Browsing Institute for Microbial Biotechnology & Metagenomics by Title
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Now showing items 9-20 of 20
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Sjoling, Sara; Cowan, Donald A. (Springer Verlag, 2003)[more][less]
Abstract: The microbial diversity in maritime meltwater pond sediments from Bratina Island, Ross Sea, Antarctica was investigated by 16S rDNA-dependent molecular phylogeny. Investigations of the vertical distribution, phylogenetic composition, and spatial variability of Bacteria and Archaea in the sediment were carried out. Results revealed the presence of a highly diverse bacterial population and a significantly depthrelated composition. Assessment of 173 partial 16S rDNA clones analyzed by amplified rDNA restriction analysis (ARDRA) using tetrameric restriction enzymes (HinP1I 5'GVCGC3'and Msp I. 5'CVGG3', BioLabs) revealed 153 different bacterial OTUs (operational taxonomic units). However, only seven archaeal OTUs were detected, indicating low archaeal diversity. Based on ARDRA results, 30 bacterial clones were selected for sequencing and the sequenced clones fell into seven major lineages of the domain Bacteria; the a, c, and d subdivisions of Proteobacteria, the Cytophaga–Flavobacterium– Bacteroides, the Spirochaetaceae, and the Actinobacteria. All of the archaeal clones sequenced belonged to the group Crenarchaeota and phylogenetic analysis revealed close relationships with members of the deep-branching Group 1 Marine Archaea. URI: http://hdl.handle.net/10566/148 Files in this item: 1
Sjoling16SrDNA.pdf (543.4Kb) -
Cowan, Donald A. (UWC, 2010)[more][less]
Abstract: The IMBM Brochure (2009) provides a summary of the staffing, activities and outputs of the Institute for the 2009 academic year Description: Institute for Microbial Biotechnology and Metagenomics brochure for 2009 URI: http://hdl.handle.net/10566/127 Files in this item: 1
IMBMbrochure2009.pdf (1.295Mb) -
Cowan, Donald A.; Stafford, William (ASM Press, 2007)[more][less]
URI: http://hdl.handle.net/10566/126 Files in this item: 1
CowanMetagenomicMethods2007.pdf (432.7Kb) -
Cowan, Donald A.; Arslanoglu, A.; Burton, Stephanie; Cameron, Rory A.; Baker, Gillian; Smith, Jacques J.; Meyer, Quinton (Portland Press, 2004)[more][less]
Abstract: With the rapid development of powerful protein evolution and enzyme-screening technologies, there is a growing belief that optimum conditions for biotransformation processes can be established without the constraints of the properties of the biocatalyst. These technologies can then be applied to find the ‘ideal biocatalyst’ for the process. In identifying the ideal biocatalyst, the processes of gene discovery and enzyme evolution play major roles. However, in order to expand the pool genes for in vitro evolution, new technologies, which circumvent the limitations of microbial culturability, must be applied. These technologies, which currently include metagenomic library screening, gene-specific amplification methods and even full metagenomic sequencing, provide access to a volume of ‘sequence space’ that is not addressed by traditional screening. URI: http://hdl.handle.net/10566/142 Files in this item: 1
CowanMetagenomicsGeneDiscovery2004.pdf (575.0Kb) -
Ah Tow, Lemese; Cowan, Donald A. (Society for General Microbiology, 2003)[more][less]
Abstract: Our results allow us to conclude that there appears to be significant conservation between the tuf genes of Planococcus, Planomicrobium and Staphylococcus spp., and that although the primer set TstaG422/TStag765 has been shown to possess high specificity, its use for the definitive identification of Staphylococcus spp. must be treated with some caution. Description: Published as a "Microbiology Comment": this provides a platform for readers of Microbiology to communicate their personal observations and opinions in a more informal way than through the submission of papers. URI: http://hdl.handle.net/10566/143 Files in this item: 1
AhTow&Cowan2003.PDF (251.5Kb) -
Baker, Gillian; Ah Tow, Lemese; Cowan, Donald A. (Elsevier, 2003)[more][less]
