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Introduction
Bacteria of the genus Thermus inhabit natural and man-made thermal environments such as hot springs, deep mines, compost manure, sewage sludge and domestic hot water (Oshima & Imahori, 1974; Munster et al., 1986; Brock & Freeze, 1969). Thermus bacteria are of major interest in this work because of their enzymes which function at higher temperatures. Some Thermus species are capable of reducing heavy metals and switching between aerobic and anaerobic respiration under certain conditions which are very essential for industrial application.
Enzymes from thermophilic organisms exhibit higher activity and stability than most synthetic and mesophilic enzymes currently been used in industry for production of food, laundry detergent, drugs, DNA replication, clothing, shoe and paper (Lioliou et al., 2004; Lasa & Berenguer, 1993). Thermophilic enzymes resist denaturing due to extreme acidity or alkaline conditions (Rocha et al., 2000; Niehaus et al., 1999). Examples of industrial important thermostable enzymes include proteases, enzymes for the conversion of carbohydrates such as starch, cellulose, xylan, lipases, ligases, DNA polymerase for DNA amplification, ribonucleases, bioleaching enzymes and many more which make strains from the genus Thermus excellent candidates for biotechnological application (Lioliou et al., 2004).
Heavy metals such as Fe(III), Cr(VI), Mn(IV), U(VI) and Co(III) have been found to be reduced by some Thermus strains (Balkwill et al., 2004; Opperman & Heerden, 2007). Reduction of Fe(III) and Mn(IV) among other heavy metals can be applied in biotechnology industry to eradicate heavy metal pollution; control global warming; remove organic contaminants in ground water; flux phosphate and to clear clogged wells among many other uses (Lovley, 1991). High levels of Cr(IV) in the human body is carcinogenic, hence its reduction eliminates toxicity in food and air for human health (Rowbotham et al., 2010). Fe(III) reduction under anaerobic conditions diverts electrons away from methane producers thereby reducing global methane fluxes into the atmosphere which lowers global warming. Since thermophilic bacteria are able to switch between aerobic and anaerobic respiration, they yield higher productivity of bio-fuels such as bio-diesel, bio-ethanol and bio-methane under anaerobic conditions when temperature rises due to biodegradation in bio-fuel cells.
Extreme levels of the biosynthetic and enzymatic activities of thermophilic bacteria have been explained by their extraordinary traits of high frequencies of natural transformations as adominant mode for horizontal gene transfer. Through this mechanism, bacteria take up free DNA from environments to incorporate it into their genome. Natural transformations permit the transportation of DNA through bacterial membranes and represent a dominant mode for transferring of genetic material between bacteria of distant evolutionary lineages even between members of different domains (Schwarzenlander et al., 2009). Horizontal gene transfer is one of the dominant players through which micro-organisms such as Thermus bacteria are able to acquire foreign genes into their genomes through mechanisms such as conjugation, transduction and natural transformation. The newly acquired genes may contribute new functionalities to the micro-organisms for adaptation and survival in hostile environments such as extreme temperature, high or low acidity and higher salt concentrates among many others.
Introduction
1.1 Introduction
1.2 Research Problem
1.3 Aims and Objectives
1.5 Thermus Bacteria
1.6 Industrial Application
1.7 Protein and Enzyme Thermostability
1.8 Genome Rearrangements
1.9 Metabolic networks
1.10 Summary and aims of the project
Genome Rearrangements
2.1 Introduction
2.2 Research Questions and Hypotheses
2.3 Analysis of the Distribution of Genes
2.4 Breakpoints Analysis
2.5 Metabolic Network Clustering
2.5.1 Data for metabolic network clustering
2.6 Gene Distribution Results
2.7 Breakpoints
2.8 Metabolic Network Clustering Results .
2.9 Discussion
2.10 Summary
3 Horizontal Gene Transfer
3.1 Introduction
3.2 Aim
3.3 Materials and Methods
3.4 Results and Discussion
3.5 Summary
4 Protein and Enzyme Thermostability
4.1 Introduction
4.2 Materials and Methods
4.3 Results and Discussion
4.4 Conclusion
5 Concluding Discussion
5.1 Introduction
Bibliography
Appendices
6.1 Appendix A
6.2 Appendix B
6.3 Appendix C
6.4 Appendix D
6.5 Appendix D
