Molecular MicrobiologyAlan Ward

Molecular MicrobiologyDefinition

Molecular microbiology is the branch of microbiology devoted to the study of the

molecular basis of the physiological processes that occur in microorganisms

study of the formation, structure, and function of macromolecules essential to life

the manipulation of DNA

Molecular MicrobiologyExample 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

Molecular Microbiology

Molecular MicrobiologyMy 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

Lab growth – flask/platesPathogenesisSymbiosisBiofilms

Classic undergraduate Central Dogma

Genetics and Biochemistry

Macromolecularmachines

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 EditionLesk, Arthur MOxford University Press, 2008

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

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

PhD studentsAnne Barrett

Characterization and discrimination of the clinically significant members of the Mycobacterium chelonae clade

Nithya RajarajanIdentification, characterization and expression of biofilm disrupting nuclease from Bacillus licheniformis

Ahmed abd-el-RazaScreening, isolation and optimization of culture conditions for the production of omega-3 and omega-6 fatty acids from marine microorganisms.

Nagamani Bora Actinomycete diversity of European smear-ripened cheeses

Expertise

Current projectsWhole 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

Expertise

Recent papersWard 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) Abd Elrazak A, Ward AC, Glassey J (2013) Polyunsaturated fatty acid production by marine bacteria. Bioprocess Biosyst Eng 36:1641–1652Abd Elrazak A, Ward AC, Glassey J (2013) Response surface methodology for optimising the culture conditions for eicosapentaenoic acid production by marine bacteria. J Ind Microbiol Biotechnol 40, 477-487Rajarajan, 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 Technology 130, 552-558 Magee JG Ward AC (2012) The Mycobacteria. In Bergey'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, 651-660Ashforth, EJ, Olive, PJW, Ward, AC (2011) Phylogenetic characterisation of bacterial assemblages and the role of sulphur-cycle bacteria in an Arenicola marina bioturbated mesocosm. 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) Verrucosispora sediminis sp. nov. a cyclodipeptide-producing actinomycete from deep-sea sediment. Int J Syst Evol Microbiol 60, 1807-1812Olive 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 marina bioturbated mesocosm Marine Ecol Prog Series 387, 223-239

Expertise

Molecular MicrobiologyAlan Ward

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