Abstract: PCR-based technologies are widely employed for the detection of specific microorganisms, and may be applied to the identification of non-indigenous microorganisms in ‘pristine’ environments. For ‘pristine’ environments such as those found on the Antarctic continent, the application of these methods to the assessment of environmental contamination from human activities must be treated with caution. Issues such as the possibility of non-human dispersal of organisms, stability and survival of non-indigenous organisms in vivo, the sensitivity, reproducibility and specificity of the PCR process (and particularly primer design) and the sampling regime employed must all be considered in detail. We conclude that despite these limitations, PCR and related technologies offer enormous scope for assessment of both natural and non-indigenous microbial distributions. URI: http://hdl.handle.net/10566/149 Files in this item: 1
BakerPCRdetection2003.pdf (391.8Kb) -
Cowan, Donald A.; Sayed, Muhammed F.; Tsekoa, Tsepo L.; Cameron, Rory A.; Sewell, B. Trevor (Academy of Science of South Africa (ASSAf), 2004)[more][less]
Abstract: Microbial nitrile hydratases are important industrial enzymes that catalyse the conversion of nitriles to the corresponding amides. Bacillus strain RAPc8 nitrile hydratase has recently been cloned and functionally expressed in E. coli. Here, the purification, crystallization and preliminary X-ray diffraction data of this nitrile hydratase are described. The heterotetrameric enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 30% PEG 400, 0.1 M MES (pH 6.5) and 0.1 M magnesium chloride were selected for X-ray diffraction studies. A data set complete to 2.5 Å was collected under cryoconditions at the in-house X-ray source at the University of the Western Cape. The space group was determined to be primitive tetragonal (P41212) with unit cell dimensions a = 106.61 Å, b = 106.61 Å, c=83.23 Å, = = =90°; with one dimer per asymmetric unit. Solution of the three-dimensional structure via molecular replacement is in progress. URI: http://hdl.handle.net/10566/167 Files in this item: 1
TsekoaPurification2004.pdf (784.0Kb) -
Baker, Gillian; Smith, J.J.; Cowan, Donald A. (Elsevier, 2003)[more][less]
Abstract: The Polymerase Chain Reaction (PCR) has facilitated the detection of unculturable microorganisms in virtually any environmental source and has thus been used extensively in the assessment of environmental microbial diversity. This technique relies on the assumption that the gene sequences present in the environment are complementary to the “universal” primers used in their amplification. The recent discovery of new taxa with 16S rDNA sequences not complementary to standard universal primers suggests that current 16S rDNA libraries are not representative of true prokaryotic biodiversity. Here we re-assess the specificity of commonly used 16S rRNA gene primers and present these data in tabular form designed as a tool to aid simple analysis, selection and implementation. In addition, we present two new primer pairs specifically designed for effective ‘universal’ Archaeal 16S rDNA sequence amplification. These primers are found to amplify sequences from Crenarchaeote and Euryarchaeote type strains and environmental DNA. URI: http://hdl.handle.net/10566/169 Files in this item: 1
BakerReviewReanalysis2003.pdf (969.0Kb) -
Burton, Stephanie; Cowan, Donald A.; Woodley, John M. (Nature Publishing Group, 2002)[more][less]
Abstract: While the use of enzymes as biocatalysts to assist in the industrial manufacture of fine chemicals and pharmaceuticals has enormous potential, application is frequently limited by evolution-led catalyst traits. The advent of designer biocatalysts, produced by informed selection and mutation through recombinant DNA technology, enables production of process-compatible enzymes. However, to fully realize the potential of designer enzymes in industrial applications, it will be necessary to tailor catalyst properties so that they are optimal not only for a given reaction but also in the context of the industrial process in which the enzyme is applied. URI: http://hdl.handle.net/10566/150 Files in this item: 1
BurtonCowanWoodley2002.pdf (768Kb) -
