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Microbiology Australia Microbiology Australia
Issue 4

From omics to systems biology: towards a more complete description and understanding of biology

Technology sets limits on what can be achieved in research. The advent of genetic engineering accompanied by the development of monoclonal antibody technology in the 1970s heralded the birth of modern ‘molecular biology’. This revolutionised the way we approach research in the biological sciences by allowing access to cellular structures and processes that were in the realm of science fiction a decade earlier. The invention of the PCR in the 1980s built on this, making cloning easier and a great deal more rapid; with PCR we no longer required a...

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Metabolomic analysis of protozoan parasites

Protozoan parasites cause a number of important diseases in humans, including malaria, African trypanosomiasis, Chagas disease and the leishmaniases. Current therapeutics for these diseases are limited and their effectiveness is being further undermined by the emergence of drug-resistant parasite strains. Parasite genome sequencing projects have provided new insights into the metabolic capacity of these pathogens and have highlighted potential drug targets. However, these genome-based reconstructions of metabolic networks are incomplete and we ...

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From omics to systems biology: Exploring the mystery box of microbial life

Microbial molecular biology has traditionally used very reductionist approaches; for example, find a gene of interest, clone it or knock it out and see if you can detect a phenotype. The genomics era has opened up the possibility of analysing microbes and communities at a systems level by combining high-throughput experimental data from genomic, transcriptomic, proteomic and phenomic techniques. This parallels earlier reductionist approaches by going from DNA to RNA to protein to phenotype, albeit on a global rather than individual gene scale. ...

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Systems biology: a new paradigm for industrial yeast strain development

One of the key challenges for industrial yeast strain development is to obtain a thorough understanding of the biology of yeast and to apply this knowledge to develop novel strains with improved features. The detailed study of individual biological components and the use of metabolic engineering have benefited the development of industrial strains enormously; however, such approaches have failed to describe yeast behaviour in the detail required to reveal the complex interactions operating within such biological systems. How can we accurately d...

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Functional genomics and mycotoxin discovery in the wheat glume blotch pathogen Stagonospora nodorum

Stagonospora nodorum is a fungal pathogen of wheat and is responsible for over $100 million in yield losses in Australia each year. Significant progress has recently been made in understanding how S. nodorum causes disease on wheat. These pathogens, known as a necrotrophs, were thought to secrete a battery of lytic and degradative enzymes during infection. These enzymes would simply degrade host tissue, allowing the infecting pathogen to feed off the lysed cellular contents. Recent studies have shown that this is not so, and that these fungi se...

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Microbial communities in Antarctic lakes: Entirely new perspectives from metagenomics and metaproteomics

Driven by advances in DNA sequencing technologies, an astounding amount of data is being generated from genetic material sourced directly from the environment, and this exponential growth of data is set to continue. By surmounting the challenges of working with such vast datasets, a whole new level of understanding is being gained about microbial diversity, microbial evolution and whole ecosystem function. For precious, pristine and logistically difficult to obtain Antarctic samples, metagenomic and metaproteomic approaches are providing the ba...

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Yeast as a system for systems biology

There are almost as many definitions of systems biology as there are workers in the field and we won’t attempt to add any further definition. In order to obtain an holistic view to the functioning of all of the processes in a cell, it is important to obtain sufficient data to understand the relationships between the many components that make up the cell.

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Quantification of microbial phenotypes using 13C-Fluxomics

Systems biology is an emerging tool in microbiology that helps us to understand cellular processes and to optimise microbes for production purposes1. It strongly relies on the use of large datasets created using omics tools followed by data mining and modelling in order to gain new insights into biology. The creation of the datasets is usually comprised of genomics defining the overall capacity of a microbe, transcriptomics and proteomics as a measure of the active set of reactions within the overall capacity and more recently metabolomics as a...

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Probing connectivity between transcriptional and post-transcriptional gene networks

The foundation for much of our current understanding of eukaryotic cell biology stems from studies exploiting the combined power of this yeast’s genetic tractability and its simple growth requirements. Furthermore, access to an early complete genome in 1996 allowed yeast researchers to spearhead the move toward genome-wide studies that underpin our thinking about systems-level biology today. Indeed, the last decade has been so rich in these studies that it has become close to impossible for most biologists to interrogate the data in an unbiased...

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Microbial proteomics: how far have we come?

It is now over 15 years since the beginning of the microbial genome era. At that time, great interest was invested in the idea of understanding bacterial genome dynamics via the analysis of their protein components or 'proteomes'. As bacterial analysis had driven the early advances in genomic squencing, these organisms were amongst the first subjected to protein-based studies. it is fair to suggest in hindsight that the original hype did not match the outcomes. At that time the term proteome was coined, en masse protein analysis meant little mo...

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Comparative genomics in the wine bacterium Oenococcus oeni

The production of wine from grape juice relies on the combined actions of both yeast and bacteria which shape the aroma and flavour of wine through the production of secondary metabolites and the biochemical transformation of many grape-derived constituents. Whereas the principal wine yeast, Saccharomyces cerevisiae, is primarily involved in the alcoholic fermentation in which glucose and fructose are converted into alcohol, the wine bacterium, Oenococcus oeni, is primarily involved in a secondary fermentation reaction where malic acid is decar...

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ASM Affairs, November 2011

Retirement of Associate Professor David Ellis from the Editorial Board; The global effort to tackle the increasing incidence of chikungunya infection; ASM Tri-State Meeting, Alice Springs 30-September- 1 October 2011; Student Special Interest Group

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