Molecular Microbiology Alan Ward Molecular
Description: Molecular Microbiology Alan Ward 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 study of the
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slide1. Molecular Microbiology Alan Ward<br>
slide2. 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 study of the formation, structure, and function of macromolecules essential to life the manipulation of DNA<br>
slide3. 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<br>
slide4. Molecular Microbiology<br>
slide5. Molecular Microbiology 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 Lab growth – flask/plates
Pathogenesis
Symbiosis
Biofilms Classic undergraduate
Central Dogma Genetics and Biochemistry Macromolecular
machines<br>
slide6. 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<br>
slide7. Molecular Microbiology Methods 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<br>
slide8. 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<br>
slide9. 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 Expertise<br>
slide10. 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 Expertise<br>
slide11. 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, 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 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 Expertise<br>
slide12. Molecular Microbiology Alan Ward What do you want to do?
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…
…
…
…
…
…<br>
slide2. 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 study of the formation, structure, and function of macromolecules essential to life the manipulation of DNA<br>
slide3. 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<br>
slide4. Molecular Microbiology<br>
slide5. Molecular Microbiology 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 Lab growth – flask/plates
Pathogenesis
Symbiosis
Biofilms Classic undergraduate
Central Dogma Genetics and Biochemistry Macromolecular
machines<br>
slide6. 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<br>
slide7. Molecular Microbiology Methods 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<br>
slide8. 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<br>
slide9. 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 Expertise<br>
slide10. 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 Expertise<br>
slide11. 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, 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 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 Expertise<br>
slide12. Molecular Microbiology Alan Ward What do you want to do?
…
…
…
…
…
…
…<br>