaturated fatty acid production by marine bacteria. Bioprocess BiosystEng36:1641–1652 AbdElrazak A, Ward AC, Glassey J (2013) Response surface methodology for optimising the culture conditions for eicosapentaenoic acid production by marine bacteria. J IndMicrobiolBiotechnol 40, 477-487 Rajarajan, N., Ward, A.C., Grant Burgess, J., Glassey, J. (2013) Use of physiological information and process optimisation enhances production of extracellular nuclease by a marine strain of Bacillus licheniformis. Bioresource Technology130, 552-558 Magee JG Ward AC (2012) The Mycobacteria. InBergey's Manual of Determinative Microbiology. 2nd Edition. Vol. 5 The Actinobacteria (editor Goodfellow, M.) Labeda, DP, Goodfellow, M, Brown, R, Ward, AC, Lanoot, B, Vanncanneyt, M Swings, J, Kim, SB, Liu, Z, Chun, J, Tamura, T, Oguchi, A, Kikuchi, T, Kikuchi, H, Nishii, T, Tsuji, K, Yamaguchi, Y, Tase, A, Takahashi, M, Sakane, T, Suzuki, KI, Hatano, K (2012) Phylogenetic study of the species within the family Streptomycetaceae. Antonie van Leeuwenhoek International 101, Special Issue: SI, 73-104 Larpin-Laborde, S, Imran, M, Bonaiti, C, Bora, N, Gelsomino, R, Goerges, S, Irlinger, F, Goodfellow, M, Ward, AC, Vancanneyt, M, Swings, J, Scherer, S, Gueguen, M, Desmasures, N (2011) Surface microbial consortia from Livarot, a French smear-ripened cheese. Canadian Journal of Microbiology 57, 651-660 Ashforth, EJ, Olive, PJW, Ward, AC (2011) Phylogenetic characterisation of bacterial assemblages and the role of sulphur-cycle bacteria in an Arenicola marina bioturbatedmesocosm. Marine Ecology Progress Series 439, 19-46 Dai HQ, Wang J, Xin YH, Pei G, Tang SK, Ren B, Ward A, Ruan JS, Li WJ, Zhang LX (2010) Verrucosisporasediminis sp. nov. a cyclodipeptide-producing actinomycete from deep-sea sediment.Int J SystEvolMicrobiol60, 1807-1812 Olive PJW Duangchinda T Ashforth E Craig S Ward AC Davies SJ (2009) Net gain of long-chain polyunsaturated fatty acids (PUFA) in a lugworm Arenicola marinabioturbatedmesocosmMarine EcolProg Series387, 223-239

12. Molecular MicrobiologyAlan Ward What do you want to do? • … • … • … • … • … • … • …