Molecular Microbiology - Newcastle University Staff Publishing

Molecular Microbiology
Alan Ward
Molecular Microbiology
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 Microbiology
Example syllabus (from Newcastle University Mres course)
 Introduction; Regulation of bacterial growth and the
stringent response
 The translation apparatus, multidrug resistance and
 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
 Bacterial transcription and its regulation
 The bacterial genome and bioinformatics
Molecular Microbiology
Molecular Microbiology
Lab growth – flask/plates
My equivalent syllabus might be:
 Bacterial growth
 DNA replication in bacteria
 Bacterial transcription
Classic undergraduate
Central Dogma
 The translation apparatus
 Regulation of transcription
Genetics and Biochemistry
 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
 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
Molecular Microbiology
• Sample preparation
– DNA extraction RNA extraction cDNA
• Band patterns
Multiplex PCR
RT-PCR (Reverse Tramscription/Real Time)
• Hybridisation
Southern/Northern blots
DNA melting – RT-PCR product validation %GC DNA:DNA similarity
• Sequencing
– Sanger sequencing
– NGS – Next/New Generation Sequencing
• Application of data analysis methods, including linear and
non-linear multivariate statistics and neural networks
– to microbial systematics, the classification and identification of
– 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
• 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 students
Anne Barrett
Characterization and discrimination of the clinically
significant members of the Mycobacterium chelonae clade
Nithya Rajarajan
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.
Nagamani Bora
Actinomycete diversity of European smear-ripened cheeses
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 (noncoding RNA regulatory chaperone) in the actinobacteria
16S phylogeny of the Streptomycetaceae
Taxonomy-guided identification of classes of chaplin genes in
the Streptomyces
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)
Abd Elrazak A, Ward AC, Glassey J (2013) Polyunsaturated fatty acid production by marine bacteria.
Bioprocess Biosyst Eng 36:1641–1652
Abd 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, 477487
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 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, 651-660
Ashforth, 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, 1807-1812
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 marina bioturbated mesocosm Marine Ecol
Prog Series 387, 223-239
Molecular Microbiology
Alan Ward
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