Pagaling, Eulyn; Haigh, Richard D.; Grant, William D.; Cowan, Donald A.; Jones, Brian; Ma, Yanhe; Ventosa, Antonio; Heaphy, Shaun (BioMed Central, 2007)[more][less]
Abstract: Background: We are profoundly ignorant about the diversity of viruses that infect the domain Archaea. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here we report the genomic sequence of a previously undescribed archaeal virus. Results: Haloarchaeal strains with 16S rRNA gene sequences 98% identical to Halorubrum saccharovorum were isolated from a hypersaline lake in Inner Mongolia. Two lytic viruses infecting these were isolated from the lake water. The BJ1 virus is described in this paper. It has an icosahedral head and tail morphology and most likely a linear double stranded DNA genome exhibiting terminal redundancy. Its genome sequence has 42,271 base pairs with a GC content of ~65 mol%. The genome of BJ1 is predicted to encode 70 ORFs, including one for a tRNA. Fifty of the seventy ORFs had no identity to data base entries; twenty showed sequence identity matches to archaeal viruses and to haloarchaea. ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified. Evidence for viral integration was obtained. Conclusion: The virus described here has a very low sequence identity to any previously described virus. Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases. Determining functions for ORFs such as these is probably easier using a simple virus as a model system. URI: http://hdl.handle.net/10566/140 Files in this item: 1
PagalingSequenceAnalysis2007.PDF (1.860Mb) -
Kimani, Serah W.; Agarkar, Vinod B.; Cowan, Donald A.; Sayed, Muhammed F.; Sewell, B. Trevor (International Union of Crystallography, 2007)[more][less]
Abstract: The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase superfamily and catalyzes the conversion of amides to the corresponding carboxylic acids and ammonia. It shows both amide-hydrolysis and acyl-transfer activities and also exhibits stereoselectivity for some enantiomeric substrates, thus making it a potentially important industrial catalyst. The crystal structure of G. pallidus RAPc8 amidase at a resolution of 1.9 A ˚ was solved by molecular replacement from a crystal belonging to the primitive cubic space group P4232. G. pallidus RAPc8 amidase is homohexameric in solution and its monomers have the typical nitrilase-superfamily α-β-β-α fold. Association in the hexamer preserves the eight-layered α-β-β-α:α-β-β-α structure across an interface which is conserved in the known members of the superfamily. The extended carboxy-terminal tail contributes to this conserved interface by interlocking the monomers. Analysis of the small active site of the G. pallidus RAPc8 amidase suggests that access of a water molecule to the catalytic triad (Cys, Glu, Lys) side chains would be impeded by the formation of the acyl intermediate. It is proposed that another active-site residue, Glu142, the position of which is conserved in the homologues, acts as a general base to catalyse the hydrolysis of this intermediate. The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity. URI: http://hdl.handle.net/10566/141 Files in this item: 1
KimaniAliphaticAmidase2007.pdf (2.155Mb) -
Cowan, Donald A. (Elsevier, 2004)[more][less]
Abstract: The newly isolated hyperthermophilic archaeal strain 121 grows slowly at 121 8C and even survives short periods at 130 8C. This is another organism that grows best at temperatures well in excess of 100 8C! We should not be astonished so much by the numerical increments but by the biochemical implications of this fact, and we should be excited by the scope provided by this and similar organisms to further our understanding of the evolution and adaptation of molecular structures and systems. And what about the upper limit of life? It appears improbable that the end-point of this search is represented by strain 121. The consensus view is that the true upper limit, where the energetic burden imposed by molecular repair and resynthesis becomes unsustainable, will probably lie in the region of 140–150 8C URI: http://hdl.handle.net/10566/147 Files in this item: 1
CowanUpperTemperature2004.pdf (331.8Kb)
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